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ICSB 2010, Edinburgh, UK. 10th-15th October 2010 - Call for Tutorials

Fiona Clark — 2009-11-23T14:19:11-00:00

REMINDER Subject: ICSB 2010, Edinburgh, UK. 10th-15th October 2010 - Call for Tutorials Call For Tutorials 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 The ICSB tutorials series is meant to prepare attendees for a better understanding of certain aspects of the main conference, by giving them an introduction to the tools and methods of general interest for systems biology and by providing hands-on experience where appropriate. We would now like to invite prospective tutorial organisers to submit proposals for ICSB2010 tutorials to the organising commitee. Proposals should include the purpose and background of the subject area, the name of organizer and speakers, a description of their organisation, an estimate of the numbers of participants and mention whether demonstration facilities other than a standard AV system will be used. If tutorial material already exists even in draft stage, it would be helpful for the programme committee to make a more informed decision, if it were included with the proposal. Tutorials will last up to 4hrs. Enquiries can be made directly to Prof. Vincent Danos (<a href="mailto:vdanos@inf.ed.ac.uk" target="_blank">vdanos@inf.ed.ac.uk</a>) and Dr. Hong Yue (<a href="mailto:hong.yue@eee.strath.ac.uk" target="_blank">hong.yue@eee.strath.ac.uk</a>). Examples of tutorials given at recent ICSB meetings can be found at <a href="http://www.icsb-2007.org/tutorials/index.html" target="_blank">http://www.icsb-2007.org/tutorials/index.html</a> <a href="http://www.icsb-2008.org/main.php?display=tutorials" target="_blank">http://www.icsb-2008.org/main.php?display=tutorials</a> <a href="http://icsb-2009.org/schedule.php#tutorial1" target="_blank">http://icsb-2009.org/schedule.php#tutorial1</a> Deadline for tutorial proposals: Jan 15 2010 Tutorial venue and date: Edinburgh International Conference Centre, Oct 10 2010 Submission can be made directly to Prof Danos and Dr Yue or via the conference website. Registration and Fees: There is no charge to present an academic/non-profit tutorial. Registration for tutorials will be handled by ICSB and participants will be charged to cover the local expenses. Tutorial presenters and attendees are expected to register for the main conference. Appropriate badging for all tutorial attendees will be provided. Commercial tutorials may be presented at a cost of GBP500. Commercial tutorials are tutorials that primarily focus on using specific commercial products or systems, or at which commercial products are advertised, promoted, or sold, or which are primarily taught by the distributors or producers of those products. The program committee will make the final determination of whether or not a tutorial is commercial. For more information about ICSB2010, please see <a href="http://www.icsb-2010.net/" target="_blank">http://www.icsb-2010.net/</a> Sent on behalf of: Chair of the Scientific Program Committee and Congress Chairman, Prof. Igor Goryanin Vice Chair of the Scientific Program Committee, Dr. Andrew B. Goryachev 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 <a href="http://www.icsb-2010.net/" target="_blank">http://www.icsb-2010.net/</a> Fiona Clark Senior Clerical Assistant Room 1.37 School of Informatics Informatics Forum University of Edinburgh 10 Crichton Street Tel: 0131 651 3291 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

FW: [Fwd: ICSB2010 workshops]

Fiona Clark — 2009-11-23T13:42:33-00:00

Call for Workshops at ICSB2010. We are now accepting proposals for workshops to be held in conjunction with the 11th International Conference on Systems Biology, which will be held October 10-15, 2010 in the Edinburgh International Edinburgh International Conference Centre (EICC), Edinburgh, UK. Deadline for Proposals for Workshops: 15 December, 2009. Notification of Acceptance: 15 January, 2010. It is expected that workshops will be held on the 15th October, 2010 at the EICC. However, additional workshops may be organised before or after ICSB2010 at a separate venue, subject to approval by the local organising committee. Please contact Prof. Igor Goryanin for further details. Workshops can vary from a half day (approximately 4 hours) to a full day, extended if necessary through participation of a local organiser. The proposal shall describe the purpose, background, estimated number of attendees, possible names of speakers, and general format of the workshop. Strong consideration will be given to workshop proposals that are of interest to an interdisciplinary community, and provide a framework for future research agendas. Early decisions may be made for workshops that require advanced preparations as well as for workshops that are held regularly with ICSB. The EICC is an international-class conference venue with a range of flexible seminar and meeting rooms (<a href="http://www.eicc.co.uk" target="_blank">http://www.eicc.co.uk</a>). Meeting rooms will be provided on a space-available basis in the Conference Centre. Space is available for up to 12 workshops to be held simultaneously, with capacities of 15 to 100 people (classroom-style seating) or 30-300 people (theatre-style seating). The smaller venues can be arranged to seat up to 36 people boardroom-style for committee meetings. An additional boardroom for up to 14 people is available. Further information about ICSB2010 workshops together with proposal forms can be found at <a href="http://www.icsb2010.org.uk/workshops." target="_blank">http://www.icsb2010.org.uk/workshops.</a>" Sent on behalf of: Chair of the Scientific Program Committee and Congress Chairman, Prof. Igor Goryanin Vice Chair of the Scientific Program Committee, Dr. Andrew B. Goryachev 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 <a href="http://www.icsb-2010.net/" target="_blank">http://www.icsb-2010.net/</a> -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

FBTC 2010

marcoxa — 2009-11-13T10:24:49-00:00

[Apologies for multiple postings] *** Deadline Extension *** 3rd Workshop "From Biology To Concurrency and back" (FBTC 2010) *** New deadline for abstracts: November 29, 2009 *** New deadline for papers: December 8, 2009 More information below or at <a href="http://www.disi.unitn.it/~fbtc2010/" target="_blank">http://www.disi.unitn.it/~fbtc2010/</a> = = = = = = = = ======================================================================== CALL FOR PAPERS: FBTC 2010 From Biology To Concurrency and back (satellite event of ETAPS 2010) March 27, 2010 Paphos, Cyprus <a href="http://www.disi.unitn.it/~fbtc2010/" target="_blank">http://www.disi.unitn.it/~fbtc2010/</a> = = = = = = = = ======================================================================== AIMS AND OBJECTIVES As in its previous editions, the workshop aims at gathering researchers with special interest at the convergence of life and computer science, with particular focus on the application of techniques and tools from concurrency. We solicit the submission of unpublished results reporting on both modelling, analysis, and validation of biological behaviours using concurrency- inspired methods and platforms, and on bio-inspired models and tools for describing distributed interactions. Topics of interest include, but are not limited to: applications of techniques from rewriting logics, process calculi, Petri Nets, graph grammars, hybrid systems, and model checking to the representation and testing of scenarios from life sciences. SUBMISSION AND PUBLICATION Submission through EasyChair, 15 pages manuscripts in EPTCS (<a href="http://www.eptcs.org/" target="_blank">http://www.eptcs.org/</a>) style. IMPORTANT DATES Submission of title and abstract: November 29, 2009 Submission of paper: December 8, 2009 Notification: January 17, 2010 Submission of final version: February 21, 2010 PROGRAMME COMMITEE (to be confirmed) Marco Antoniotti (University of Milan Bicocca, IT) Chiara Bodei (University of Pisa, IT) Luca Bortolussi (University of Udine, IT) Luca Cardelli (Microsoft Research Cambridge, UK) Erik de Vink (Technische Universiteit Eindhoven, NL) Vincent Danos (CNRS and University of Edinburgh, UK) François Fages (INRIA Paris-Rocquencourt, F) Anthony Finkelstein (University College London, UK) Walter Fontana (Harvard Medical School, US) Radu Grosu (Stony Brook University, US) Jane Hillston (University of Edinburgh, UK) Anna Ingólfsdóttir (Reykjavik University, IS) John Lygeros (Automatic Control Laboratory, CH) Emanuela Merelli (University of Camerino, IT) (Co-chair) Paola Quaglia (CoSBi and Trento University, IT) (Co-chair) Carolyn Talcott (SRI International, US) Adelinde Uhrmacher (University of Rostock, DE) Cristian Versari (University of Bologna, IT) -- Marco Antoniotti, Associate Professor tel. +39 - 02 64 48 79 01 DISCo, Università Milano Bicocca U14 2043 Viale Sarca 336 I-20126 Milan (MI) ITALY Please note that I am not checking my Spam-box anymore. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Call for software demos - CCB 2010

Nicolas Le Novere — 2009-11-04T09:25:08-00:00

Dear colleagues, The forthcoming WT/CSHL meeting Computational Cell Biology (CCB) 2010, that will be held near Cambridge (UK) on February 10-13, will feature sessions dedicated to software demonstrations. An IT room will be provided with 20 desktops and provision for pluging 20 more computers. If you wish to organise a demo of your software, please register to the meeting and submit an abstract. For more information on the meeting, see: <a href="http://meetings.cshl.edu/meetings/compuk10.shtml" target="_blank">http://meetings.cshl.edu/meetings/compuk10.shtml</a> For registering, see: <a href="https://meetings.cshl.edu/meetings/meetingsregistration_uk.asp" target="_blank">https://meetings.cshl.edu/meetings/meetingsregistration_uk.asp</a> Best regards, -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:<a href="mailto:nlenovere@hotmail.com" target="_blank">nlenovere@hotmail.com</a>(NOT email) <a href="http://www.ebi.ac.uk/~lenov/," target="_blank">http://www.ebi.ac.uk/~lenov/,</a> <a href="http://www.ebi.ac.uk/compneur/" target="_blank">http://www.ebi.ac.uk/compneur/</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

High Performance Computing Symposium Paper Submission Deadline Extended.

thackerw — 2009-10-31T14:41:07-00:00

Call for Papers - Date Extended - Submissions accepted until December 4. 18th Annual High Performance Computing Symposium (HPC 2010) Florida Mall Hotel and Conference Center - Orlando, Florida Topics of interest include: High Performance/Large Scale Simulation Numerical Methods High Performance Applications and Case Studies Distributed and Grid Computing Asynchronous numerical methods Visualization and Data Management Advanced Simulation Frameworks Problem Solving Environments Parallel Algorithms for Emerging Architectures High Performance Software Tools Tools and Environments for Coupling Parallel Codes Component Technologies for High Performance Computing Power-aware Computing <a href="http://hosting.cs.vt.edu/hpc2010" target="_blank">http://hosting.cs.vt.edu/hpc2010</a> General Chair: Adrian Sandu <<a href="mailto:sandu@cs.vt.edu" target="_blank">sandu@cs.vt.edu</a>> General Vice-Chair: Layne Watson <<a href="mailto:watson@cs.vt.edu" target="_blank">watson@cs.vt.edu</a>> Program Chair: William I. Thacker <<a href="mailto:thackerw@winthrop.edu" target="_blank">thackerw@winthrop.edu</a>> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Re: Tenure-track faculty positions

Colin Nichols — 2009-10-09T19:39:30-00:00

My apologies, here is the advertisement. -----Original Message----- From: Colin Nichols [mailto:<a href="mailto:cnichols@wustl.edu]" target="_blank">cnichols@wustl.edu]</a> Sent: Thursday, October 08, 2009 5:33 PM To: <a href="mailto:bioinfo@sfbi.fr" target="_blank">bioinfo@sfbi.fr</a>; <a href="mailto:sysbio@caltech.edu" target="_blank">sysbio@caltech.edu</a> Subject: RE: Tenure-track faculty positions Dear Colleagues The attached Ad was recently placed in Nature and Cell, to advertise positions on tenure-track, at the level of Assistant Professor or higher, in appropriate pre-clinical or clinical Departments, in the Center for Membrane Excitabiltiy Disorders at WUMS. I would greatly appreciate if you would publicize these opportunities via the attached description. Thank you! Colin --- Colin G. Nichols Carl Cori Professor, Department of Cell Biology and Physiology, and Director, CIMED Washington University School of Medicine Campus Box 8228 660 South Euclid Avenue Saint Louis, MO 63110 <a href="mailto:cnichols@wustl.edu" target="_blank">cnichols@wustl.edu</a> www.nicholslab.wustl.edu For FedEx and Packages please use the following address: Washington University School of Medicine Cell Biology & Physiology Department 8228 4566 Scott Avenue Saint Louis, MO 63110

(no subject)

les — 2009-10-07T18:31:56-00:00

Dear Colleagues, I am please to announce opportunities for positions in biophysics here at UCHC. We are seeking to fill a tenure track faculty position (at any level), as well as several post-doctoral openings. My apologies for the mass mailing, but I would greatly appreciate if you would publicize these opportunities via the attached descriptions. Best wishes, Les ----------------------- Leslie M. Loew Boehringer Ingelheim Chair in Cell Sciences Professor of Cell Biology Professor of Computer Science and Engineering Director, R. D. Berlin Center for Cell Analysis and Modeling University of Connecticut Health Center Farmington, CT 06030-1507 (860)679-3568 <a href="mailto:les@volt.uchc.edu" target="_blank">les@volt.uchc.edu</a> CCAM: www.ccam.uchc.edu<<a href="file:///C:/Documents%20and%20Settings/les/Application%20Data/Microsoft/Signatures/www.ccam.uchc.edu" target="_blank">file:///C:/Documents%20and%20Settings/les/Application%20Data/Microsoft/Signatures/www.ccam.uchc.edu</a>> Virtual Cell: www.vcell.org<<a href="file:///C:/Documents%20and%20Settings/les/Application%20Data/Microsoft/Signatures/www.vcell.org" target="_blank">file:///C:/Documents%20and%20Settings/les/Application%20Data/Microsoft/Signatures/www.vcell.org</a>>

Computational Cell Biology (CCB) 2010

Nicolas Le Novere — 2009-09-23T16:32:28-00:00

########################################################################### ## ## ## Joint Cold Spring Harbor Laboratory/Wellcome Trust Conference ## ## Computational Cell Biology - February 10 - 13, 2010 ## ## ## ########################################################################### Organizers: Dennis Bray, University of Cambridge, UK Nicolas Le NovÃ¨re, EMBL-EBI, UK Leslie Loew, University of Connecticut, USA Following the success of the previous meeting on Computational Cell Biology another meeting on the same theme will be held at the Wellcome-Trust Conference Centre in Hinxton, near Cambridge, UK. The meeting will begin in the afternoon of Wednesday February 10 (3 pm), and end with a banquet on Saturday evening February 13, with normal departure on Sunday morning. Plenary Speakers: James Ferrell, Stanford University, USA Ben Scheres, University of Utrecht, The Netherlands Topics & Intracellular Signalling - Michael White Session Chairs: Tools and Software - Nicolas Le NovÃ¨re Self-organization in Cells - Bela Mulder/ Karsten Kruse Cell Motility - FranÃ§ois NÃ©dÃ©lec Patterns in Development - Jan Traas The specific goal for this meeting is to foster fruitful and creative dialogs between experimental cell biologists and mathematical-computational modelers with common interests in the regulation of cell physiology. The format of the meeting will consist of oral sessions including a combination of invited talks and talks selected from the abstracts, plus sessions devoted to posters and new software development. Abstracts should contain only new and unpublished material and must be submitted electronically by the abstract deadline. Selection of material for oral and poster presentation will be made by the organizers and individual session chairs. Status (talk/poster) of abstracts will be posted on our web site as soon as decisions have been made by the organizers. Abstracts due: November 20, 2009 Abstracts must be submitted electronically at www.cshl.edu/meetings We are eager to have as many young people as possible attend since they are likely to benefit most from this meeting. We have some funds to partially support graduate students and postdocs. Apply in writing to <a href="mailto:meetings@cshl.edu" target="_blank">meetings@cshl.edu</a> stating need for financial support - preference is given to those submitting abstracts. We look forward to seeing you at Hinxton in February. Conference Enquiries: Cold Spring Harbor Laboratory, Meetings & Courses Program, Cold Spring Harbor, NY 11724-2213. <a href="http://www.cshl.edu/meetings/" target="_blank">http://www.cshl.edu/meetings/</a> Email: <a href="mailto:meetings@cshl.edu" target="_blank">meetings@cshl.edu</a>, Phone: (516) 367-8346, Fax: (516) 367-8845 Conference Venue: Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK. <a href="http://www.wtconference.org.uk." target="_blank">http://www.wtconference.org.uk.</a> Email: <a href="mailto:info@wtconference.org.uk" target="_blank">info@wtconference.org.uk</a>, Tel: +44 (0)1223 495000, Fax: +44 (0)1223 495114 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Post-doctoral position at EMBL: identifying the neural circuits of anxiety

Nicolas Le Novere — 2009-09-13T21:41:25-00:00

EMBL INTERDISCIPLINARY POSTDOC (EIPOD) <a href="http://www.embl.de/training/postdocs/eipod/index.html" target="_blank">http://www.embl.de/training/postdocs/eipod/index.html</a> Brain rhythms: identifying the neural circuits of anxiety Coordinator: Cornelius Gross, EMBL Monterotondo <a href="http://www.embl.it/research/unit/gross/index.html" target="_blank">http://www.embl.it/research/unit/gross/index.html</a> Partner: Nicolas Le NovÃ¨re, EMBL-EBI Hinxton <a href="http://www.ebi.ac.uk/compneur-srv/" target="_blank">http://www.ebi.ac.uk/compneur-srv/</a> Anxiety is a mental state characterized by rumination and trepidation in the anticipation of threat. In its pathological form, anxiety is a debilitating disease. At present the most effective anti-anxiety drugs are benzodiazepines, allosteric agonists of fast inhibitory GABA-A receptors. However, very little is know about how these drugs work and in particular we do not know where in the brain and on which cells these drugs act to reduce anxiety. Fortunately, benzodiazepines are effective in reducing anxiety in a wide range of species and studies in animal models have begun to identify their mechanism of action. In rodents, injection of benzodiazepines into the hippocampus replicates the anxiolytic effect of systemic treatment, and recent data suggests that such treatment is accompanied by changes in the rhythmic firing patterns of this brain structure. This interdisciplinary project we will use a combination of behavioral, pharmaco-genetic, and computational methods to map the neuronal circuits and physiological substrates of anxiety in mice. The project will include a theoretical and an experimental part, executed at the European Bioinformatics Institute in Hinxton, UK and the Mouse Biology Unit in Rome, Italy, respectively. The theoretical part will encompass neuronal circuit modelling using available software platforms to make predictions about changes in firing rates and rhythmic firing patterns following benzodiazepine treatment. These models will allow us to make predictions about which synapses are likely to be the substrates of benzodiazepines and will help us to model the effects of cell-type specific manipulations of neuronal activity deriving from the experimental part of the project. The experimental part will involve a combination of pharmaco-genetic technology in transgenic mice to rapidly and selectively inhibit/activate specific cell-types in behaving mice and in vivo behaving electrophysiology to directly measure the physiological correlates of these manipulations. By combining computational and experimental approaches in this way we hope to determine the cell-type(s) and rhythmic activities underlying anxiety. We seek a postdoctoral candidate who has completed a PhD in mathematics, physics, engineering, computer science and who expresses a strong motivation to gain experience in experimental neurobiology. Online application is open until 31 October 2009. <a href="https://www-db.embl.de/jss/eipod" target="_blank">https://www-db.embl.de/jss/eipod</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

High Performance Computing Symposium (HPC '10) CFP and Conference Announcement

thackerw — 2009-09-10T20:34:16-00:00

Call for Papers 18th Annual High Performance Computing Symposium (HPC 2010) Part of the 2010 Spring Simulation Multiconference (SpringSim'10) Sponsored by: The Society for Modeling and Simulation International (SCS) April 12-15, 2010 Florida Mall Hotel and Conference Center The 2010 Spring Simulation Multiconference will feature the High Performance Computing Symposium (HPC 2010). This will be the 18th special symposium devoted to the impact of high performance computing and communications. Advances in networking, high-end computers, large data stores, and middleware capabilities are ushering in a new era of high-performance parallel and distributed simulations. Along with these new capabilities come new challenges in computing and system modeling. The goal of HPC 2010 is to encourage innovation in high performance computing and communication technologies and to promote synergistic advances in modeling methodologies and simulation. It will promote the exchange of ideas and information between universities, industry, and national laboratories about new developments in system modeling, high performance computing and communication, and scientific computing and simulation. Topics of interest include: High Performance/Large Scale Simulation Numerical Methods High Performance Applications and Case Studies Distributed and Grid Computing Asynchronous numerical methods Visualization and Data Management Advanced Simulation Frameworks Problem Solving Environments Parallel Algorithms for Emerging Architectures High Performance Software Tools Tools and Environments for Coupling Parallel Codes Component Technologies for High Performance Computing Power-aware Computing Key Information HPC 2010 Organization: <a href="http://hosting.cs.vt.edu/hpc2010/organization.php" target="_blank">http://hosting.cs.vt.edu/hpc2010/organization.php</a> HPC 2010 Program: <a href="http://hosting.cs.vt.edu/hpc2010/program.php" target="_blank">http://hosting.cs.vt.edu/hpc2010/program.php</a> HPC 2010 Submission guidelines: <a href="http://hosting.cs.vt.edu/hpc2010/submission.php" target="_blank">http://hosting.cs.vt.edu/hpc2010/submission.php</a> Key Dates 23 Oct 2009 Paper Submission due. 11 Dec 2009 Program committee will review the papers and notify authors. 8 Jan 2010 The final version of accepted papers, incorporating changes based on reviewer comments, are due. There is also a poster session at SpringSim'10 that welcomes HPC posters (see <a href="http://www.scs.org/confernc/springsim/springsim10/cfp/poster.htm" target="_blank">http://www.scs.org/confernc/springsim/springsim10/cfp/poster.htm</a>) Papers should be submitted to the SCS Conference Proceedings Management System: <a href="http://www.scs.org/springsim/submission" target="_blank">http://www.scs.org/springsim/submission</a> HPC 2010 Chairs General Chair: Adrian Sandu <<a href="mailto:sandu@cs.vt.edu" target="_blank">sandu@cs.vt.edu</a>> General Vice-Chair: Layne Watson <<a href="mailto:watson@cs.vt.edu" target="_blank">watson@cs.vt.edu</a>> Program Chair: William I. Thacker <<a href="mailto:thackerw@winthrop.edu" target="_blank">thackerw@winthrop.edu</a>> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Ph.D. student selections open in Milan Bicocca, Italy

marcoxa — 2009-09-10T12:26:46-00:00

Dear all apologies for the mutliple postings. The selections for Ph.D. students are now open in Milan Bicocca. Deadlines and procedures are described at <a href="http://www.unimib.it/XML/contenuti/news/dett.jsp?_cid=cb3d9349¶m1=146¶m2=2473512322652572250&_crc=453d7a28" target="_blank">http://www.unimib.it/XML/contenuti/news/dett.jsp?_cid=cb3d9349¶m1=146¶m2=2473512322652572250&_crc=453d7a28</a> The Computer Science Department (DISCo) welcomes applications from candidates interested in Bioinformatics and Systems Biology. Please do not hesitate to contact me for more details. The University web site is <a href="http://www.unimib.it" target="_blank">http://www.unimib.it</a> The Department web site (under heavy renovation right now) is <a href="http://www.disco.unimib.it" target="_blank">http://www.disco.unimib.it</a> The BIMIB group web site is <a href="http://bimib.disco.unimib.it" target="_blank">http://bimib.disco.unimib.it</a> best regards -- Marco Antoniotti, Associate Professor tel. +39 - 02 64 48 79 01 DISCo, Università Milano Bicocca U14 2043 Viale Sarca 336 I-20126 Milan (MI) ITALY Please note that I am not checking my Spam-box anymore. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Entelos is hiring (and at ICSB) - Dynamics engineers, CV scientists

Alex Bangs — 2009-08-28T20:24:14-00:00

Entelos will be at the ICSB meeting next week at Stanford, please stop by our booth to meet our engineers and scientists. We are hiring and would be happy to talk with people about these open positions: ************************************************************************** Scientist/Senior Scientist in Cardiovascular - Entelos is seeking scientists with experience in vascular biology and atherosclerosis to join our interdisciplinary modeling team that is building large scale physiological models and performing research with our collaboration partners; please see the Entelos site for details of this position: <a href="http://www.entelos.com/careers.php?ID=main" target="_blank">http://www.entelos.com/careers.php?ID=main</a> ************************************************************************** Dynamics Engineer - Entelos is seeking engineers and applied mathematicians for full-time positions in our In Research and Development group. The Dynamics Engineer works with scientists and other engineers to perform in silico research and development. He or she provides mathematical modeling expertise, helps develop complex mathematical models that meet the needs of pharmaceutical researchers, uses these models in research projects, identifies novel experiments that can be done to address major knowledge gaps, writes project proposals and reports, and makes technical presentations of their work. This position is located at Entelos’ Foster City, California headquarters on San Francisco Bay. The ideal candidate will have: * A Ph.D. or substantial experience in Engineering, Applied Mathematics, Physics, or a closely related field with a strong background in nonlinear dynamics and control theory. * Substantial experience in developing and analyzing mathematical models of complex, real world problems. * Experience with collaborative, multidisciplinary research projects. * A strong interest in biology. * Very strong communication skills, both verbal and written, including technical writing and presentation. * The ability to work independently in a diverse, cross-functional team environment. * Biology background is desirable. * Industry or post-graduate experience is desirable, preferably in pharmaceutical or life sciences field. Entelos is an equal opportunity employer. Upon hiring, proof of eligibility to work in the United States is required. For more information on the company and to apply for this position, please go to <a href="http://www.entelos.com/careers.php?ID=main" target="_blank">http://www.entelos.com/careers.php?ID=main</a> ************************************************************************** Alex L. Bangs Co-Founder & CTO Entelos, Inc. 110 Marsh Drive, Foster City, CA 94404 USA +1(650)572-5510 Phone / +1(413)431-5130 Fax <a href="mailto:bangs@entelos.com" target="_blank">bangs@entelos.com</a> / www.entelos.com Get to know your DigitalSelf™ at www.MyDigitalHealth.com – the world’s first personal health simulator ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Interdisciplinary PhD Position in Experimental and Computational Molecular Biology at ETH Zurich

Beerenwinkel Niko — 2009-07-30T13:46:01-00:00

Interdisciplinary PhD Position in Experimental and Computational Molecular Biology An interdisciplinary PhD position is available in the groups of Dr. Gunter Merdes (Molecular Biology) and Prof. Niko Beerenwinkel (Computational Biology) at the Department of Biosystems Science and Engineering of ETH Zurich in Basel. Our research is at the interface of mathematics, statistics, and computer science with biology and medicine. We are particularly interested in disease-associated cellular networks and their evolutionary dynamics. The PhD project is concerned with the prediction of functional redundancy in protein networks, and the student will be involved in an alternating cycle between experiment and computational method development. The successful candidate will be a member of both research groups and receive intense interdisciplinary training. Applicants should have a strong background in molecular biology and a solid background in mathematics and statistics. Experience in the area of computational biology is a plus but not a necessity. We seek highly motivated and enthusiastic students with the willingness to cross scientific borders. Good knowledge of English both in writing and speaking is expected. The salary is according to the guidelines of the Swiss National Science Foundation. The position is funded by a SystemsX.ch interdisciplinary PhD fellowship for an initial three years with a possible extension to four years. The Department of Biosystems Science and Engineering of ETH Zurich is an integral part of SystemX.ch, the Swiss initiative in Systems Biology. It is located in Basel, a European hot-spot for biomedical research, in close proximity of the Biozentrum of the University of Basel, the Friedrich Miescher Institute for Biomedical Research, and the pharmaceutical and biotech industry. ETH Zurich is a major research university, offering an excellent environment for innovative and collaborative research across disciplines. Please send the usual application material, including at least two references, as a single PDF file to <a href="mailto:niko.beerenwinkel@bsse.ethz.ch" target="_blank">niko.beerenwinkel@bsse.ethz.ch</a> and <a href="mailto:gunter.merdes@bsse.ethz.ch." target="_blank">gunter.merdes@bsse.ethz.ch.</a> For further information, please visit our web sites: Department of Biosystems Science and Engineering, <a href="http://www.bsse.ethz.ch/" target="_blank">http://www.bsse.ethz.ch/</a> Niko Beerenwinkel, <a href="http://www.cbg.ethz.ch" target="_blank">http://www.cbg.ethz.ch</a> Gunter Merdes, <a href="http://www.bsse.ethz.ch/people/gmerdes/" target="_blank">http://www.bsse.ethz.ch/people/gmerdes/</a>

FOSBE 2009 Late Abstract Submission

Mike Henson — 2009-07-26T14:05:40-00:00

Foundations of Systems Biology in Engineering (FOSBE 2009) Inverness Hotel and Conference Center Denver, Colorado August 9-12, 2009 <<a href="http://www.fosbe.org" target="_blank">http://www.fosbe.org</a>> www.fosbe.org The Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009) sponsored by the CACHE Corporation will take place in Denver, Colorado August 9-12, 2009. Late Abstract Submission We will be accepting late abstract submissions for poster presentations. Authors should submit their abstracts electronically to: <<a href="https://www.softconf.com/s08/fosbe09/submit.html" target="_blank">https://www.softconf.com/s08/fosbe09/submit.html</a>> <a href="https://www.softconf.com/s08/fosbe09/submit.html." target="_blank">https://www.softconf.com/s08/fosbe09/submit.html.</a> Papers will not be accepted. August 3, 2009: Final deadline for contributed abstracts. Conference Registration The following rates apply: $900 Standard registration $500 Graduate student registration $50 Training workshop Additional information and online registration are available on the conference website ( <<a href="http://www.fosbe.org/?fosbe=registration" target="_blank">http://www.fosbe.org/?fosbe=registration</a>> <a href="http://www.fosbe.org/?fosbe=registration" target="_blank">http://www.fosbe.org/?fosbe=registration</a>). Lodging Information The conference will take place at the scenic Inverness Hotel and Conference Center in Englewood, Colorado. The room rate is $195 per night. Additional information and online reservations are available on the conference website (<a href="http://www.fosbe.org/?fosbe=lodging" target="_blank">http://www.fosbe.org/?fosbe=lodging</a>). ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

[HiBi09] Call For Poster - Participation: Registration is now open

mazza — 2009-07-16T14:39:48-00:00

*CALL FOR POSTER & PARTICIPATION* ************************************************************************************ *International Workshop on High Performance Computational Systems Biology* (HiBi 2009) Trento, Italy, October 14-16, 2009 <a href="http://www.cosbi.eu/hibi09/" target="_blank">http://www.cosbi.eu/hibi09/</a> ************************************************************************************ The HiBi (High performance computational systems Biology) workshop establishes a forum to link researchers in the areas of parallel computing and computational systems biology. One of the main limitations in managing models of biological systems comes from the fundamental difference between the high parallelism evident in biochemical reactions and the sequential environments employed for the analysis of these reactions. Such limitations affect all varieties of continuous, deterministic, discrete and stochastic models; undermining the applicability of simulation techniques and analysis of biological models. The goal of HiBi is therefore to bring together researchers in the fields of high performance computing and computational systems biology. Experts from around the world will present their current work, discuss profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology. *Poster presentation *is a unique opportunity to present significant work in progress or novel ideas that are not quite ready for a regular full-length paper. Moreover, it is an important chance to obtain direct feedback about their work from a wide audience present during the dedicated poster session. A 1 page poster abstract describing the work will be reviewed and published in the conference proceedings. The poster will be shown in the main conference room, and a dedicated session will be arranged. A selection of best posters will be invited to submit an extended abstract to the International Journal of Advanced Science and Technology or to the International Journal of Bio-Science and Bio-Technology. *Topics of interest include, but are not limited to:* * Parallel Stochastic simulation * Biological and Numerical parallel computing * Parallel and distributed architectures * Emerging processing architectures (e.g., Cell processors, GPUs, mixed CPU-FPGA) * Parallel Model Checking techniques * Parallel parameters estimation * Parallel algorithms for biological analysis * Application of concurrency theory to biology * Parallel visualization algorithms * Web-services and internet computing for e-Science * Tools and applications *Poster guidelines:* Posters should be: * brief and clearly organized; * simple, with an obvious theme; and * easy to read from 4 to 6 feet away. *Poster dimension:* * All posters must fit into a 36" x 48" space. *Important dates:* * August 10, 2009: submission of poster abstract * August 10, 2009: early registration to workshop deadline *Program Committee Members:* * Tommaso Mazza (CoSBi, Italy) - chair * Mateo Valero (Technical University of Catalonia, Spain) - co-chair * Yutaka Akiyama (Tokyo Institute of Technology, Japan) * Paolo Ballarini (CoSBi, Italy) * Gianfranco Balbo (University of Torino, Italy) * Lubos Brim (Masaryk University, Czech Republic) * Kevin Burrage (University of Oxford, UK) * Hidde De Jong (INRIA Rhône-Alpes, France) * François Fages (INRIA Paris-Rocquencourt, France) * Fabrizio Gagliardi (Microsoft Research Cambridge, United Kingdom) * Martin Leucker (Technische Universität München, Germany) * Gethin Norman (Oxford University Computing Laboratory, United Kingdom) * Dave Parker (Oxford University Computing Laboratory, United Kingdom) * Davide Prandi (CoSBi, Italy) * Assaf Schuster (Israel Institute of Technology, Israel) * Koichi Takahashi (RIKEN, Japan) * David Torrents Arenales (Barcelona Supercomputing Center, Spain) * Adelinde Uhrmacher (University of Rostock, Germany) Information related to HiBi 2009 is available at the official HiBi 2009 Web site: <a href="http://www.cosbi.eu/hibi09/" target="_blank">http://www.cosbi.eu/hibi09/</a> Best regards, HiBi organizing committee ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

FOSBE 2009 Late Abstract Submission

Mike Henson — 2009-07-15T12:27:34-00:00

Foundations of Systems Biology in Engineering (FOSBE 2009) Inverness Hotel and Conference Center Denver, Colorado August 9-12, 2009 <<a href="http://www.fosbe.org" target="_blank">http://www.fosbe.org</a>> www.fosbe.org The Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009) sponsored by the CACHE Corporation will take place in Denver, Colorado August 9-12, 2009. Late Abstract Submission We will be accepting late abstract submissions for poster presentations. Authors should submit their abstracts electronically to: <<a href="https://www.softconf.com/s08/fosbe09/submit.html" target="_blank">https://www.softconf.com/s08/fosbe09/submit.html</a>> <a href="https://www.softconf.com/s08/fosbe09/submit.html." target="_blank">https://www.softconf.com/s08/fosbe09/submit.html.</a> Papers will not be accepted. August 3, 2009: Final deadline for contributed abstracts. Conference Registration The following rates apply: $900 Standard registration $500 Graduate student registration $50 Training workshop Additional information and online registration are available on the conference website ( <<a href="http://www.fosbe.org/?fosbe=registration" target="_blank">http://www.fosbe.org/?fosbe=registration</a>> <a href="http://www.fosbe.org/?fosbe=registration" target="_blank">http://www.fosbe.org/?fosbe=registration</a>). Lodging Information The conference will take place at the scenic Inverness Hotel and Conference Center in Englewood, Colorado. The room rate is $195 per night. Additional information and online reservations are available on the conference website (<a href="http://www.fosbe.org/?fosbe=lodging" target="_blank">http://www.fosbe.org/?fosbe=lodging</a>). ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Announcing ChiBE: Chisio BioPAX Editor

Ugur Dogrusoz — 2009-07-15T03:53:32-00:00

Dear All, We are happy to announce the release of ChiBE (Chisio BioPAX Editor) version 1.0. ChiBE is a free, open-source editing and visualization tool for pathway models represented by the BioPAX format (level 2). The tool features user-friendly display, viewing, and editing of pathway models. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art layout and visualization technologies. In addition, facilities for querying a set of integrated pathways in Pathway Commons are provided. Furthermore, visualization of experimental data overlaid on pathway views is supported in ChiBE. ChiBE is a Java application running on Windows XP/Vista and Linux. It was built using Chisio 1.0 and Eclipse GEF 3.1 for graph visualization, Paxtools for accessing and manipulating BioPAX files, and PATIKAmad for experiment data analysis. For details: <a href="http://www.bilkent.edu.tr/~bcbi/chibe.html" target="_blank">http://www.bilkent.edu.tr/~bcbi/chibe.html</a> Best, Ugur Dogrusoz Center for Bioinformatics Bilkent University ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

More miscellaneous SBML news

mhucka — 2009-07-13T21:27:55-00:00

I hope people won't mind another brief update on miscellaneous SBML news: * We have produced an updated description of changes planned for the SBML Level 3 Core specification. We very much want to get people's feedback; please contact the SBML Editors directly or (better) post your comments to the sbml-discuss mailing list. The Level 3 description is at <a href="http://sbml.org/Community/Wiki/SBML_Level_3_Core" target="_blank">http://sbml.org/Community/Wiki/SBML_Level_3_Core</a> * The next SBML Forum meeting will be held Sep. 3-4 at Stanford as a satellite of ICSB 2009. It's getting close to that time, and we need to know how many people will be there so that we can make venue arrangements. If you're coming, please register using the link on this page: <a href="http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting" target="_blank">http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting</a> * There have been several additional document errata published for the SBML Level 2 Version 4 specification. The specification and an errata list are available at <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> * The SBML community recently achieved a new record of 170 software tools worldwide known to support SBML. A guide to the known tools is at <a href="http://sbml.org/SBML_Software_Guide" target="_blank">http://sbml.org/SBML_Software_Guide</a> * We highly recommend that anyone even remotely interested in SBML please subscribe to the sbml-announce mailing list, or at least monitor the RSS or Twitter feeds. The mailing list is extremely low-volume, and it's used only for very significant news, such as announcements of SBML releases and SBML workshops. Visit <a href="http://sbml.org/Forums" target="_blank">http://sbml.org/Forums</a> for more information. Mike on behalf of the SBML Editors and the SBML Team -- Mike Hucka, Ph.D. <a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a> <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a> Senior Research Fellow, Control and Dynamical Systems Co-director, Biological Network Modeling Center (BNMC) Beckman Institute @ the California Institute of Technology ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Symposium year on The Mathematics of Complexity Science and Systems Biology

David Wild — 2009-07-07T12:40:56-00:00

Warwick Mathematics Research Centre EPSRC Symposium year on The Mathematics of Complexity Science and Systems Biology >From September 2009 to July 2010, we will run an intensive year of research workshop, conference and visitor activity, to summarise the state of play, identify and address the main challenges and develop key ideas in a range of topics in the Mathematics of Complexity Science and Systems Biology. Complexity Science is the study of systems with many interdependent components. Its remit spans a wide range of areas, from physical to technological to biological and social systems. One important such area to which particular attention will be given is Systems Biology, the study of organisms from the point of view of systems rather than individual components. We believe that these subjects depend heavily on Mathematics for their healthy development and conversely they provide rich sources of stimulation for new Mathematics. Programme of events Information extraction from complex data sets, 14-18 Sep 09 European Conference on Complex Systems ECCS09, 21-25 Sep 09 Networks: dynamics & flows, 28 Sep - 2 Oct 09 >From molecules to bodies: spanning levels of biological organisation in medicine, 14-15 Dec 09 Space-time phases for spatially extended systems, 6-8 Jan 10 Non-equilibrium dynamics of spatially extended interacting particle systems, 11-13 Jan 10 Game theory for finance, social and biological sciences, 14-16 Apr 10 Ecology, epidemiology & evolution: biological processes & artificial analogues, 20-22 Apr 10 Dendrites, neurones & networks: space & stochasticity in the brain, 24-27 May 10 Clocks, switches & signals, 14-19 Jun 10 Spatio-temporal dynamics challenges from fluorescence data, Jul 10 All are welcome to attend. Except for ECCS09, there are no registration fees. Please register via <a href="http://www2.warwick.ac.uk/fac/sci/maths/research/events/2009-2010/symposium/" target="_blank">http://www2.warwick.ac.uk/fac/sci/maths/research/events/2009-2010/symposium/</a> We are grateful to EPSRC for financial support for the speakers and long-term visitors, but regret that we are unlikely to be able to offer expenses to any others. Organisers: Robert MacKay and David Wild ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

FOSBE 2009 Registation and Late Abstract Submission - Corrected Version

Mike Henson — 2009-07-06T16:37:37-00:00

FOSBE 2009 Registation and Late Abstract Submission

Mike Henson — 2009-07-06T13:29:06-00:00

Post-doc position in Systems Biology at UTC

Frederic.BOIS — 2009-07-06T07:40:42-00:00

Post-Doctoral Position in Systems Biology at UTC The newly created Chair in Mathematical Modeling for Predictive Toxicology and Ecotoxicology at CompiÃ¨gne University of Technology (UTC), and INERIS (French National Institute for Industrial Environment and Risks), collaborate on the development of Systems Biology tools and concepts for predictive toxicology. An important part of the on-going work focuses on the development of ab initio methods for modeling drug-drug interactions and metabolic interactions in complex mixtures of chemicals. Development and application of Bayesian numerical techniques to pathway identification and parameterization is another research theme. The research is performed in co-operation with the Biomechanics and Bioengineering laboratory (UMR6600) at UTC, which develops bio-artificial organs, to mimic in vitro the in vivo conditions. Research links also exist with a large consortium of laboratories working in the framework of the European Integrated Projects "PREDICT-IV" and "2-FUN". The goal of the post-doctoral position now opened is to further develop, validate and illustrate an original approach for automatic integration of SBML and physiologically-based models for many-reactant metabolic / signaling / transcription /regulation schemes. Issues of parameter estimation and structural identifiability will be treated as needed. Under the supervision of the chairperson, the candidate will in particular: - Participate in the development of the GNU MCSim software, - Further the development of theoretical foundations of the approach developed, - Develop case studies and applications, - Propose the design of needed experiments and supervise the data collection, - Actively publish in peer reviewers journals, - Disseminate the results to the pharmacology, toxicology and systems biology research communities and industrial partners, - Supervise students working on the project. Candidate profile: We are seeking a highly motivated individual interested in collaborating with an interdisciplinary group of modelers, biologists and bioengineers. A Ph.D. in computational biology, bioengineering, biomathematics or related fields is essential. Communication skills and fluency in English are a requirement. Applications include a statement of interest, CV, and names and contact for two academic references. Applications or requests for further information should be sent to Frederic Y. Bois (<a href="mailto:Frederic.Bois@ineris.fr" target="_blank">Frederic.Bois@ineris.fr</a>). Location: CompiÃ¨gne University of Technology and INERIS, Verneuil-en-Halatte, Oise, France (60 kilometers North of Paris) Duration: 24 months ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Post-doc position in Bioinformatics and Computational Systems Biology of Breast Cancer research

Emmanuel Barillot — 2009-07-04T21:28:48-00:00

*Post-doc position in Bioinformatics and Computational Systems Biology of Breast Cancer research at the Institut Curie, Paris, France.* A postdoc position is open at Institut Curie in the context of the GEPIG (Genetics and Epigenetics of Tumor, <a href="http://gepig.curie.fr" target="_blank">http://gepig.curie.fr</a>) project, an integrated approach to profile Breast Cancer from model systems to biological resources. Project: This project is funded through the INCa (National Institute of Cancer) and Institut Curie. It proposes an integrated program to decipher genomic and epigenetic defects using a combination of complementary expertise, tools, models, and a unique tumor bank with the aim to improve the understanding of the biological mechanisms of tumoral progression. A strong emphasis will be given to the generation and analysis of large sets of data in particular using new generation sequencing approaches. This project brings together research groups from the Institute, covering a range of expertises from pathology (X. Sastre, A. Vincent Salomon) to genetics (O. Delattre, A. Nicolas, M-H. Stern), epigenetics (G. Almouzni, E. Heard, F. Radvanyi, A. Taddei), bioinformatics and mathematical modelling (E. Barillot). The position is for a duration of 2 years with possible extension. An immediate start is possible. Mission of the postdocs: The postdoc will work under the joint supervision of Dr Geneviève Almouzni (Laboratory of nuclear dynamics and genome plasticity) and Dr Emmanuel Barillot (Laboratory of Bioinformatics and Computational Systems Biology of Cancer). She/he will be involved in the generation (experimental design) and computational analysis of data encompassing several levels of observations including transcriptome profiling (including small RNAs), DNA methylation and histone variants and modification analyses ... Profile of candidates: The ideal candidate will have a strong background both in bioinformatics or statistics, and in molecular biology. Previous experience in sequence analysis will constitute an advantage. The candidate must have a strong capability to collaborate simultaneously with experimentalists and theoreticians. Location: Institut Curie (<a href="http://www.curie.fr/" target="_blank">http://www.curie.fr/</a>), Paris, France. Institut Curie is one of the largest European institutions for cancer research with strong and longstanding interdisciplinary traditions. The existence of Curie hospital specialized in cancer treatment located on the same site, provides a continuum of expertise from fundamental research to patient care. Its situation in the center of Paris offers a unique environment both culturally and scientifically. Contact: Please send CV, letter of motivation and letters of references to <a href="mailto:bcsb32@curie.fr" target="_blank">bcsb32@curie.fr</a> Deadline for application is July 31st, 2009 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Post-Doc and PhD positions at ETH Zurich

Dagmar Iber — 2009-07-03T15:45:44-00:00

Applications are invited for a PhD studentship and a Post-Doc position, within the Computational Biology Group at the Department of Biosystems Science and Engineering of ETH Zurich. The group focuses on the development of detailed, predictive models for cellular signaling networks with a view to develop a comprehensive understanding of the dynamics and evolution of cellular signaling. Projects are carried out in close collaboration with experimental groups so that quantitative data is available and model predictions can be tested in experiments. Applicants should have a strong background in mathematical and computational modeling or statistics, and demonstrated experience in nonlinear dynamics and numerical calculations. PhD candidates should hold or expect to obtain an MSc degree or diploma in a numerate discipline (e.g. mathematics, physics, statistics, computational biology, or related areas). The Department of Biosystems Science and Engineering of ETH Zurich is an integral part of SystemX.ch, the Swiss initiative in Systems Biology. It is located in Basel, a European hotspot for biomedical research, in close proximity of the Biozentrum of the University of Basel, the Friedrich Miescher Institute for Biomedical Research, and the pharmaceutical and biotech industry. ETH Zurich is a major research university, offering an excellent environment for innovative and collaborative research across disciplines. Please send the usual application material, including at least two references, as a single PDF file to <a href="mailto:dagmar.iber@bsse.ethz.ch" target="_blank">dagmar.iber@bsse.ethz.ch</a> (preferred), or via surface mail to: Prof Dagmar Iber ETH Zurich D-BSSE Mattenstrasse 26 4058 Basel Switzerland For further information please visit our web page at <a href="http://www.dbsse.ethz.ch/research/group_iber" target="_blank">http://www.dbsse.ethz.ch/research/group_iber</a>

"Models, minds, machines" by Marvin Minsky

Nicolas Le Novere — 2009-06-19T22:10:47-00:00

Dear Colleagues, I am looking for a copy of the following paper: M Minsky (1965) Models, minds, machines. Proceedings IFIP Congress, pp 45-49. Any help appreciated. Best regards, -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:<a href="mailto:nlenovere@hotmail.com" target="_blank">nlenovere@hotmail.com</a>(NOT email) <a href="http://www.ebi.ac.uk/~lenov/," target="_blank">http://www.ebi.ac.uk/~lenov/,</a> <a href="http://www.ebi.ac.uk/compneur/" target="_blank">http://www.ebi.ac.uk/compneur/</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Position of group leader at EMBL-EBI

Nicolas Le Novere — 2009-06-17T15:43:25-00:00

Job description: We are seeking a dynamic computational biologist, with a proven track record, to establish a new research group to complement our current programme. The EMBL-EBI, located near Cambridge, UK on the Welcome Trust Genome Campus, is a global centre for biological data, hosting the very large sequence, structure and expression data resources in Europe as well as eight dedicated research groups. It provides an excellent research environment including access to outstanding students and post-doctoral scientists from around Europe, and computational facilities and support At the EBI, research is pursued in many different aspects of biology, exploiting and helping to interpret the biological data held in the databases. Currently research topics include sequence analysis, computational genomics, phylogeny, structural biology, regulatory control networks, functional genomics, neurobiology and literature/text mining. In addition, research activities are an important part of several of the large data resource teams, which also provide services. We are keen to expand our research into the areas of comparative genomics, human variation, biomedical informatics and novel algorithms/statistical approaches, but will favour outstanding candidates from any area of computational biology. The candidate will join a strong and supportive group of young research group leaders and will interact closely with the large database teams, benefiting from their technical expertise and scientific knowledge. Contract: An initial contract of 5 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of the review. Closing date: 31. July 2009 EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. Please note that EMBL does not return CVs or attached documents to applicants. To apply, please send a CV, three written references and a concise description of research interests and future plans , by email, quoting ref. no. W/09/052/EBI in the subject line, to: <a href="mailto:applications@ebi.ac.uk." target="_blank">applications@ebi.ac.uk.</a> General enquiries may also be sent to this e-mail address. Further information about EMBL-EBI can be obtained at <a href="http://www.embl.org/" target="_blank">http://www.embl.org/</a> and <a href="http://www.ebi.ac.uk/" target="_blank">http://www.ebi.ac.uk/</a> and on the position from the Director of the EMBL-EBI Janet Thornton (<a href="mailto:doffice@ebi.ac.uk" target="_blank">doffice@ebi.ac.uk</a>) ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Call For Poster: (HiBi 2009) International Workshop on High Performance Computational Systems Biolog

HiBi09 — 2009-06-16T10:06:20-00:00

____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

BioNetGen Rule Based Modeling Short Course and Microscopes to Models Workshop

blinov — 2009-06-05T21:36:18-00:00

We are pleased to announce the BioNetGen Rule Based Modeling Short Course and Microscopes to Models Workshop. BioNetGen Rule Based Modeling Short Course June 23rd-24th. This hands-on course is designed to enable biologists and modelers to develop a rule- based model of signal transduction for experimental systems. The course will consist of one morning of introductory lectures, followed by continuous interactive, hands-on sessions using the BioNetGen ( <a href="http://vcell.org/bionetgen" target="_blank">http://vcell.org/bionetgen</a>) and Virtual Cell ( <a href="http://vcell.org" target="_blank">http://vcell.org</a> ) software. Contact Dr. Michael Blinov, <a href="mailto:blinov@uchc.edu" target="_blank">blinov@uchc.edu</a>, for more details and to register. Microscopes to Models Workshop, July 13-14th. We invite you and your colleagues to attend this two day workshop designed for biologists who are new to modeling and have some experience with microscopy. The hands-on workshop combines microscopy based experiments, e.g. Fluoresence Redistribution After Photobleaching (FRAP), with model-based simulation analysis with Virtual Cell and Virtual FRAP. See <a href="http://vcell.org/education/submit_registration.html" target="_blank">http://vcell.org/education/submit_registration.html</a> for more information and to register. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

ICSB 2009 at Stanford in August-September 2009

Markus Covert — 2009-05-23T01:07:05-00:00

Dear Systems Biology Community, We would like to call your attention to the 2009 International Conference on Systems Biology Meeting which will take place at Stanford University this year. This 10th ICSB continues an annual series of conferences initiated by Hiroaki Kitano in Tokyo in 2000. The most recent meetings were held in Yokohama (2006), in Long Beach (2007), and in Goteborg (2008). Stanford University is situated in the San Francisco Bay Area -- birthplace of both recombinant DNA and the personal computer, and home to major academic and industrial efforts in vital aspects of systems biology, notably biotechnology, informatics and computing. Please see the website for schedule, speaker and registration information: <a href="http://www.icsb-2009.org/" target="_blank">http://www.icsb-2009.org/</a> We look forward to seeing you there! Markus -- Markus Covert Assistant Professor Department of Bioengineering Stanford University ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Foundations of Systems Biology in Engineering (FOSBE 2009) Registation and Late Abstract Submission

Mike Henson — 2009-05-21T22:24:36-00:00

Foundations of Systems Biology in Engineering (FOSBE 2009) Inverness Hotel and Conference Center Denver, Colorado August 9-12, 2009 www.fosbe.org Registration is now open for the Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009) sponsored by the CACHE Corporation. The primary objectives of the FOSBE 2009 conference will be to provide an in-depth review and critical assessment of the current state-of-the-art, to discuss current and future needs of research, education and training, and to identify new directions, opportunities, and challenges in systems biology. We anticipate strong attendance from academia, industry, and government. Late Abstract Submission We will be accepting late abstract submissions for poster presentations. Authors should submit their abstracts electronically to: <a href="https://www.softconf.com/s08/fosbe09/submit.html." target="_blank">https://www.softconf.com/s08/fosbe09/submit.html.</a> Papers will not be accepted. June 19, 2009: Deadline for contributed abstracts to be included in conference proceedings and deadline for early registration August 3, 2009: Final deadline for contributed abstracts Registration Fees $800 Early registration before June 19, 2009 $900 Regular registration after June 19, 2009 $500 Graduate student registration $50 Training Workshop (Sunday) The conference fee includes one copy of the proceedings CD, an abstract book, the opening reception, hospitalities during the poster session, the conference banquet and refreshments during program breaks. There is an additional $50 fee for the optional Training Workshop. Sessions Alternative Fuels Circadian Systems Drug Development Network Modeling and Analysis Synthetic Biology Systems Biology Education Systems Biology Training Workshop Invited Speakers Erin O'Shea, Harvard University, USA (keynote) Adam Arkin, University of California, Berkeley, USA David Balaban, Amgen, USA Bill Bentley, University of Maryland, USA Frank Doyle, University of California, Santa Barbara, USA Dan Gillespie, Gillespie Consulting, USA Albert Goldbeter, University of Brussels, Belgium Bruce Gomes, Pfizer, USA Vassily Hatzimanikatis, Swiss Institute of Technology (EPFL), Switzerland Erik Herzog, Washington University, USA Ravi Iyengar, Mount Sinai Medical School, USA Iya Khalil, Gene Network Sciences, USA John Lamb, Merck, USA Art Lander, University of California, Irvine, USA Doug Lauffenburger, Massachusetts Institute of Technology, USA Jim Liao, University of California, Los Angeles, USA Jens Nielsen, Chalmers University of Technology, Sweden Bodo Stern, Harvard University, USA Masaru Tomita, Keio University, Japan Hiroki Ueda, Kyushu University, Japan Eberhard Voit, Georgia Institute of Technology, USA Huimin Zhao, University of Illinois, USA ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

post-doc position

kblackw1 — 2009-05-20T12:47:48-00:00

George Mason University, Krasnow Institute for Advanced Study invites applications for a Postdoctoral Research position available immediately to contribute to ongoing cutting-edge research in computational systems biology / neuroscience funded by the National Institutes of Health (NIH) through the National Institute of Alcohol Abuse and Alcoholism. The initial focus is on the signaling pathways underlying learning and synaptic plasticity in the basal ganglia. The overall project involves a variety of techniques including computer simulations, software development, and electrophysiology, as well as close collaboration between modelers and experimentalists. The incumbent will join the Center for Neural Informatics, Structures, and Plasticity--an interdisciplinary, dynamic and creative research group at George Mason University's Krasnow Institute for Advanced Study, located in northern Virginia (15 miles west of Washington, D.C.). The successful applicant will have office space, a new computer, and a salary on the NIH postdoctoral scale supplemented by excellent state employee benefits. Research experience with programming languages (e.g. C++, JAVA), modelling packages (e.g. XPPAUT, Genesis), and knowledge of diffusion and stochastic processes is highly desirable. All highly motivated candidates with a recent Ph.D. in a relevant field (e.g. biology, computer science, physics, bioinformatics, engineering) are encouraged to apply. All applicants must apply at <a href="http://jobs.gmu.edu" target="_blank">http://jobs.gmu.edu</a> for position number F8816Z, then send resume, (p)reprints, a one-page description of your motivation, and three recommendation letters either to <a href="mailto:kblackw1@gmu.edu" target="_blank">kblackw1@gmu.edu</a>, or to Prof. Kim Blackwell, V.M.D., Ph.D. Molecular Neuroscience Department Krasnow Institute for Advanced Study George Mason University 4400 University Drive, MS 2A1 Fairfax, VA 22030-4444 (USA) Phone: 703-993-4381/Fax: 703-993-4325 Position will be filled as soon as a suitable candidate is found. George Mason University is an equal opportunity employer encouraging diversity. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Miscellaneous SBML news

mhucka — 2009-05-20T03:44:59-00:00

It's been a long time since SBML was mentioned on this list, so I wanted to bring up a few news items that may interest people. You can find out more at <a href="http://sbml.org" target="_blank">http://sbml.org</a> * The next SBML Forum meeting will be held Sep. 3-4 at Stanford University, California, as a satellite of ICSB 2009: <a href="http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting" target="_blank">http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting</a> * The most recent specification of SBML is Level 2 Version 4, released last December. Since then, a few document errors have been found. The specification and an errata list are available at <a href="http://sbml.org/Documents/Specifications" target="_blank">http://sbml.org/Documents/Specifications</a> * SBML recently surpassed a total of 160 software tools worldwide known to support SBML. A guide to the known tools is available at <a href="http://sbml.org/SBML_Software_Guide" target="_blank">http://sbml.org/SBML_Software_Guide</a> (If you have an SBML-compatible software tool and it's not listed, we apologize for the omission, and ask that you please notify us using the web form on that page.) * We are currently seeking people's feed about future development plans for libSBML. If you use libSBML and haven't already done so, please fill out the short survey! <a href="http://sbml.org/SBML_Projects/Development/LibSBML_survey_2009" target="_blank">http://sbml.org/SBML_Projects/Development/LibSBML_survey_2009</a> * There have been many additions and edits to the FAQ in the last several months, and it might be worth perusing if you haven't seen it recently: <a href="http://sbml.org/Documents/FAQ" target="_blank">http://sbml.org/Documents/FAQ</a> * There is a new area on sbml.org for small user-contributed programs and scripts. It's still new and nascent, but it'll surely grown in time: <a href="http://sbml.org/Community/Programs" target="_blank">http://sbml.org/Community/Programs</a> * SourceForge is currently holding a vote for community choice awards. Won't you please nominate the SBML project? <a href="http://sbml.org/vote-for-sbml" target="_blank">http://sbml.org/vote-for-sbml</a> * Life would not be complete without a Twitter feed for SBML: <a href="http://twitter.com/sbmlnews" target="_blank">http://twitter.com/sbmlnews</a> Everyone on the SBML Team and the SBML Editors heartily thank all of you who have supported SBML by using it, creating models with it, developing software to work with SBML, attending workshops, engaging in discussions on the mailing lists and in person, writing articles about SBML, and in all other ways both large and small. Thank you! Mike on behalf of the SBML Editors and the SBML Team -- Mike Hucka, Ph.D. <a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a> <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a> Senior Research Fellow, Control and Dynamical Systems Co-director, Biological Network Modeling Center (BNMC) Beckman Institute @ the California Institute of Technology ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

SABIO-RK User Meeting

martin.golebiewski — 2009-05-08T17:10:04-00:00

Dear Colleagues, now the meeting program is available for the SABIO-RK User Meeting <a href="http://projects.eml.org/sdbv/events/SABIORK_UserMeeting/index.html" target="_blank">http://projects.eml.org/sdbv/events/SABIORK_UserMeeting/index.html</a> <<a href="http://projects.eml.org/sdbv/events/SABIORK_UserMeeting/index.html" target="_blank">http://projects.eml.org/sdbv/events/SABIORK_UserMeeting/index.html</a>> which will be held in Heidelberg, Germany on June 15-16, 2009. SABIO-RK (<a href="http://sabio.villa-bosch.de/SABIORK/" target="_blank">http://sabio.villa-bosch.de/SABIORK/</a>) is a curated database containing data about biochemical reactions and their kinetic properties based on literature information. The Meeting will focus on: - the understanding of current SABIO-RK functionalities - delivering insight into the curation process - presentations of experiences by SABIO-RK users - future developments Beside presentations of SABIO-RK users and members of the development team there will be tutorials and discussions. Participants interested in a short oral presentation (5-10 minutes) about their work in progress are invited to send the title of the talk by using the registration form. The deadline for registration is May 15, 2009. We hope to see you there. The SABIO-RK team Martin Golebiewski Tel: +49-6221-533281 FAX: +49-6221-533298 Email: <a href="mailto:martin.golebiewski@eml-r.villa-bosch.de" target="_blank">martin.golebiewski@eml-r.villa-bosch.de</a> ________________________________________________________________________ ____________________________________ EML Research gGmbH Schloss-Wolfsbrunnenweg 33 D-69118 Heidelberg Germany Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira, Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter <a href="http://www.eml-r.org" target="_blank">http://www.eml-r.org</a> <<a href="http://www.eml-r.org/" target="_blank">http://www.eml-r.org/</a>> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Postdoctoral Position in modelling nicotine-dopamine interactions

boris.gutkin — 2009-04-29T11:30:52-00:00

We are searching for one postdoc to develop computational models of nicotine addiction in the brain. The candidate will participate in a project in which the interaction between nicotine and dopamine pathways are studied on the level of receptor dynamics and microcircuit behavior in the ventral tegmental area (VTA). Initial research directions include: 1. to construct spiking network models of the VTA in order to understand how addictive drugs, and nicotine specifically, usurp the normal function of the dopaminergic signalling by controlling the activity modes of the neurons. 2. to integrate the VTA circuit in the mesocorticolimbic feedback loop model. The candidate will have the opportunity to develop further directions together with the project leaders and collaborators. This work is carried out in close interaction with experimental labs in the Paris region and abroad. The ideal candidate will have a doctoral degree, or equivalent, with an emphasis on computational approaches to the biology of neuronal systems. Basic knowledge of neuronal signal integration and signal transmission in spiking neuronal networks is required. Programming in Matlab and C/C++ will be part of the project. The position is funded until 01/2011 with possible extensions. Salary is commensurate with experience and the position carries a full social security and health coverage. Generous travel allowances will be provided. Applications should include a CV, a motivation letter and two recommendation letters. Applications will be reviewed on a rolling basis until a suitable candidate has been found. Please send applications (preferred format pdf) and further inquiries via email to Boris Gutkin boris.gutkin-at-ens.fr . Dr. Boris S Gutkin Senior Research Scientist Group for Neural Theory DEC-ENS 29 rue d'Ulm 75005 Paris tel: +33 (0)1 44 32 29 56 fax: +33 (0)1.44.32.29.74 www.gnt.ens.fr ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

MCSim v 5.3.1 support of SBML

Frederic.BOIS — 2009-04-26T20:56:38-00:00

Hi! GNU MCSim (<a href="http://www.gnu.org/software/mcsim/" target="_blank">http://www.gnu.org/software/mcsim/</a>) is a simulation package, written in C, which allows you to: * design your own statistical or simulation models (eventually dynamic, via ODEs), * perform Monte Carlo stochastic simulations, * do Bayesian inference through Markov Chain Monte Carlo simulations. Current version 5.3.1 supports importing SBML models. You can then use the Bayesian numerical computation features of GNU MCSim to calibrate your models (see <a href="http://www.gnu.org/software/mcsim/supplement_bioinformatics_2009.html" target="_blank">http://www.gnu.org/software/mcsim/supplement_bioinformatics_2009.html</a> for a demo). Version 5.3.1 does not use LibSBML. We are currently working on a version calling for LibSBML with extensive and more robust processing of SBML. Do not hesitate to contact me if you have questions on MCSim. Even better is to post on <a href="http://lists.gnu.org/mailman/listinfo/help-mcsim" target="_blank">http://lists.gnu.org/mailman/listinfo/help-mcsim</a> to share with everyone. Frederic Bois ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Registration for Pathway Tools Tutorial & Workshop (August 19-28, 2009) Now Open

Tomer Altman - Workshop Coordinator — 2009-04-24T19:13:39-00:00

Pathway Tools Tutorial & Workshop Registration Now Open Registration is now open for the Pathway Tools Tutorial & Workshop on August 19-28, 2009 in Menlo Park, CA Please visit our registration website for details on fees, travel, and hotels: <a href="http://brg.ai.sri.com/ptools09/reg.html" target="_blank">http://brg.ai.sri.com/ptools09/reg.html</a> Registration fees go up on June 15th, so please sign up soon! Best regards, ~Tomer Altman (650)859-2692 Pathway Tools Workshop Coordinator --- Pathway Tools Workshop August 19-28, 2009 Hosted by the Bioinformatics Research Group <<a href="http://brg.ai.sri.com/" target="_blank">http://brg.ai.sri.com/</a>> at SRI International <<a href="http://www.sri.com" target="_blank">http://www.sri.com</a>> <a href="http://brg.ai.sri.com/ptools09/" target="_blank">http://brg.ai.sri.com/ptools09/</a> This two-part workshop oriented around SRI's Pathway Tools software and BioCyc Database Collection will explore pathway bioinformatics and Pathway/Genome Databases. The workshop will be held at SRI International in Menlo Park, CA in the San Francisco Bay Area, with proximity to redwood forests, the Napa Valley, Lake Tahoe, and Northern California beaches. Part 1: Tutorial, August 19-21 This introductory tutorial will educate the new user on aspects of Pathway Tools including basic use of the Pathway/Genome Navigator, Editors, and PathoLogic. Students can bring a genome and leave with a draft Pathway/Genome Database. Tutorial space is limited. Part 2: Workshop August 24-28 The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to: * Share expertise on how to develop new organism-specific databases with Pathway Tools * Present new scientific results achieved with Pathway Tools and BioCyc * Share experiences on how to make the most of Pathway Tools * Presentations by users on extensions they have developed to Pathway Tools * Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs * Discussions of requested future enhancements to Pathway Tools and BioCyc * Ideas for other software tools to integrate with Pathway Tools * Group development of new Pathway Tools enhancements Should you wish to make a presentation at the meeting, please submit a proposed title and abstract to <a href="mailto:ptools-info@ai.sri.com" target="_blank">ptools-info@ai.sri.com</a> Please check the following website for updates: <a href="http://brg.ai.sri.com/ptools09/" target="_blank">http://brg.ai.sri.com/ptools09/</a> -- Pathway Tools Workshop: August 19 - 28, 2009 <a href="http://bioinformatics.ai.sri.com/ptools09" target="_blank">http://bioinformatics.ai.sri.com/ptools09</a> --- Tomer Altman <a href="mailto:taltman@ai.sri.com" target="_blank">taltman@ai.sri.com</a> (650)859-2692 <a href="http://www.ai.sri.com/people/taltman" target="_blank">http://www.ai.sri.com/people/taltman</a> Bioinformatics Research Group: Artificial Intelligence Center SRI, International <a href="http://bioinformatics.ai.sri.com/" target="_blank">http://bioinformatics.ai.sri.com/</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Announcement: SABIO-RK User Meeting

wittig — 2009-03-16T10:48:25-00:00

Dear Colleague, we would like to draw your attention to the SABIO-RK User Meeting <a href="http://projects.eml.org/sdbv/events/SABIORK_UserMeeting/index.html" target="_blank">http://projects.eml.org/sdbv/events/SABIORK_UserMeeting/index.html</a> which will be held in Heidelberg, Germany on June 15-16, 2009. SABIO-RK (<a href="http://sabio.villa-bosch.de/SABIORK/" target="_blank">http://sabio.villa-bosch.de/SABIORK/</a>) is a curated database containing data about biochemical reactions and their kinetic properties based on literature information. The Meeting will focus on: - the understanding of current SABIO-RK functionalities - delivering insight into the curation process - presentations of experiences by SABIO-RK users - future developments Beside presentations of SABIO-RK users and members of the development team there will be tutorials and discussions. Participants interested in a short oral presentation (5-10 minutes) about their work in progress are invited to send the title of the talk by using the registration form. The deadline for registration is May 15, 2009. We hope to see you there. Dr. Ulrike Wittig Scientific Databases and Visualization EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany <a href="mailto:ulrike.wittig@eml-r.villa-bosch.de" target="_blank">ulrike.wittig@eml-r.villa-bosch.de</a> Phone +49-6221-533-217 Fax +49-6221-533-298 www.eml-r.villa-bosch.de <<a href="http://www.eml-r.villa-bosch.de/" target="_blank">http://www.eml-r.villa-bosch.de/</a>> Amtsgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira, Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

KITP: Morphodynamics of Plants, Animals and Beyond

emj — 2009-02-23T20:29:59-00:00

Dear colleagues, We are writing to remind you of the mini-program titled "Morphodynamics of Plants, Animals and Beyond", to be held at the Kavli Institute for Theoretical Physics at the University of California, Santa Barbara, during the period August 24 - September 25, 2009, and to alert you that applications are now being accepted with a rapidly approaching deadline of March 1. This five-week program will seek to bring to bear current developments and foundational work in models of morphodynamic processes. Beneficiaries will include biologists who bring their problems, and physicists, applied mathematicians, and computer scientists who bring capabilities to more deeply understand such spatially dynamic problems. KITP programs differ from many conferences and workshops in that they create a situation where scientists learn from each other and actually do substantive research, often collaborating with other participants. To foster these interactions, KITP strongly encourages all theorists to stay for as long as possible, with three weeks being the minimum stay for a regular participant. We understand, however, that experimentalists usually cannot manage long visits but can have a big impact even in a week, so we can be more flexible for them. The latest information about this program and how to apply is available at the program home page on the KITP web site at <a href="http://www.kitp.ucsb.edu/activities/auto/?id=976." target="_blank">http://www.kitp.ucsb.edu/activities/auto/?id=976.</a> For examples of other KITP activities, please see <a href="http://www.kitp.ucsb.edu/activities." target="_blank">http://www.kitp.ucsb.edu/activities.</a> It is necessary for every participant to set up an account and apply online, even if we have already corresponded with you about the program. Because of space and budget limitations, participation is by invitation only, and we may not be able to accommodate everyone who applies. Late applications will be considered as budget and space permit. Some level of financial support will be available to invitees, the amount depending both on the needs of the participants and the availability of funds. KITP provides office and computing facilities on its site at UC Santa Barbara and also provides help in finding affordable living accommodations. For participants considering bringing children for periods of four weeks or more, there may be some additional support available through our Rice Family Fund. Please understand that actual commitments of office space and financial support can be made only by written formal invitations from the KITP Director, David Gross, regardless of any communications you may have had with us. Sincerely yours, Eric Mjolsness (<a href="mailto:emj@uci.edu" target="_blank">emj@uci.edu</a>) Elliot M. Meyerowitz (<a href="mailto:meyerow@caltech.edu" target="_blank">meyerow@caltech.edu</a>) Clare Yu (<a href="mailto:cyu@uci.edu" target="_blank">cyu@uci.edu</a>) -- Eric Mjolsness Institute for Genomics and Bioinformatics, and Computer Science Department University of California, Irvine <a href="mailto:emj@uci.edu" target="_blank">emj@uci.edu</a> <a href="http://www.ics.uci.edu/~emj" target="_blank">http://www.ics.uci.edu/~emj</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Molecular Systems Biology of the Cell, April 19-20

mhucka — 2009-02-19T04:39:50-00:00

The Institute for Systems Biology in Seattle, Washington, is presenting its 8th annual systems biology symposium. This year it is "Molecular Systems Biology of the Cell" The event is April 19-20, 2009. Please visit the following site for more information, registration, and a schedule: <a href="http://systemsbiology.org/symposium/index.html" target="_blank">http://systemsbiology.org/symposium/index.html</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

2009 NSF Computational Cell Biology Course

mhucka — 2009-02-17T22:37:06-00:00

Announcing the 2009 NSF Computational Cell Biology Course Cold Spring Harbor Laboratory June 26 - July 16 --> APPLICATIONS BY MARCH 15 <-- <a href="http://meetings.cshl.edu/courses/c-comp09.shtml" target="_blank">http://meetings.cshl.edu/courses/c-comp09.shtml</a> Computational cell biology is the field of study that applied the mathematics of dynamical systems together with computer simulation techniques to the study of cellular processes. The field encompassed several topics that have been studied long enough to be well established in their own right, such as calcium signaling, molecular motors and cell motility, the cell cycle, and gene expression during development. In addition to providing a recognizable larger community for topics such as these, this course provides a base for the development of newer areas of inquiry -- for example, the dynamics of intracellular second-messenger signaling, of programmed cell death, of mitotic chromosome movements, and of synthetic gene networks. Unlike computational genomics or bioinformatics, Computational Cell Biology is focused on simulation of the molecular machinery (genes-proteins-metabolites) that underlie the physiological behavior (input-output characteristics) of living cells. This three week course in Computational Cell Biology incorporates a series of didactic lectures on the mathematics of dynamical systems, computational simulation techniques, cell biology and molecular biology. Practicing theoreticians and experimentalists will rotate in for 1-3 day visits during the course to give lectures and interact with the students. Midway through the course, students will select an area for independent study, and the focus of the last week of the course will be largely on these projects, supplemented by continued visiting lecturers. Some scholarship support is available to students - please see applications materials. Further information can be found on the CSHL website: <a href="http://meetings.cshl.edu/courses/c-comp09.shtml" target="_blank">http://meetings.cshl.edu/courses/c-comp09.shtml</a> A flyer is attached in PDF format.

Computational Methods in Systems Biology (CMSB'09) -- call for papers

Roberto Gorrieri — 2009-02-10T10:33:43-00:00

*********************************************************************** ** CMSB 2009 ** ** The 7th Conference on Computational Methods in Systems Biology ** ** Bologna, Italy, August 31st - September 1st, 2009 ** ** <a href="http://cmsb09.cs.unibo.it/" target="_blank">http://cmsb09.cs.unibo.it/</a> ** *********************************************************************** Call for papers The CMSB (Computational Methods in Systems Biology) conference series was established in 2003 to help catalyze the convergence of modellers, physicists, mathematicians, and theoretical computer scientists (from fields such as language design, concurrency theory, program verification) with molecular biologists, physicians and neuroscientists interested in a systems-level understanding of cellular physiology and pathology. CMSB 2009 solicits original research articles, surveys of current research and posters. These may cover theoretical or applied contributions that are motivated by a biological question and can demonstrate actual or potential usefulness towards answering that question. Additionally, they may cover models of computation inspired by biological processes; of which the motivation may be either computational or biological. In particular, relevant case studies and open biological questions that demand modelling of systems are of significant interest. Topics of interest (biological systems and networks: inference, properties, modelling, dynamics, simulation and reverse engineering) include, but are not limited to: * Modelling: o Re-engineering and synthesis of biological systems and networks o Definition and study of theoretical properties of biologically-inspired formal languages o Qualitative and quantitative languages and calculi o Theoretical comparisons between different formal models of cellular processes o Models including symbolic evolution and learning o Spatial, multi-level, and multi-formalism modeling * Simulation / Analysis: o Simulation and analysis methods for computational biology o Biologically-inspired extensions to concurrency theory, constraint programming, logical methods or language equivalences o Emergence of properties in complex biological systems o Parallel, distributed, and multi-resolution simulation methods o Methods to predict biological network behavior from incomplete information * Tools / Frameworks / Libraries: o Modelling, analysis and simulation tools o Differential, discrete and/or stochastic modeling-language frameworks o Visualization methods for computational biology o Biological databases and exchange formats for biological data and standards * Applications: o Detailed biological case-studies on which formal models successfully apply o Computer models in nano-sciences applied to biological domains o Model-driven analysis of biological systems Submission The CMSB 2009 conference solicits high quality papers reporting research results and/or experience reports related to the topics mentioned above. All papers must be original, unpublished, and not submitted for publication elsewhere. Contributions should be submitted electronically as PDF via Easychair at * <a href="http://www.easychair.org/conferences/?conf=cmsb09" target="_blank">http://www.easychair.org/conferences/?conf=cmsb09</a> using the Springer LNCS style. Papers should not exceed 15 pages in length. If necessary, the paper may be supplemented with a clearly marked appendix, which will be reviewed at the discretion of the program committee. The proceedings of the conference will be published with Springer under the series named Lecture Notes in Bioinformatics, sub-series of Lecture Notes in Computer Science. The best papers presented at the Conference will be selected for a special issue of a Journal. Important Dates March, 16: Submission of abstracts March, 23: Submission of full papers May, 18: Notification of paper acceptance June, 15: Revised version of papers August 31 – September 1: Conference Invited speakers * Rita Casadio, Università di Bologna, Italy * John K. Heath, University of Birmingham, UK * Corrado Priami, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (Italy) Steering Committee * Finn Drabløs, Norwegian University of Science and Technology, Trondheim (Norway) * François Fages, INRIA Rocquencourt, France * David Harel, Weizmann Institute of Science, Israel * Monika Heiner, TU Cottbus (Germany) * Michael Hörnquist , Linköping University, Sweden * Satoru Miyano, University of Tokyo, Japan * Gordon Plotkin, University of Edinburgh, UK * Corrado Priami, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (Italy) * Adelinde M. Uhrmacher, University of Rostock, Germany Program Committee * Pierpaolo Degano, Università di Pisa, Italy (co-chair) * Finn Drabløs, Norwegian University of Science and Technology, Trondheim, Norway * François Fages, INRIA Rocquencourt, France * Stephen Gilmore, University of Edinburgh, UK * Roberto Gorrieri, Università di Bologna, Italy (co-chair) * Monika Heiner, TU Cottbus, Germany * Adaoha Elizabeth C. Ihekwaba, CoSBI, Italy * Marta Kwiatkowska, University of Oxford, UK * Pietro Liò, Computing Lab Cambridge, UK * Satoru Miyano, University of Tokyo, Japan * Mark van Rossum, University of Edinburgh, UK * Grzegorz Rozenberg, Leiden University, Leiden, NL * Carolyn Talcott, Stanford Research Institute, USA * Adelinde M. Uhrmacher, University of Rostock, Germany Organizing Committee * Cinzia Di Giusto, Università di Bologna, Italy * Roberto Gorrieri, Università di Bologna, Italy * Cristian Versari, Università di Bologna, Italy (chair) * Antonio Vitale, Università di Bologna, Italy * Gianluigi Zavattaro, Università di Bologna, Italy ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Supported doctoral program

eric_minch — 2009-02-10T01:14:00-00:00

For those working in health in space, and human applications on earth, here's a supported doctoral program of interest: <a href="http://www.dlr.de/me/desktopdefault.aspx/tabid-4960/." target="_blank">http://www.dlr.de/me/desktopdefault.aspx/tabid-4960/.</a> Please apply here: <a href="http://www.dlr.de/me/desktopdefault.aspx/tabid-5036/" target="_blank">http://www.dlr.de/me/desktopdefault.aspx/tabid-5036/</a> Best-- --Eric -- Dr. Eric Minch, Senior Research Fellow Applied Computer Science and Mathematics WP 37B-200, West Point, PA 19486-0004 tel: (215) 652-0194 fax: (215) 993-6016 email: <a href="mailto:eric_minch@merck.com" target="_blank">eric_minch@merck.com</a> Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at <a href="http://www.merck.com/contact/contacts.html" target="_blank">http://www.merck.com/contact/contacts.html</a>) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Post-Doc and PhD positions: Computational Systems Biology, ETH Zurich

Dagmar Iber — 2009-01-19T17:32:25-00:00

Post-Doc and PhD positions: Computational Systems Biology, ETH Zurich Applications are invited for a PhD studentship and a Post-Doc position, within the Computational Biology Group at the Department of Biosystems Science and Engineering of ETH Zurich. The group focuses on the development of detailed, predictive models for cellular signaling networks with a view to develop a comprehensive understanding of the dynamics and evolution of cellular signaling. All projects are carried out in close collaboration with experimental groups so that quantitative data is available and model predictions can be tested in experiments. Applicants should have a strong background in mathematical and computational modeling, and demonstrated experience in nonlinear dynamics and numerical calculations. PhD candidates should hold or expect to obtain a degree in a numerate discipline (e.g. mathematics, physics, computational biology, or related areas). Candidates are expected to engage in interdisciplinary research and to foster in-house collaborations with biologists and bioengineers. The Department of Biosystems Science and Engineering of ETH Zurich is an integral part of SystemX.ch, the Swiss initiative in Systems Biology. It is located in Basel, a European hotspot for biomedical research, in close proximity of the Biozentrum of the University of Basel, the Friedrich Miescher Institute for Biomedical Research, and the pharmaceutical and biotech industry. ETH Zurich is a major research university, offering an excellent environment for innovative and collaborative research across disciplines. Please send the usual application material, including at least two references, as a single PDF file to <a href="mailto:dagmar.iber@bsse.ethz.ch" target="_blank">dagmar.iber@bsse.ethz.ch</a> (preferred), or via surface mail to: Prof. Dr. Dr. Dagmar Iber ETH Zurich D-BSSE Mattenstrasse 26 4058 Basel Switzerland For further information please visit our web page at <a href="http://www.dbsse.ethz.ch/iber" target="_blank">http://www.dbsse.ethz.ch/iber</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

CFP: (HiBi 2009) International Workshop on High Performance ComputationalSystems Biology

mazza — 2009-01-19T11:21:31-00:00

Please find attached the Call For Papers for: **************************************************************************** International Workshop on High Performance Computational Systems Biology (HiBi 2009) Trento, Italy, October 14-16, 2009 <a href="http://www.cosbi.eu/hibi09/" target="_blank">http://www.cosbi.eu/hibi09/</a> **************************************************************************** The HiBi (High performance computational systems Biology) workshop establishes a forum to link researchers in the areas of parallel computing and computational systems biology. One of the main limitations in managing models of biological systems comes from the fundamental difference between the high parallelism evident in biochemical reactions and the sequential environments employed for the analysis of these reactions. Such limitations affect all varieties of continuous, deterministic, discrete and stochastic models; undermining the applicability of simulation techniques and analysis of biological models. The goal of HiBi is therefore to bring together researchers in the fields of high performance computing and computational systems biology. Experts from around the world will present their current work, discuss profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology. IMPORTANT DEADLINES: paper submission deadline (abstract only) April 24, 2009 paper submission deadline May 1, 2009 acceptance notification June 23, 2009 revised papers due July 15, 2009 early registration deadline July 31, 2009 Best regards, HiBi organizing committee ******************************************************************************** We apologize if you received multiple copies of this Call for Papers. Please feel free to distribute it to those who might be interested. ******************************************************************************** -------------------------------------------------------------------------------- International Workshop on High Performance Computational Systems Biology (HiBi 2009) October 14-16, 2009 Trento, Italy --------------------------------------------------------------------------------- 1st Call for Papers (<a href="http://www.cosbi.eu/hibi09/cfp.pdf" target="_blank">http://www.cosbi.eu/hibi09/cfp.pdf</a>) ***************** The HiBi (High performance computational systems Biology) workshop establishes a forum to link researchers in the areas of parallel computing and computational systems biology. One of the main limitations in managing models of biological systems comes from the fundamental difference between the high parallelism evident in biochemical reactions and the sequential environments employed for the analysis of these reactions. Such limitations affect all varieties of continuous, deterministic, discrete and stochastic models; undermining the applicability of simulation techniques and analysis of biological models. The goal of HiBi is therefore to bring together researchers in the fields of high performance computing and computational systems biology. Experts from around the world will present their current work, discuss profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology. Topics of interest include high performance algorithms, systems, architecture, and tools for the following: (but are not limited to the following list) - Parallel and distributed Stochastic simulation - Biological and Numerical parallel computing - Parallel and distributed architectures - Emerging processing architectures (Cell processors, GPUs, mixed CPU-FPGA) - Parallel Model Checking techniques - Parallel parameters estimation - Parallel algorithms for biological analysis - Application of concurrency theory to biology - Parallel visualization algorithms - Web-services and internet computing for e-Science - Tools and applications SUBMISSION INFORMATION: HiBi welcomes submissions for: - *full research papers* describing recent advances at the border between parallel computing and systems biology; - *short tool papers* describing implemented parallel techniques and tools for systems biology. PROCEEDINGS: All submitted papers will be reviewed by the Program Committee. The review process will include a rebuttal phase whereby authors will be given the possibility to send their comments on the received review. Full papers as well as short (tool) papers will be published in the proceedings of the workshop. Detailed information about papers format and publisher will be available soon. A selection of best (full) papers will also be published on a dedicated special issue of the Briefings in Bioinformatics journal. Submission of papers to HiBi09 will be through the EasyChair conference system. PROGRAM COMMITTEE MEMBERS: - Tommaso Mazza (CoSBi, Italy) - chair - Mateo Valero (Technical University of Catalonia, Spain) - co-chair - Yutaka Akiyama (Tokyo Institute of Technology, Japan) - Paolo Ballarini (CoSBi, Italy) - Gianfranco Balbo (University of Torino, Italy) - Lubos Brim (Masaryk University, Czech Republic) - Kevin Burrage (University of Oxford, UK) - Hidde De Jong (INRIA RhÃ´ne-Alpes, France) - FranÃ§ois Fages (INRIA Paris-Rocquencourt, France) - Fabrizio Gagliardi (Microsoft Research Cambridge, United Kingdom) - Martin Leucker (Technische UniversitÃ¤t MÃ¼nchen, Germany) - Gethin Norman (Oxford University Computing Laboratory, United Kingdom) - Dave Parker (Oxford University Computing Laboratory, United Kingdom) - Davide Prandi (CoSBi, Italy) - Assaf Schuster (Israel Institute of Technology, Israel) - Koichi Takahashi (RIKEN, Japan) - David Torrents Arenales (Barcelona Supercomputing Center, Spain) - Adelinde Uhrmacher (University of Rostock, Germany) Information related to HiBi 2009 is available at the official HiBi 2009 Web site: <a href="http://www.cosbi.eu/hibi09/" target="_blank">http://www.cosbi.eu/hibi09/</a>

Call for Papers: Data Integration in the Life Sciences

Norman Paton — 2009-01-18T18:24:22-00:00

*6th International Workshop on Data Integration in the Life Sciences * <a href="http://www.cs.manchester.ac.uk/DILS09/" target="_blank">http://www.cs.manchester.ac.uk/DILS09/</a> The DILS workshop provides a forum for the discussion of emerging challenges for data integration in the life sciences, and the techniques that seek to address them. Topics of interest include, but are not limited to: * Architectures and data management techniques for the life sciences * Query processing and optimization for biological data * Biological Data sharing and update propagation * Query formulation assistance for scientists * Modeling of life sciences data * Biological Metadata management * Annotation in scientific data integration * Provenance modeling and management for the life sciences * Scientific Workflows and analysis pipelines * Laboratory information management systems in biology * Biological data quality and data cleaning * Life sciences ontologies * Semantic web for the life sciences * Mining integrated life sciences data * Text mining in the life science literature * Machine learning in data integration in the life sciences * Grid Computing and Grid technologies for the life sciences * System prototypes for biology * Commercial solutions in the life sciences Submission Guidelines Authors are invited to submit original contributions of practical relevance and technical rigor, experience reports and demonstrations of relevance to data integation in the life sciences. DILS 2009 invites two types of papers: * *Research papers* (up to 16 pages). * *System/Demonstration papers* (up to 8 pages). Papers describing commercial solutions are welcome as long as sufficient detail of the problem and its technical solution are provided. The proceedings of DILS will be published by Springer in Lecture Notes in Bioinformatics. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Final call for abstracts for the 3rd InternationalBiocuration Conference 2009

martin.golebiewski — 2009-01-14T11:10:01-00:00

Final call for abstracts for the 3rd International Biocuration Conference 2009 which will take place in Berlin, Germany, on April 16th - 19th, 2009. <a href="http://projects.eml.org/Meeting2009" target="_blank">http://projects.eml.org/Meeting2009</a> <<a href="http://projects.eml.org/Meeting2009" target="_blank">http://projects.eml.org/Meeting2009</a>> Abstract submission deadline: January 15th, 2009 ------------------------------------------------------------------------ - Workshops/tutorials There will be two workshops and two tutorials. For more information please visit the following website: <a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutorial" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutorial</a> .html <<a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutoria" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutoria</a> l.html> ------------------------------------------------------------------------ ----- For questions or technical difficulties with the submission or registration, please contact Renate Kania at <a href="mailto:kania@eml-r.org" target="_blank">kania@eml-r.org</a> Please feel free to forward this announcement to interested parties. This announcement has been sent to multiple mailing lists. Apologies if you have been sent this email more than once or in error. Kind regards, The Organizing Committee ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

3rd International Biocuration Conference- reminder:abstract submission deadline is January 15, 2009

martin.golebiewski — 2009-01-12T09:51:03-00:00

Call for abstracts for The 3rd International Biocuration Conference 2009 which will take place in Berlin, Germany, on April 16th - 19th, 2009. <a href="http://projects.eml.org/Meeting2009" target="_blank">http://projects.eml.org/Meeting2009</a> Abstract submission deadline: January 15th, 2009 ------------------------------------------------------------------------ - Workshops/tutorials There will be two workshops and two tutorials. For more information please visit the following website: <a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutorial" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutorial</a> .html ------------------------------------------------------------------------ ----- For questions or technical difficulties with the submission or registration, please contact Renate Kania at <a href="mailto:kania@eml-r.org" target="_blank">kania@eml-r.org</a> Please feel free to forward this announcement to interested parties. This announcement has been sent to multiple mailing lists. Apologies if you have been sent this email more than once or in error. Kind regards, The Organizing Committee ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Call for paper: International Conference on Molecular Systems Biology 2009 (ICMSB09)

Fenny Xue — 2009-01-09T14:50:21-00:00

Dear colleagues, Please see below for CFP of International Conference on Molecular Systems Biology 2009 (ICMSB09). Please feel free to distribute to people who might be interested. Thank you on behalf of the organizers. Best regards, Fenny Xue CAS-MPG Partner Institute for Computational Biology(PICB) NO. 320, Yue Yang Road, Shanghai, 200031, China Tel: (86)-21-54920453 Fax: (86)-21-54920451 Email: <a href="mailto:fxue@sibs.ac.cn" target="_blank">fxue@sibs.ac.cn</a> ---------------------------------------------------------------- 11th International Conference on Molecular Systems Biology <a href="http://www.picb.ac.cn/icmsb2009" target="_blank">http://www.picb.ac.cn/icmsb2009</a> June 21-25, 2009 Chinese Academy of Sciences - Max Planck Society Partner Institute for Computational Biology, Shanghai, China For the past years, active research in systems biology has generated many promising and intriguing experimental, theoretical, and computational results. At the 11th International Conference on Molecular Systems Biology (ICMSB'09, Shanghai), world experts from many relevant fields will meet in Shanghai to present and discuss recent advances and new applications in molecular systems biology, and exchange emerging research ideas. We strongly encourage participation by young researchers and graduate students from all over the world. The ICMSB'09 will be hosted by the CAS-MPG Partner Institute for Computational Biology (PICB). The city of Shanghai is a dynamic center of economy, commerce, science and technology in . It provides an excellent environment for scientists to interact and identify potential collaborations. We are now open to accept contributed talks and posters for all areas in molecular systems biology including (but not limited to) the following topics: * Mathematical modeling and simulation of biosystems and their evolution * Functional genomics and proteomics * Identification and analysis of gene regulatory networks * Identification and analysis of protein-protein interaction networks * Identification and analysis of metabolic networks * Computational approaches to complex genetic diseases * Synthetic biology and circuitry ABSTRACT SUBMISSION DEADLINE March 15, 2009 SCIENCE ADVISORY BOARD Rui Alves, Universidad de Lleida, Spain William Atchley, North Carolina State University, USA Xiaoya Chen, Institute of Plant Physiology and Ecology, CAS Andreas Dress, CAS-MPG Partner Institute for Computational Biology Jianfeng Feng, Warwick University, UK Bailin Hao, Fudan University, China Li Jin, Fudan University | CAS-MPG Partner Institute for Computational Biology Eduardo Mendoza, Ludwig Maximilians University, Germany Albert Sorribas, Universidad de Lleida, Lleida, Spain Martin Vingron, Max Planck Institute for Molecular Genetics, Germany Eberhardt Voit, Georgia Institute of Technology, USA ORGANIZING COMMITTEE Su-shing Chen, CAS-MPG PICB, CAS Haipeng Li, CAS-MPG PICB, CAS Kun Tang, CAS-MPG PICB, CAS Shuhua Xu, CAS-MPG PICB, CAS Jin Yang, CAS-MPG Partner Institute for Computational Biology

3rd International Biocuration Conference - second announcement

martin.golebiewski — 2008-12-17T15:10:53-00:00

Second announcement ------------------------------------------------------------------------ - Call for abstracts for The 3rd International Biocuration Conference 2009 which will take place in Berlin, Germany, on April 16th - 19th, 2009. <a href="http://projects.eml.org/Meeting2009" target="_blank">http://projects.eml.org/Meeting2009</a> <<a href="http://projects.eml.org/Meeting2009" target="_blank">http://projects.eml.org/Meeting2009</a>> Abstract submission deadline: January 15th, 2009 ------------------------------------------------------------------------ - Workshops/tutorials There will be two workshops and two tutorials. For more information please visit the following website: <a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutorial" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutorial</a> .html <<a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutoria" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop_tutoria</a> l.html> ------------------------------------------------------------------------ ----- Travel Fellowships For more information please visit the following website: <a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/travel_fellowship" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/travel_fellowship</a> .html <<a href="http://projects.eml.org/sdbv/events/BiocurationMeeting/travel_fellowshi" target="_blank">http://projects.eml.org/sdbv/events/BiocurationMeeting/travel_fellowshi</a> p.html> ------------------------------------------------------------------------ ----- For questions or technical difficulties with the submission or registration, please contact Renate Kania at <a href="mailto:kania@eml-r.org" target="_blank">kania@eml-r.org</a> Please feel free to forward this announcement to interested parties. This announcement has been sent to multiple mailing lists. Apologies if you have been sent this email more than once or in error. Kind regards, The Organizing Committee Martin Golebiewski ________________________________________________________________________ ____________________________________ EML Research gGmbH Schloss-Wolfsbrunnenweg 33 D-69118 Heidelberg Germany Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira, Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter <a href="http://www.eml-r.org" target="_blank">http://www.eml-r.org</a> <<a href="http://www.eml-r.org/" target="_blank">http://www.eml-r.org/</a>> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Computational Methods in Systems Biology (CMSB) - first call for papers

Roberto Gorrieri — 2008-12-15T07:09:48-00:00

(Apologies if you receive multiple copies of this message) **************************************************** International Conference on COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY (CMSB 2009) **************************************************** (first call for papers) August 31 -- September 1, 2009 Bologna, Italy <a href="http://cmsb09.cs.unibo.it/" target="_blank">http://cmsb09.cs.unibo.it/</a> ***************************************************** The CMSB (Computational Methods in Systems Biology) conference series was established in 2003 to help catalyze the convergence of modelers, physicists, mathematicians, and theoretical computer scientists (from fields such as language design, concurrency theory, program verification) with molecular biologists, physicians and neuroscientists interested in a systems-level understanding of cellular physiology and pathology. CMSB 2009 solicits original research articles, surveys of current research and posters. These may cover theoretical or applied contributions that are motivated by a biological question and can demonstrate actual or potential usefulness towards answering that question. Additionally, they may cover models of computation inspired by biological processes; of which the motivation may be either computational or biological. In particular, relevant case studies and open biological questions that demand modeling of systems are of significant interest. Topics of interest (biological systems and networks: inference, properties, modeling, dynamics, simulation and reverse engineering) include, but are not limited to: Modeling: -------- * Re-engineering and synthesis of biological systems and networks * Definition and study of theoretical properties of biologically-inspired formal languages * Qualitative and quantitative languages and calculi * Theoretical comparisons between different formal models of cellular processes * Models including symbolic evolution and learning * Spatial, multi-level, and multi-formalism modeling Simulation/Analysis: ------------------- * Simulation and analysis methods for computational biology * Biologically-inspired extensions to concurrency theory, constraint programming, logical methods or language equivalences * Emergence of properties in complex biological systems * Parallel, distributed, and multi-resolution simulation methods * Methods to predict biological network behavior from incomplete information Tools/Frameworks/Libraries: -------------------------- * Modeling, analysis and simulation tools * Differential, discrete and/or stochastic modeling-language frameworks * Visualization methods for computational biology * Biological databases and exchange formats for biological data and standards Applications: ------------ * Detailed biological case-studies on which formal models successfully apply * Computer models in nano-sciences applied to biological domains * Model-driven analysis of biological systems All submissions will be reviewed by the program committee. The proceedings of the conference will be published with Springer under the series named Lecture Notes in Bioinformatics, sub-series of Lecture Notes in Computer Science. The best papers presented at the Conference will be selected for a special issue of a Journal. Important Dates --------------- March, 16: Submission of abstracts March, 23: Submission of full papers May, 18: Notification of acceptance/rejection June, 15: Revised version of accepted papers due August 31 -- September 1: Conference PROGRAM COMMITTEE (provisional) ----------------- Pierpaolo Degano, Università di Pisa, Italy (co-chair) Finn Drablos, Norwegian University of Science and Technology, Norway François Fages, INRIA Rocquencourt, France Stephen Gilmore, University of Edinburgh, UK Roberto Gorrieri, Università di Bologna, Italy (co-chair) Monika Heiner, TU Cottbus, Germany Adaoha Elizabeth C. Ihekwaba, CoSBI, Italy Marta Kwiatkowska, University of Oxford, UK Pietro Liò, Computing Lab Cambridge, UK Satoru Miyano, University of Tokyo, Japan Mark van Rossum, University of Edinburgh, UK Grzegorz Rozenberg, Leiden University, Leiden, NL Carolyn Talcott, Stanford Research Institute, USA Adelinde M. Uhrmacher, University of Rostock, Germany ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

SBML Hackathon 2009: March 26-28

mhucka — 2008-12-12T23:28:02-00:00

Announcing the ------------------- SBML Hackathon 2009 ------------------- <a href="http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon" target="_blank">http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon</a> March 26-28 European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Hosted and co-organized by the Le Novere group (<a href="http://ebi.ac.uk/compneur" target="_blank">http://ebi.ac.uk/compneur</a>) SBML Hackathons are an opportunity to get together with other software developers who use SBML as their model exchange format. The objective of the meeting is to collaborate and exchange ideas and software to accelerate development of SBML-enabled software. The 2009 SBML Hackathon will be held at the familiar EBI in Hinxton, UK, which was also the site of the 2004 SBML Hackathon. The EBI is the home of many SBML-related efforts and resources, including the BioModels Database, the Systems Biology Ontology, MIRIAM Resources, and more. This year's event will be immediately followed by the BioModels Annual Meeting, held March 28-30. Interested persons may register for one or both events using the registration page at <a href="http://tinyurl.com/sb2009" target="_blank">http://tinyurl.com/sb2009</a> This year's Hackathon is also preceded by BioSysBio on March 23-25 in Cambridge (<a href="http://conferences.theiet.org/biosysbio/" target="_blank">http://conferences.theiet.org/biosysbio/</a>) and will be followed shortly thereafter by the combined CellML-SBGN-SBO-MIRIAM-BioPAX super-workshop in Auckland, New Zealand, April 5 (<a href="http://www.cellml.org/workshop/workshop2009/" target="_blank">http://www.cellml.org/workshop/workshop2009/</a>). Please visit the SBML Hackathon 2009 information page for more information, and please make sure to fill out the registration form as soon as you can: <a href="http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon" target="_blank">http://sbml.org/Events/Hackathons/The_7th_SBML_Hackathon</a> We will have a limited amount of travel support funding available for the SBML/BioModels events. We emphasize *limited amount*. If you truly need it, please get in touch with us as soon as possible and we will try to work something out. We hope to see you all there in 2009! Mike, the Le Novere group, and the SBML Team ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

PhD stipends in computational systems biology, Heidelberg

Sven Sahle — 2008-12-02T14:29:38-00:00

Dear colleagues, I would like to draw your attention to available stipends for PhD projects in computational systems biology in Heidelberg. The stipends are offered by the Heidelberg MathComp Graduate School and the VIROQUANT center. Details about the projects are listed on the following page: <a href="http://www.mathcomp.uni-heidelberg.de/application/viroquant.php" target="_blank">http://www.mathcomp.uni-heidelberg.de/application/viroquant.php</a> Specifically, in our group we are looking for applicants with a strong mathematical background for projects involving the development of computational methods for the analysis of stochastical models. For further information about these projects you can contact <a href="mailto:sven.sahle@bioquant.uni-heidelberg.de" target="_blank">sven.sahle@bioquant.uni-heidelberg.de</a> Dr. Sven Sahle Abteilung Modellierung biologischer Prozesse Universität Heidelberg, BIOQUANT/Zoologie ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Two Pathway Commons Positions @ MSKCC, New York

Emek Demir — 2008-11-24T17:36:23-00:00

Hi All, Please see the announcement for two new Pathway Commons positions at MSKCC. I would be grateful if you can announce this locally and forward it to the people who might be interested in. Thanks! Emek *Biological Pathway Information Resource* *Content Manager and Software Developer* Join us building *Pathway Commons*, a research resource for biological pathways and cellular processes. Collaborate with scientists around the world to refine the standard *BioPAX* language for exchanging pathway data. Aggregate and integrate information and make it available to the scientific world for use in the scientific discovery process. Become part of the revolutionary expansion of biological knowledge connecting molecular behavior to system properties. Two pathway informatics positions are available immediately in Chris Sander's Computational and Systems Biology Group in the *Computational Biology Center* at Memorial Sloan Kettering Cancer Center (MSKCC) in New York City. Pathway Commons is a collaborative project with Gary Bader's group at the University of Toronto. MSKCC is one of the world's premier cancer centers with an emphasis on leading-edge research. Apply to *pathway-commons-jobscbio.mskcc.org* preferably by *8 Dec 2008.* *Content Manager - Research Scientist* As Content Manager, collaborating with biological pathway database teams, you will be responsible for aggregating, validating and *integrating pathway information* and maintaining Pathway Commons releases. You also will work on BioPAX development, test Pathway Commons information services and organize outreach programs for biologists. You have the opportunity to participate in research projects applying pathway-based ideas, tools, and algorithms to cancer genomics. You have a PhD or equivalent in or a related field and have an excellent understanding of the biology reflected in pathway representations. Exceptional* organizational and communication* skills are required. Experience in Java, ontologies, pathway databases and bioinformatics analysis tools is a plus. * Infrastructure Developer - Research Fellow* As Infrastructure Developer, working with the Pathway Commons team, you will build tools and develop *software systems* for aggregating, integrating, querying and analyzing biological pathway information. Your tasks include helping develop a software library for BioPAX, designing and developing a state-of-the-art query backend, new algorithms for comparing and merging pathways and an internet application for efficient capture of biological factoids. You have a postgraduate degree in computer science, computational biology or a related field, excellent *programming skills, preferably in Java*, and experience in knowledge representation. A strong interest in molecular biology and previous experience in developing bioinformatics applications is a big plus.

Joint CMU-Pitt Ph.D. Program in Computational Biology

NEP7 — 2008-11-12T18:57:22-00:00

____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or

Positions Available in Seattle

Herbert M Sauro — 2008-10-27T17:58:31-00:00

Applications are invited for a post doctoral position at the Systems and Synthetic Biology group in the University of Washington, Seattle. The offer is for an NIH funded position for four years to work in the following areas: 1) In collaboration with the Glazier group in Indiana, explore ways in which standards such as SBML or CellML can be used to describe multicellular systems.Communication with the exiting standards community is critical to this effort. 2) Develop a C/C++ based software library for ODE simulation (possibly based on SOSLib or other existing C/C++ based simulators) that uses SBML (via libSBML) and collaborate with the compucell3d group in Indiana to integrate this library into their software to enable cellular network simulation in multicellular models. 3) Investigate ways to run multicellular systems at high efficiency on multicore systems. 4) Enhance existing or develop new visualization tools (particularly cell network visualizers) that can be added as plugins to the compucell3D framework. 5) Work with the Indiana group to develop multicellular models or enhance the general modeling environment. The Indiana group already has an advanced modeling system for multicellular systems based on the Potts model. This approach can model different cell-types in the same model as well as migration of cells in a tissue or organ containing 1000s of cells. This approach is ideally suited to modeling systems such as development or wound healing. However the model does not incorporate any internal cellular dynamics in the individual cells. One of the aims of this project is to enhance the modeling capacity by incorporating cellular network modeling. For more general information see the press release at <a href="http://newsinfo.iu.edu/news/page/normal/9038.html" target="_blank">http://newsinfo.iu.edu/news/page/normal/9038.html</a> This project is a joint effort between UW and the University of Indiana with James Glazier as PI. Salary is based on the NIH post-doctoral pay scale but the exact salary point will depend on the applicant's experience. The successful applicant will be based in Seattle. Please send applications, including at least two references, as a single PDF file to <a href="mailto:hsauro@uw.washington.edu" target="_blank">hsauro@uw.washington.edu</a> , or via surface mail to: Dr. Herbert Sauro Department of Bioengineering University of Washington Seattle, WA, 98195 -- Herbert M Sauro Associate Professor Department of Bioengineering University of Washington Seattle, WA, 98195-5061 Check out our simulation software at www.sys-bio.org Tel: 206-685-2119 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Post-Doc and PhD positions at ETH Zurich

Dagmar Iber — 2008-10-21T12:58:16-00:00

Applications are invited for a PhD studentship and a Post-Doc position, within the Computational Biology Group at the Department of Biosystems Science and Engineering of ETH Zurich. The group focuses on the development of detailed, predictive models for cellular signaling networks with a view to develop a comprehensive understanding of the dynamics and evolution of cellular signaling. All projects are carried out in close collaboration with experimental groups so that quantitative data is available and model predictions can be tested in experiments. Applicants should have a strong background in mathematical and computational modeling, and demonstrated experience in nonlinear dynamics and numerical calculations. PhD candidates should hold or expect to obtain a degree in a numerate discipline (e.g. mathematics, computational science, computational biology, physics, biotechnology, chemical or bio- engineering, or related areas). Candidates are expected to engage in interdisciplinary research and to foster in-house collaborations with biologists and bioengineers. The Department of Biosystems Science and Engineering of ETH Zurich is an integral part of SystemX.ch, the Swiss initiative in Systems Biology. It is located in Basel, a European hotspot for biomedical research, in close proximity of the Biozentrum of the University of Basel, the Friedrich Miescher Institute for Biomedical Research, and the pharmaceutical and biotech industry. ETH Zurich is a major research university, offering an excellent environment for innovative and collaborative research across disciplines. Please send the usual application material, including at least two references, as a single PDF file to <a href="mailto:dagmar.iber@bsse.ethz.ch" target="_blank">dagmar.iber@bsse.ethz.ch</a> (preferred), or via surface mail to: Prof. Dr. Dr. Dagmar Iber ETH Zurich D-BSSE Mattenstrasse 26 4058 Basel Switzerland For further information please visit our web page at <a href="http://www.dbsse.ethz.ch/research/group_iber" target="_blank">http://www.dbsse.ethz.ch/research/group_iber</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

3rd International Biocuration Conference Announcement

martin.golebiewski — 2008-10-16T09:45:46-00:00

Dear Colleagues, We cordially invite you to join us for the 3rd International Biocuration Conference in Berlin, Germany, from April 16-19, 2009. This conference will provide a forum for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this active and growing area of research. Furthermore, we will introduce the newly formed International Society for Biocuration (ISB). The past two Biocuration Meetings have been a great success. We are looking forward to your participation in the 3rd Conference! Meeting announcement & Call for abstracts Event date: April 16-19, 2009 Abstract Submission deadline: January 15th Early registration discount until: February 15th Location: SEMINARIS CampusHotel Berlin, Science & Conference Center, Berlin, Germany Website: <a href="http://projects.eml.org/Meeting2009" target="_blank">http://projects.eml.org/Meeting2009</a> For questions or technical difficulties with the registration, please contact Renate Kania at <a href="mailto:kania@eml-r.org" target="_blank">kania@eml-r.org</a> Please feel free to forward this announcement to interested parties. This announcement has been sent to multiple mailing lists. Please accept our apologies if you have received this email in duplicates or in error. Kind regards, The Organizing Committee ____________________________________________________________________________ Martin Golebiewski EML Research gGmbH Schloss-Wolfsbrunnenweg 33 D-69118 Heidelberg Germany Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira, Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter <a href="http://www.eml-r.org" target="_blank">http://www.eml-r.org</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Barcelona School on Biomedical Informatics 2009

jvilla — 2008-10-07T17:17:16-00:00

Dear colleague, We apologize for multiple messages. We would appreciate if you distribute the announcement for the 1st Barcelona School on Biomedical Informatics, organized by the Universitat Pompeu Fabra, to be held at the premises of the Barcelona Biomedical Research Park ( <a href="http://www.prbb.org" target="_blank">http://www.prbb.org</a>) on February 16th to 20th, 2009. The school aims at demonstrating the use of tools in the field of translational bioinformatics, in part based on the results of two EC-FP6 STREP projects that are about to finnish in a few months, BioBridge ( <a href="http://www.biobridge.eu" target="_blank">http://www.biobridge.eu</a>) and QosCosGrid (<a href="http://www.qoscosgrid.eu" target="_blank">http://www.qoscosgrid.eu</a>). The school will include intense hands-on training on computational systems biology methods and on their application to the biomedical research. The computational infrastructure for some of these tools will be demonstrated on the qoscosgrid environment. The students will be included into interdisciplinary groups targetting a particular question relevant to biomedical informatics from different perspectives. More details on the BSBMI, as well as the instructions for registration, can be found at <a href="http://www.bsbmi.eu" target="_blank">http://www.bsbmi.eu</a> On behalf of the organization Àlex Gómez Adrián López García de Lomana Marta Dies Pau Rué Jordi Villà-Freixa -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biomèdica de Barcelona C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: <a href="mailto:jvilla@imim.es" target="_blank">jvilla@imim.es</a> <a href="http://cbbl.imim.es" target="_blank">http://cbbl.imim.es</a> MSc Bioinformatics for Health Sciences <a href="http://www.upf.edu/postgraubiomed/bioinfo" target="_blank">http://www.upf.edu/postgraubiomed/bioinfo</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

GROUP LEADER POSITION IN BIOPHYSICS

martin.golebiewski — 2008-10-01T15:10:21-00:00

GROUP LEADER POSITION IN BIOPHYSICS Job Location: EML Research gGmbH, Heidelberg Germany General Description: EML Research gGmbH is a private non-profit research laboratory dedicated to basic and applied research in IT with a focus on bioinformatics and natural language processing. We offer a stimulating interdisciplinary environment, excellent computational facilities and support, and a competitive salary. Job Description: We are seeking outstanding candidates to establish an independent research group addressing fundamental questions in biophysics from a theoretical and/or computational perspective. The activities of the new research group should complement the existing groups at EML Research (see www.eml-research.de <<a href="http://www.eml-research.de" target="_blank">http://www.eml-research.de</a>> ) as well as related activities at the University of Heidelberg and other research organizations in the region. Through a collaboration agreement with the University of Heidelberg group leaders at EML Research can assume various academic responsibilities. The successful candidate will be expected to develop an internationally recognized research program. Group leaders at EML Research are encouraged to obtain additional funding through grant applications to national and international funding agencies. Requirements: Candidates must hold a doctorate in Physics, Biophysics, Chemistry or a related discipline. They should have at least 3 years of post-doctoral work experience in their scientific field. In addition they should have demonstrated independent research and leadership skills. Application: Applications should comprise a detailed CV, a list of publications, references, and a draft proposal for the scientific agenda of a research group in the field of biophysics. Send your applications to: Prof. Dr.-Ing. Andreas Reuter EML Research gGmbH EMLR-05-2008 Schloss-Wolfsbrunnenweg 33 D-69118 Heidelberg Or by e-mail to: Baerbel.Mack at eml-r.villa-bosch.de ________________________________________________________________________ ____________________________________ Martin Golebiewski Tel: +49-6221-533281 FAX: +49-6221-533298 Email: <a href="mailto:martin.golebiewski@eml-r.villa-bosch.de" target="_blank">martin.golebiewski@eml-r.villa-bosch.de</a> EML Research gGmbH Schloss-Wolfsbrunnenweg 33 D-69118 Heidelberg Germany Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira, Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter <a href="http://www.eml-r.org" target="_blank">http://www.eml-r.org</a> <<a href="http://www.eml-r.org/" target="_blank">http://www.eml-r.org/</a>> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Enhanced VCell Versions

rholmes — 2008-09-18T19:39:20-00:00

New VCell 4.5 (release) and VCell 4.6 (beta) Dear Colleague, We are pleased to announce the release of VCell 4.5 (release) and VCell 4.6 (beta). New features in VCell 4.5 (release) include the capacity for Hybrid stochastic simulations (HYSS), implementation of Differential Algebraic Equation (DAE) solver for fast systems, and refined VCML format. New features in VCell 4.6 (beta) include: enhanced SBML compatibility, explicit global parameters available for reaction kinetics, and improved user interfaces for model writing and data analysis. VCell 4.6 also provides links and import functions to models in BioModels DB <<a href="http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=home" target="_blank">http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=home</a>> (<a href="http://www.ebi.ac.uk/biomodels-main" target="_blank">http://www.ebi.ac.uk/biomodels-main</a>) and image data in PSLID DB <<a href="http://pslid.cbi.cmu.edu/public4/" target="_blank">http://pslid.cbi.cmu.edu/public4/</a>> (<a href="http://pslid.cbi.cmu.edu/public4/" target="_blank">http://pslid.cbi.cmu.edu/public4/</a>). A full list of new features is in Release Notes <<a href="http://vcell.org/login/release_notes.html" target="_blank">http://vcell.org/login/release_notes.html</a>> (<a href="http://vcell.org/login/release_notes.html" target="_blank">http://vcell.org/login/release_notes.html</a>), a description of HySS implementation can be found in the most recent user guide. Run VCell 4.5 (release <<a href="http://vcell.org/webstart/Rel/vcell.jnlp" target="_blank">http://vcell.org/webstart/Rel/vcell.jnlp</a>> - <a href="http://vcell.org/webstart/Rel/vcell.jnlp" target="_blank">http://vcell.org/webstart/Rel/vcell.jnlp</a>) or VCell 4.6 (beta <<a href="http://vcell.org/webstart/Beta/vcellbeta.jnlp" target="_blank">http://vcell.org/webstart/Beta/vcellbeta.jnlp</a>> - <a href="http://vcell.org/webstart/Beta/vcellbeta.jnlp" target="_blank">http://vcell.org/webstart/Beta/vcellbeta.jnlp</a>) to update your local cache and make use of the new functions. We look forward to your feedback on our new developments. VCell Team <a href="mailto:vcell@uchc.edu" target="_blank">vcell@uchc.edu</a> Raquell M. Holmes, Ph.D. <a href="http://raquell.us" target="_blank">http://raquell.us</a> <<a href="http://raquell.us/" target="_blank">http://raquell.us/</a>> Center for Cell Analysis and Modeling University of Connecticut Health Center <a href="http://www.ccam.uchc.edu" target="_blank">http://www.ccam.uchc.edu</a> <<a href="http://www.ccam.uchc.edu/" target="_blank">http://www.ccam.uchc.edu/</a>> Center for Computational Science Boston University <a href="http://ccs.bu.edu" target="_blank">http://ccs.bu.edu</a> <<a href="http://ccs.bu.edu/" target="_blank">http://ccs.bu.edu/</a>> <a href="http://raquell.us/" target="_blank">http://raquell.us/</a> <<a href="http://raquell.us/" target="_blank">http://raquell.us/</a>> <a href="http://ccs.bu.edu/" target="_blank">http://ccs.bu.edu/</a> <<a href="http://ccs.bu.edu/" target="_blank">http://ccs.bu.edu/</a>> <a href="http://www.ccam.uchc.edu/" target="_blank">http://www.ccam.uchc.edu/</a> <<a href="http://www.ccam.uchc.edu/" target="_blank">http://www.ccam.uchc.edu/</a>> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Postdoctoral Research Associate in Computational Cell Biology

Andrew Goryachev — 2008-09-01T14:46:54-00:00

POSTDOCTORAL RESEARCH ASSOCIATE IN COMPUTATIONAL CELL BIOLOGY A three-year position in computational cell biology is available in the group of Dr. Andrew B. Goryachev at the Centre for Systems Biology (CSBE), School of biological sciences, University of Edinburgh. An energetic, motivated and highly qualified researcher is required to spearhead the computational modeling effort in an international joint experiment-theory systems biology project to study cell polarity in budding yeast. The successful applicant will utilize published and novel experimental data to build detailed, realistic models of morphogenetic processes on a cell scale. Beyond the analysis of yeast molecular mechanisms, the project aims to reveal fundamental biophysical principles underlying self-organization of dynamic structures on biological membranes. Salary, up to GBP 32,000 per year, will be commensurate with the candidate’s skills and experience. Collaborative nature of the project provides an opportunity for international travel. REQUIREMENTS: A solid background in modeling chemical or biochemical reactive systems is required. Expertise in pattern-formation in far-from-equilibrium reactive media is particularly welcome. Understanding of principles of cell biology and experience in spatio-temporal modeling of cellular processes are desirable. Candidate should possess strong programming skills and experience of scientific computing in major programming languages and/or Matlab. Excellent communication skills are a must. APPLICATION: Interested individuals should send inquires and applications directly to Dr. A. Goryachev (<a href="mailto:Andrew.Goryachev@ed.ac.uk" target="_blank">Andrew.Goryachev@ed.ac.uk</a>). The position will be available from the 1st of October, 2008 and will remain open until filled. -- Dr. Andrew B. Goryachev Centre for Systems Biology School of Biological Sciences The University of Edinburgh +44 131 650 7807 <a href="http://www.biology.ed.ac.uk/research/groups/goryachev/" target="_blank">http://www.biology.ed.ac.uk/research/groups/goryachev/</a> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Biosimilars 2008 Announcement - Sept 22-23 - Washington, DC

Scherago International — 2008-08-27T13:56:11-00:00

Biosimilars 2008 Sept 22-23 George Washington University PRE-REGISTRATION DEADLINE SEPTEMBER 1, 2008 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Conference Announcement Juue/25/2008 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For Immediate Release Contact: Darrin Scherago <a href="mailto:biosimilars@scherago.com" target="_blank">biosimilars@scherago.com</a> [mailto:<a href="mailto:biosimilars@scherago.com]" target="_blank">biosimilars@scherago.com]</a> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Organizing Committee: James Green, Ph.D - Biogen Idec, USA Takao Hayakawa, Ph.D - Pharmaceuticals and Medical Devices Agency, Japan Rachelle Heller, Ph.D - George Washington University, USA Steven Kozlowski, M.D., FDA Curtis Meuse, Ph.D - NIST, USA Rudy Potenzone, Ph.D. - Microsoft, USA Emily Shacter, Ph.D. - FDA, USA Lincoln Tsang, Ph.D - Arnold & Porter LLP, UK Gillian Woollett, MA, DPhil - Engel & Novitt LLP, USA PRE-REGISTRATION DEADLINE: SEPTEMBER 1, 2008 www.biosimilarstoday.com [<a href="http://rs6.net/tn.jsp?e=0015le4iNNxq8b9qOnAtbc0o_6mT_7pz3CdvPA6TDqMNnVFL9D4_otl0KwqfbeRfaaH16L6AL6XaO84iG3cXA2MuVqfsuqthxg6a4b4WbmMR72W1XoVHrj_0q0yTrPP42WR" target="_blank">http://rs6.net/tn.jsp?e=0015le4iNNxq8b9qOnAtbc0o_6mT_7pz3CdvPA6TDqMNnVFL9D4_otl0KwqfbeRfaaH16L6AL6XaO84iG3cXA2MuVqfsuqthxg6a4b4WbmMR72W1XoVHrj_0q0yTrPP42WR</a>] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Biosimilars 2008 will be a two day conference to "air the issues" associated with the proposed legislation for biotech medicines currently under consideration in the US Congress to provide the authority for the FDA to regulate Biosimilars (also called follow-on biologics or generic biologicals). The conference will cover the main areas and issues of interest and concern to the innovator and generic Pharma industry and the public - legislative, legal and patent/intellectual property, the economic/financial, regulatory, scientific and standards issues, the experience of the EU procedures, the public sector concerns, and the health care industry interests. The global development of biosimilars is now recognized to be a critical part of the future of biotechnology, as the pharma, legal and payor/patient communities consider the legal, scientific, technical, financial and economic impacts. Participants will hear from, and interact with, leading professionals from government, non-governmental organizations and the private sector over the two-day Biosimilars2008 Conference. There will be four sessions with a broad and diverse spectrum of leading and knowledgeable speakers addressing the various issues and positions regarding Biosimilars or follow-on biologicals. There will be a panel session at the conclusion of each session for conference attendees to ask questions and interact with the speakers. Session Topics: 1. Legislative & Policy 2. Legal/Patent 3. Economic & Financial 4. Regulatory & Technical Who Should Attend: Pharma/Biotech Industry from the USA, Europe, Japan, India, Singapore, China, Israel, and other countries with biotech and generic biotech organizations: · Legal Affairs / Corporate Strategy / Regulatory Affairs · Intellectual Property / Patent Attorneys / Regulatory Compliance · New Product Development / Business Development / Business Operations · Project Management / Laboratory Heads/Chiefs / Scientific Affairs · Principal Scientists / Chief Scientific Officer Speakers: (Additional speakers listed on website) Senator Orrin Hatch, US Senate Hon. Henry Waxman, US House of Representatives Hon. Joe Barton, US House of Representatives (Invited) Elizabeth Dickinson, FDA John Emgel, Engel & Novitt LLP Bruce Artim, Eli Lilly Bill Tauzin, PhRMA David Dorsey, US Senate/HELP Patrick Vink, Mylan Pharmaceuticals Lisa Layman, GPhA Elizabeth Dickinson, FDA Geoffrey Allan, Ph.D, Insmed, Inc. Michale King, Rodman & Renshaw Sandra Dennis, BIO Brian Seiz, M.D., Express Scripts Diane Edquist Dorman, National Organization for Rare Disorders Anna Schwamlein Howard, AARP Jim Furniss, Bridgehead International Limited David Martin, M-CAM, Inc. Pamela Jones Harbour, FTC Commissioner Les Jordan, Microsoft Steve Miller, M.D., Express Scripts Diane Edquist Dorman, NORD Mark Merritt, Pharmaceutical Care Management Assoc. Jeffery Kushan, Sidley Austin, LLP William Schultz, Zuckerman Spaeder, LLP Ingrid Schwarzenberger, Ph.D, Sandoz Biopharmecuticals Development Susan Kirshner, Ph.D., FDA/CDER Milt Axley, Ph.D., MedImmune Falk Ehmann, M.D./Ph.D., EMEA Save by registering early - deadline is September 1. Register online at: www.biosomilarstoday.com [<a href="http://rs6.net/tn.jsp?e=0015le4iNNxq8Z_YWYH22pPf1BjjsNL38aVczCk2K-ifaAvumG0uNagZgEKKCNoqYtNeCoLMNViszsL8pAkJn8hmW9b7odNNtVjkpwAP_XNdm_QZ0xueO52i4wGx2uyGTMt" target="_blank">http://rs6.net/tn.jsp?e=0015le4iNNxq8Z_YWYH22pPf1BjjsNL38aVczCk2K-ifaAvumG0uNagZgEKKCNoqYtNeCoLMNViszsL8pAkJn8hmW9b7odNNtVjkpwAP_XNdm_QZ0xueO52i4wGx2uyGTMt</a>] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Organizer: Scherago International * 525 Washington Blvd, Ste 3310 * Jersey City, NJ 07310 Tel: 201-653-4777 * Fax: 201-653-5705 Email: <a href="mailto:biosimilarstoday@scherago.com" target="_blank">biosimilarstoday@scherago.com</a> * Website: www.biosimilarstoday.com [<a href="http://rs6.net/tn.jsp?e=0015le4iNNxq8b9qOnAtbc0o_6mT_7pz3CdvPA6TDqMNnVFL9D4_otl0KwqfbeRfaaH16L6AL6XaO84iG3cXA2MuVqfsuqthxg6a4b4WbmMR72W1XoVHrj_0q0yTrPP42WR" target="_blank">http://rs6.net/tn.jsp?e=0015le4iNNxq8b9qOnAtbc0o_6mT_7pz3CdvPA6TDqMNnVFL9D4_otl0KwqfbeRfaaH16L6AL6XaO84iG3cXA2MuVqfsuqthxg6a4b4WbmMR72W1XoVHrj_0q0yTrPP42WR</a>] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Forward email <a href="http://ui.constantcontact.com/sa/fwtf.jsp?m=1101300054303&ea=sysbio@caltech.edu&a=1102217489017" target="_blank">http://ui.constantcontact.com/sa/fwtf.jsp?m=1101300054303&ea=sysbio@caltech.edu&a=1102217489017</a> This email was sent to <a href="mailto:sysbio@caltech.edu" target="_blank">sysbio@caltech.edu</a> by <a href="mailto:darrins@scherago.com." target="_blank">darrins@scherago.com.</a> Update Profile/Email Address <a href="http://visitor.constantcontact.com/d.jsp?v=001U6LRkZXdabaZIKxTyuwA2G3g2jiAgzUy8EXmAdM0plO4TYyQtsPkMjt_YGazg4SttLWkjDYBwR7hU8kPZZacrA%3D%3D&p=oo" target="_blank">http://visitor.constantcontact.com/d.jsp?v=001U6LRkZXdabaZIKxTyuwA2G3g2jiAgzUy8EXmAdM0plO4TYyQtsPkMjt_YGazg4SttLWkjDYBwR7hU8kPZZacrA%3D%3D&p=oo</a> Instant removal with SafeUnsubscribe(TM) <a href="http://visitor.constantcontact.com/d.jsp?v=001U6LRkZXdabaZIKxTyuwA2G3g2jiAgzUy8EXmAdM0plO4TYyQtsPkMjt_YGazg4SttLWkjDYBwR7hU8kPZZacrA%3D%3D&p=un" target="_blank">http://visitor.constantcontact.com/d.jsp?v=001U6LRkZXdabaZIKxTyuwA2G3g2jiAgzUy8EXmAdM0plO4TYyQtsPkMjt_YGazg4SttLWkjDYBwR7hU8kPZZacrA%3D%3D&p=un</a> Privacy Policy: <a href="http://ui.constantcontact.com/roving/CCPrivacyPolicy.jsp" target="_blank">http://ui.constantcontact.com/roving/CCPrivacyPolicy.jsp</a> Email Marketing by Constant Contact(R) www.constantcontact.com Scherago International | 525 Washington Blvd. | Suite 3310 | Jersey city | NJ | 07310 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

First release of SBGN Process Diagrams

Nicolas Le Novere — 2008-08-23T13:00:02-00:00

23 August 2008. Dear Colleagues, After three years of hard work, we are happy to announce the first specification for Process Diagrams of the Systems Biology Graphical Notation! The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual representation of essential biochemical and cellular processes studied in Systems Biology. SBGN defines a comprehensive though limited set of symbols with precise semantics, together with detailed syntactic rules defining their use. It also describes the manner in which such graphical information should be interpreted. Standardizing graphical notations for describing biological interactions is an important step towards the efficient and accurate transmission of biological knowledge between different communities. Traditionally, diagrams representing interactions among genes and molecules have been drawn in an informal manner, using simple unconstrained shapes and edges such as arrows. Until the development of SBGN, no standard agreed-upon convention existed defining exactly how to draw such diagrams in a way that helps readers interpret them consistently, correctly, and unambiguously. By standardizing the visual notation, SBGN can serve as a bridge between different communities such as computational and experimental biologists, and even more broadly in education, publishing, and more. SBGN is formed of three languages offering different views of a biological system. The present specification defines the Level 1 of the Process Diagram notation, aimed to describe the causal sequences of molecular processes and their results. It is the result of numerous discussions and exchanges, between many individual and groups, and is very much a community work. The result should hopefully suits the result of most users while being unambiguous. More information on SBGN and SBGN Process Diagram Level 1 can be found at <a href="http://www.sbgn.org/" target="_blank">http://www.sbgn.org/</a> and through the mailing-list <a href="mailto:sbgn-discuss@sbgn.org" target="_blank">sbgn-discuss@sbgn.org</a> SBGN Principal Authors: Nicolas Le Novere (EMBL European Bioinformatics Institute, UK) Stuart Moodie (University of Edinburgh, UK) Anatoly Sorokin (University of Edinburgh, UK) Michael Hucka (California Institute of Technology, USA) Falk Schreiber (IPK Gatersleben & MLU Halle, Germany) Emek Demir (MSKCC Computational Biology Center, USA) Huaiyu Mi (SRI International, USA) Yukiko Matsuoka (The Systems Biology Institute, Japan) Katja Wegner (University of Hertfordshire, UK) and Hiroaki Kitano (The Systems Biology Institute, Japan) The authors are grateful to all the attendees of the SBGN meetings, as well as to the subscribers of the <a href="mailto:sbgn-discuss@sbgn.org" target="_blank">sbgn-discuss@sbgn.org</a> mailing list. The authors would like to acknowledge especially the help of Frank Bergmann, Sarala Dissanayake, Ralph Gauges, Peter Ghazal, and Lu Li. SM and AS would also like to acknowledge Igor Goryanin whose financial support and encouragement enabled us to commit the necessary time to the development of this specification. A more comprehensive list of people involved in SBGN development is available in the appendix D of the specification. The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO). The Okinawa Institute of Science and Technology (OIST), the AIST Computational Biology Research Center (AIST CBRC), the British Biotechnology and Biological Sciences Research Council (BBSRC), through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH), and the Beckman Institute at the California Institute of Technology provided additional support for SBGN workshops. Some help was provided by the Japan Science and Technology Agency (JST) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT) for the development of the gene regulation network aspect of SBGN, and from the British Engineering and Physical Sciences Research Council (EPSRC) during the redaction of the specification. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

BioModels Database 11th Release

Nicolas Le Novere — 2008-08-21T14:54:52-00:00

Hinxton, Thursday 21st August 2008 Dear colleagues, We are pleased to announce the eleventh release of BioModels Database. In this new release, 17 new models entered the curated branch. That brings the public version of BioModels Database to 259 models representing 27117 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 11000 cross-references. With the new release of BioModels Database software version 3, the interface for viewing the models is enhanced. Now, beside the model lists, the user also can browse a model-tree based on Gene Ontology. Model's elements are presented into several sections, which represent different aspects of the model. Furthermore, a submodel of any model can be generated, based on elements selected by the users. Finally, a simple embedded simulation tool is also provided, beside the links to the more powerful JWS interface. For more details on this release, please consult: <a href="http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_21August2008" target="_blank">http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_21August2008</a> BioModels Database is developed by the teams of Nicolas Le NovÃ¨re (EMBL-EBI, United-Kingdom) and Michael Hucka (SBML Team, Caltech, USA) in collaboration with Upinder Bhalla (DOQCS, National Center for Biological Sciences, India), Ion Moraru (the Virtual Cell), Jacky Snoep (JWS Online, Stellenbosch (ZA) University, ZA). BioModels Database development is funded by the European Molecular Biology Laboratory (Le NovÃ¨re team), the Biotechnology and Biological Sciences Research Council (Le NovÃ¨re team), the National Institute of General Medical Sciences (SBML team and Le NovÃ¨re team) and the National Center for Research Resources (Virtual Cell team). A big thank-you to all our collaborators and submitters! BioModels Database Team www.ebi.ac.uk/biomodels ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Minimum Information for Biological and Biomedical Investigations

Nicolas Le Novere — 2008-08-08T17:00:57-00:00

Dear colleagues, We would like to inform you that the paper describing the Minimum Information for Biological and Biomedical Investigations (MIBBI) project -- <a href="http://www.mibbi.org/" target="_blank">http://www.mibbi.org/</a> -- has been published this month in Nature Biotechnology. This represents a significant step towards a comprehensive set complementary reporting guidelines for the biosciences; both by describing our work to date, and by acting as a beacon for new participants. A PDF of the paper is freely-available for download: <a href="http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf" target="_blank">http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf</a> This paper: 1. Describes the foundational work performed by the ever-growing list of participants in this project. 2. Provides analysis of the various MI specifications registered at the site (scope, conflicts, etc.). 3. Addresses the view of funders and publishers on the enforcement of consensual reporting guidelines. 4. Outlines our plans for future work, which all are strongly encouraged to monitor, and in which all are invited to participate. Any questions can be directed to: Chris Taylor (<a href="mailto:chris.taylor@ebi.ac.uk" target="_blank">chris.taylor@ebi.ac.uk</a>) Dawn Field (<a href="mailto:dfield@ceh.ac.uk" target="_blank">dfield@ceh.ac.uk</a>) Susanna-Assunta Sansone (<a href="mailto:sansone@ebi.ac.uk" target="_blank">sansone@ebi.ac.uk</a>) Yours Sincerely, Chris, Dawn and Susanna on behalf of all authors. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Tutorial on SBGN at ICSB 2008

Nicolas Le Novere — 2008-07-31T09:00:11-00:00

Dear colleagues, The editors of the Systems Biology Graphical Notation will run a tutorial on SBGN process diagram before the ICSB in Goteborg, Sweden. See: <a href="http://www.icsb-2008.org/downloads/tutorials/sbgn-tutorial.pdf" target="_blank">http://www.icsb-2008.org/downloads/tutorials/sbgn-tutorial.pdf</a> The tutorial will take place on August 23, from 11:00 to 13:00. Registration is open until August 10 from the ICSB website. The aim of the tutorial is to provide participants with an understanding of what SBGN is, what problems it is designed to cover, and how SBGN constructs can be used to represent biological graphs such as signaling pathways, metabolic networks, or gene regulatory networks. To this end the tutorial will have the following structure: History of SBGN Rationale for a standardised graphical language, how SBGN started, what its goals are. Presentation of the three languages. SBGN-PD Level 1 We will introduce the concepts behind the Process Diagram notation. The set of symbols will be presented, and we will teach the drawing rules (syntax and semantics). We will start of by describing how to draw a simple pathway diagram, and then move on to progressively more complex examples that illustrate some of the more complex rules of SBGN-PD. Futures plans We will outline the roadmap for future SBGN releases, in particular those for the Entity-Relationship and Activity Flow notations as well as SBGN Level 2. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

SYCAMORE�a SYstems biology Computatio =?windows-1252?q?nal_Analysis_and_MOdeling_Research_Environmen

Rebecca Wade — 2008-07-11T11:42:02-00:00

Dear Sysbio listmanager: Could you post this to the sysbio list please? Best, Rebecca Wade SYCAMORE—a SYstems biology Computational Analysis and MOdeling Research Environment EML Research and the University of Heidelberg would like to announce the availability of SYCAMORE at <a href="http://sycamore.eml.org/." target="_blank">http://sycamore.eml.org/.</a> Finding answers to the complexity of questions emerging in modern biology requires the use of quantitative, computational approaches. Mathematical modelling is a critical component of systems biology studies of biochemical networks. However, the use and applicability of computational methods in systems biology is often hampered by the complexity of the software tools available for the modelling and simulation tasks. SYCAMORE has been developed in order to support the user, particularly the non-expert user, in setting up, simulating and analysing biochemical models. SYCAMORE is a web browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Functions include database supported modelling, basic model checking, model simulation and the estimation of unknown kinetic parameters based on protein structures. It interfaces with other tools such as the COPASI Complex Pathway Simulator (www.copasi.org) and databases such as BRENDA (www.brenda-enzymes.info) and SABIO-RK (sabio.villa-bosch.de/SABIORK) which contain enzymatic kinetic data. In addition, it offers guidance in order to allow non-expert users to perform basic computational modelling tasks. SYCAMORE is described in the following article: Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca Wade and Ursula Kummer SYCAMORE—a systems biology computational analysis and modeling research environment Bioinformatics 2008 24(12):1463-1464; doi:10.1093/bioinformatics/btn207 SYCAMORE is freely available for academic use at <a href="http://sycamore.eml.org." target="_blank">http://sycamore.eml.org.</a> Commercial users may acquire a license. SYCAMORE is a joint project of the Molecular and Cellular Modeling Group (MCM) and Scientific Databases and Visualization Group (SDBV) at EML Research, as well as the department for Modeling of Biological Processes at the University of Heidelberg. The development of SYCAMORE is supported by the Klaus Tschira Foundation and the German Ministry of Research and Education (BMBF) (HepatoSys Grant 0313078C) The authors can be contacted at: <a href="mailto:sycamore_support@eml-r.villa-bosch.de" target="_blank">sycamore_support@eml-r.villa-bosch.de</a> Dr. Ursula Kummer Dept. Modeling of Biological Processes Institute of Zoology/BIOQUANT BQ18 Im Neuenheimer Feld 267 Ruprecht-Karls-Universität Heidelberg D-69120 Heidelberg Phone: +49 (0)6221 - 5451 - 375 Dr. Rebecca Wade Molecular and Cellular Modeling Group EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Telephone: +49 (0)6221 - 533 - 247 -- Rebecca Wade Tel: +49-6221-533 247 Fax: +49-6221-533 298 Email: <a href="mailto:rebecca.wade@eml-r.villa-bosch.de" target="_blank">rebecca.wade@eml-r.villa-bosch.de</a> <a href="http://www.eml-r.org/english/homes/wade/" target="_blank">http://www.eml-r.org/english/homes/wade/</a> --------------------------------------------------------------- EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany <a href="http://www.eml-r.org" target="_blank">http://www.eml-r.org</a> Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter --------------------------------------------------------------- ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Berkeley Labs Seek 2 Research Associates for Exciting EBI Project

Susan McAllister — 2008-05-22T13:38:38-00:00

Dr's. Adam Arkin and Terry Hazen, have an exciting opportunity for 2 Research Associates to work as team members of the Energy Biosciences Institute program. For more information and too apply on-line, please go to: <a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid=21620&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid=21620&P=1</a> <<a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21620&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21620&P=1</a>> <a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid=21621&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid=21621&P=1</a> <<a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21621&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21621&P=1</a>> Susan McAllister -- Susan McAllister, PHR Senior Human Resources Division Partner Lawrence Berkeley National Laboratory HR 90 Center Phone 510-486-5683 Fax 510-486-7793 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Berkeley Labs Research Associate positions

Susan McAllister — 2008-05-17T00:31:28-00:00

Hello: I was given your email by one of our Scientists, Adam Arkin, who requested that I provide two new openings for Research Associates that Berkeley Labs, working as a team member of Energy Biosciences Institute program has just opened. Is it possible to distribute these web links to your mailing list? If you prefer a complete copy of the ads, please let me know. <a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21620&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21620&P=1</a> <<a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21620&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21620&P=1</a>> <a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21621&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21621&P=1</a> <<a href="http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21621&P=1" target="_blank">http://cjo.lbl.gov/LBNLCareers/details.asp?jid+21621&P=1</a>> I appreciate your assistance, Susan McAllister -- Susan McAllister, PHR Senior Human Resources Division Partner Lawrence Berkeley National Laboratory HR 90 Center Phone 510-486-5683 Fax 510-486-7793 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Please announce the following Job Opening

JLClarke — 2008-05-16T21:39:37-00:00

*Systems Administrator 3* The Joint BioEnergy Institute (JBEI) is a new multi-organizational research center comprising world-class resources and expertise located in one facility at Emeryville, California. The goal of JBEI is to use rapidly advancing scientific techniques, such as systems and synthetic biology, to accelerate development of the nation's biofuels industry. JBEI is a U.S. Department of Energy funded Bioenergy Research Center, managed by Lawrence Berkeley National Laboratory (LBNL) with partners from 5 internationally recognized scientific institutions: Sandia National Laboratories (SNL), Lawrence Livermore National Laboratory (LLNL), University of California-Davis (UCD), University of California-Berkeley (UCB), and the Carnegie Institution for Science. *Summary* The Joint BioEnergy Institute is seeking a Systems Administrator, to be a part of the Technology Division. The scope of this position includes managing research and administrative computing resources, especially linux servers and Apple/Windows desktops, and making project and public data accessible in a timely manner to project participants, and integrating the data with existing data from other databases. *Duties --* * Plan, organize, prioritize and complete assigned tasks and projects in a timely manner * Frequently and clearly communicate task or project status to customers to either set or negotiate expectations Under the broad supervision of the Vice President of Technology and the Computational Analysis Director: 50% - Provide linux system administration and user support for research groups. * System installations, software installations from packages or from source code * Distribution upgrades * security patches * System monitoring * Disk and file system management * System hardware and peripheral management * Backup and recovery management, troubleshooting, and crash recovery * Configure, administer, and troubleshoot various web servers and other services and daemons * Participate in the formulation, planning, organizing, implementation and support of new services or capabilities 40% - Provide similar desktop and laptop support as above, for both Apple and Windows systems 10% - Assist researchers with program compilation, commercial and public domain software installation, and use of UNIX tools and utilities * Participate in the development of research tools for data analysis *Qualifications --* * At least five years linux system administration experience, with responsibility for a wide range of hardware and distributions * Specific areas of required experience include Apache; Python/Perl; bash/tcsh, including writing complex Bourne shell scripts; runlevel 1 for critical update or recovery purposes; remote administration, including ssh, remote serial consoles, and remote PDUs; NFS; LDAP, primarily the OpenLDAP server and clients and RAID controllers * Firm understanding of linux internals including the boot process, kernel versions, and recovery scenarios * Familiarity with sendmail and with email protocols in general * Experience developing applications in Python/Perl and developing Web-based applications using CGI * Experience with a code management system, preferably SVN or CVS, as both administrator and code contributor * Demonstrated ability to incorporate disparate protocols to provide services to researchers and collaborators * Experience with relational database operation and maintenance, specifically with MySQL, PostgreSQL or Oracle * Database experience should include database design, implementation, installation, and administration, including backup and restore of large databases * Ability to employ a flexible approach to solving software problems, and to balance independent approaches to software issues, with specifications developed by others, including project management, project researchers, and other software developers * Demonstrated ability to make progress on multiple tasks simultaneously, and to work both independently and as a member of a team * Must be available as needed nights and weekends for critical system updates that cannot be performed during regular lab hours Marginal - * Bachelor's degree in computer science, or in a physical science discipline, or equivalent experience * Experience with installing, configuring, and troubleshooting cluster queuing software * Experience developing software in a research or technical (preferably biological) field, or for scientific applications *Notes* This is a full-time one-year Term appointment, renewable under the same conditions, contingent upon the continued availability of funding and work. For consideration apply online at: <a href="http://jobs.lbl.gov," target="_blank">http://jobs.lbl.gov,</a> select "Search Jobs", and enter job number 21565 in the keyword search field. For more information about JBEI go to: www.jbei.org -- Tina Clarke JBEI HR Manager Lawrence Berkeley National Laboratory Tel. 510-486-6593 Fax 510-486-7074 <a href="mailto:JLClarke@lbl.gov" target="_blank">JLClarke@lbl.gov</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Faculty Positions Open at Berkeley at the Energy Biosciences Institute

Adam Paul Arkin — 2008-05-15T23:42:49-00:00

13th Workshop of the ISGSB - new registration deadline

David Fell — 2008-05-11T20:55:31-00:00

I announced previously that the 13th Workshop of the International Study Group for Systems Biology (formerly known as the International Study Group for BioThermoKinetics) is taking place at Elsinore in Denmark on 17-20th August 2008, just before the International Conference on Systems Biology in nearby Gothenburg, Sweden. However, we had requests to extend the rather short registration period, and so we have done so. The deadline for registering to give a talk or poster is now 21st May 2008. See <a href="http://sysbio.brookes.ac.uk/index.php/ISGSB-08" target="_blank">http://sysbio.brookes.ac.uk/index.php/ISGSB-08</a> for details Foe those unfamiliar with the scope of the workshops, further details have been added of previous meetings here: <a href="http://sysbio.brookes.ac.uk/index.php/Main_Page" target="_blank">http://sysbio.brookes.ac.uk/index.php/Main_Page</a> David Fell -- =================================================== Prof David A Fell, School of Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, UK Tel: +44 (0)1865 483247 Fax: +44 (0)1865 483242 Mob: +44 (0)7786 515729 New web pages: <a href="http://mudshark.brookes.ac.uk/" target="_blank">http://mudshark.brookes.ac.uk/</a> 17th-20th August 2008: 13th Workshop of the International Study Group for Systems Biology. See: <a href="http://sysbio.brookes.ac.uk/index.php/ISGSB-08" target="_blank">http://sysbio.brookes.ac.uk/index.php/ISGSB-08</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

5th Workshop on Computation of Biochemical Pathways

Ursula Kummer — 2008-05-07T13:51:54-00:00

We would like to announce the 5th Workshop on Computation of Biochemical Pathways and Genetic Networks in Heidelberg, Germany. It will take place on the 22nd and 23rd of September 2008. Like its predecessors the workshop focuses on recent methodological developments in computational systems biology. This year the sessions will be: - Model merging - Model identification - Analysis of stochastic systems - New methods in nonlinear dynamics Informations are frequently updated on: <a href="http://otto.bioquant.uni-heidelberg.de/workshop08" target="_blank">http://otto.bioquant.uni-heidelberg.de/workshop08</a> Registration is now open. The number of participants is strictly limited to 60 and is on a first-come, first-serve basis. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

13th Workshop of the International Study Group for Systems Biology

David Fell — 2008-05-03T21:13:32-00:00

The 13th Workshop of the International Study Group for Systems Biology (formerly known as the International Study Group for BioThermoKinetics) is taking place at Elsinore in Denmark on 17-20th August 2008, just before the International Conference on Systems Biology in nearby Gothenburg, Sweden. As usual, the focus is on the interaction between theory and experiment and the presentation of on-going work. From postgrads to professors, everyone has the opportunity to participate with a talk and/or poster. The deadline for registering to give a talk or poster is 7th May 2008. See <a href="http://sysbio.brookes.ac.uk/index.php/ISGSB-08" target="_blank">http://sysbio.brookes.ac.uk/index.php/ISGSB-08</a> for details Regards, David Fell Prof David Fell, Chair. International Study Group for Systems Biology (<a href="http://sysbio.brookes.ac.uk" target="_blank">http://sysbio.brookes.ac.uk</a>) 13th Workshop, 17th-20th August 2008, Elsinore, Denmark <a href="http://sysbio.brookes.ac.uk/index.php/ISGSB-08" target="_blank">http://sysbio.brookes.ac.uk/index.php/ISGSB-08</a> -- No virus found in this outgoing message. Checked by AVG. Version: 7.5.523 / Virus Database: 269.23.8/1413 - Release Date: 03/05/2008 11:22 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

GRC on Cellular Systems Biology, July 27 to August 1, 2008

Douglas Bruce Kell — 2008-05-02T09:04:48-00:00

Folk may well be interested in the Gordon Conference on "Macromolecular Organisation and Cell Function: Cellular Systems Biology" that will be held at Magdalen College, Oxford from 27th July to 1st August, to BTK members. <a href="http://www.grc.org/programs.aspx?year=2008&program=macromol" target="_blank">http://www.grc.org/programs.aspx?year=2008&program=macromol</a> -- Douglas B. Kell EPSRC/RSC Research Chair in Bioanalytical Science, and Director, Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, MANCHESTER M1 7DN. Tel: 0161 306 4492 Fax: 0161 306 4556 <a href="mailto:dbk@manchester.ac.uk" target="_blank">dbk@manchester.ac.uk</a> <a href="http://dbkgroup.org/" target="_blank">http://dbkgroup.org/</a> <a href="http://www.mcisb.org/" target="_blank">http://www.mcisb.org/</a> <a href="http://www.mib.ac.uk/" target="_blank">http://www.mib.ac.uk/</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Please post the following Postdoctoral Researcher Position

JLClarke — 2008-04-23T22:33:53-00:00

Computing Engineering Postdoctoral Researcher --------------------------------------------- Be Part of Something Great! Lawrence Berkeley National Laboratory (Berkeley Lab) is located in the San Francisco Bay Area on a 200-acre site in the hills above the University of California's Berkeley campus and is managed by the University of California for the U.S. Department of Energy. A leader in science and engineering research for 75 years, Berkeley Lab is the oldest of the U.S. Department of Energy's national laboratories. We are seeking a dynamic Postdoctoral Researcher interested in using comparative functional genomics and computational systems biology techniques to aid in the synthetic biological engineering of proteins and pathways in support of bioenergy research. The candidate would be involved in planning and executing research in this area and in working with the JBEI team in optimizing experimental design, statistical analysis and interpretation of data across the institute. The initial focus would be on microbial pathway engineering for biomass depolymerization and biofuel production. Work would be performed as part of the Arkin laboratory at the Lawrence Berkeley National Laboratory and the Joint BioEnergy Institute, JBEI. Information on the Arkin Lab can be found at <a href="http://bioeng.berkeley.edu/cv.php?facultyid=3016." target="_blank">http://bioeng.berkeley.edu/cv.php?facultyid=3016.</a> Information about JBEI can be found at <a href="http://jbei.org." target="_blank">http://jbei.org.</a> Duties - The primary duties of this position are to provide core primary research in (initially) o microbial functional genomics spanning transcriptomics, metabolomics, genetics and proteomics in the context of pathway engineering and optimization of production o Protein functional analysis and engineering for processing of feedstock and creation of biofuel pathways o Computational support for metabolic pathway engineering and knowledge - Maintain an accurate and detailed laboratory notebook of all work performed to ensure that others could duplicate results - Prepare presentations and manuscripts for internal use and peer reviewed publication. - Maintain accurate documentation and source-code control for all work-product Key Success Factors: - PhD. in an Engineering or Quantitative Biological discipline or a related field of science - Demonstrated high-level skills, knowledge and work experience in engineering, computer science, and biology especially in regard protein biochemistry, structure and genome-scale data - Must have high analytical skill and programming skill (language unspecified but prefer C, C++, or Java and PERL), familiarity with tools such as matlab and Mathematica, experience with SQL database construction and maintenance as well as web-based, user-friendly, interfaces to these tools and databases - Ability to creatively work, within a team of scientists, with problems in microbial comparative functional genomics with emphasis on metabolic pathway analysis and protein functional prediction and design - Effective interpersonal, verbal and written communication skills with ability to accomplish goals as a team member - Demonstrated ability to work collaboratively with programmers, engineers, post-docs, graduate students, and undergraduates from multiple backgrounds - Must have ability to handle multiple projects and tasks in parallel and meet programmatic milestones and project timelines - Demonstrated experience with high-level problem solving in computational biology Notes This is a one year Term appointment, renewable under the same conditions, contingent upon the continued availability of funding and work. For immediate consideration please apply at: <a href="http://jobs.lbl.gov/LBNLCareers/details.asp?jid=21607&p=1." target="_blank">http://jobs.lbl.gov/LBNLCareers/details.asp?jid=21607&p=1.</a> Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce. For more information about LBNL and its programs, visit www.lbl.gov. -- Tina Clarke JBEI HR Manager Lawrence Berkeley National Laboratory Tel. 510-486-6593 Fax 510-486-7074 <a href="mailto:JLClarke@lbl.gov" target="_blank">JLClarke@lbl.gov</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Cytoscape software engineer, Pasteur Institute, Paris (France)

Benno Schwikowski — 2008-04-23T10:30:30-00:00

Postdoc position: Identification of functional modules; Pasteur Institute, Paris, France

Benno Schwikowski — 2008-04-12T08:34:46-00:00

*** Postdoctoral position: Approaches for the identification of functional modules The Systems Biology Group at the Pasteur Institute in Paris is looking for a motivated computational scientist to join our multidisciplinary research group developing new approaches for the identification of functional modules in biological subcellular systems. We develop and implement algorithms to identify functional modules (i.e., groups of functionally related genes and proteins) from high-throughput, large- scale data, such as transcriptomic, proteomic, and metabolomic data. We develop algorithms and the underlying biological hypotheses in close collaboration with computational biologists and experimentalists from the BaSysBio consortium (see below). We are looking for a candidate with a solid background in numerical/ optimization algorithms, and programming, and a strong interest in molecular and systems biology. Good communication skills and good knowledge of English are necessary. Experiences with the computational- statistical analysis of large-scale biological data, machine learning, and intracellular interactions networks are a plus. Profile: Ph.D. in a quantitative science, such as applied mathematics, statistics, computer science, or physics. Starting date: June 2008 or later, initially 12 months, extendable to 2 ½ years. Please send your CV along with three references until April 27, 2008 to: Benno Schwikowski, <a href="mailto:benno@pasteur.fr" target="_blank">benno@pasteur.fr</a>, <a href="http://www.systemsbiology.fr/" target="_blank">http://www.systemsbiology.fr/</a> *** BaSysBio, a European Integrated Project for Systems Biology BaSysBio (<a href="http://www.basysbio.eu/" target="_blank">http://www.basysbio.eu/</a>) is a multidisciplinary project involving 16 institutions from 9 countries, in which a systems biology approach is used to understand the dynamic transcriptional regulation at a global scale in bacteria. In living cells, the regulation of transcription is embedded into a hierarchical flow of information from genes to phenotype. BaSysBio is generating quantitative data about the cellular components at all the levels of the information flow in order to understand at the system’s level the highly dynamic regulation of genes. High-throughput technologies are developed and adapted to facilitate quantitative measurements, in conjunction with the development and validation of computational systems biology methodologies to enable the quantitative interpretation of the data and to unravel the underlying principles of regulatory network interactions. Experimental data are generated in the highly tractable Gram-positive model bacterium Bacillus subtilis with two specific goals: (1) to unravel the global regulatory structure of B. subtilis metabolism and understand how transcriptional regulation is integrated with the other levels of control; (2) to achieve a quantitative understanding of the cellular transcriptional responses under conditions mimicking pathogenesis and to apply the acquired knowledge and the integrated modelling/experimental strategy developed in the model bacterium to understand the regulatory networks controlling pathogenesis in the closely related disease-causing bacteria Bacillus anthracis and Staphylococcus aureus. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

2nd CfP - CMSB 2008

mh — 2008-04-10T15:07:18-00:00

------------------------------------- Deadline is approaching! ------------------------------------- International Conference on *COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY * 12th to 15th October 2008, Rostock, Germany <a href="http://wwwmosi.informatik.uni-rostock.de/cmsb08/" target="_blank">http://wwwmosi.informatik.uni-rostock.de/cmsb08/</a> The conference proceedings will be published by Springer LNCS/LNBI. There will be a follow-up volume in LNCS journal TCSB with extended versions of the best papers. *important deadlines:* May, 5 - submission of abstracts May, 5 - submission of tutorial proposals May, 12 - submission of full papers June, 16 - notification of paper acceptance June, 16 - notification of tutorial acceptance July, 21 - revised version of papers Please note, the deadline for the full paper submission has been postponed by one week, provided an abstract is submitted until May, 5. ----------------------------------------------- Prof. Dr.-Ing. Monika Heiner Brandenburg University of Technology at Cottbus Computer Science Institute = Data Structures and Software Dependability = Postbox 10 13 44, 03013 Cottbus, Germany <a href="http://www-dssz.informatik.tu-cottbus.de/" target="_blank">http://www-dssz.informatik.tu-cottbus.de/</a> <a href="mailto:monika.heiner@informatik.tu-cottbus.de" target="_blank">monika.heiner@informatik.tu-cottbus.de</a> phone (+49-355) 69 3884,fax (+49-355) 69 3830 ----------------------------------------------- ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

3 Week Computational Cell Biology at Cold Spring Harbor

les — 2008-04-04T14:41:06-00:00

Dear Colleagues, Here is a flyer about the upcoming course on Computational Cell Biology at CSHL. Please spread the word. We are especially interested in applications from talented experimentalists who are interested in using mathematical modeling in their research. Best, Les Loew

Postdoc in Computational Systems Biology

jtk — 2008-04-01T10:19:36-00:00

Dear Colleagues, I'd be grateful if you could circulate / advertise this as appropriate. Best regards & thanks in advance, Jan -- +- Jan T. Kim -------------------------------------------------------+ | email: <a href="mailto:jtk@cmp.uea.ac.uk" target="_blank">jtk@cmp.uea.ac.uk</a> | | WWW: <a href="http://www.cmp.uea.ac.uk/people/jtk" target="_blank">http://www.cmp.uea.ac.uk/people/jtk</a> | *-----=< hierarchical systems are for files, not for humans >=-----* ----- 8< ----------------------------------------------------------------- University of East Anglia, UK School of Computing Sciences POST-DOCTORAL RESEARCH ASSOCIATE (Ref: RA477) <a href="http://www.uea.ac.uk/hr/jobs/ra/ra477.htm" target="_blank">http://www.uea.ac.uk/hr/jobs/ra/ra477.htm</a> GBP 28,290 - 32,795 per annum (w.e.f. 01/05/08) A postdoctoral position is available for a computational systems biologist, to work on computational models of biological networks. The project is to develop a platform for scoring network models based on their consistency with gene expression data, and to apply this platform to investigate the networks that organise wounding responses in plants. The project team will be comprised of members from the School of Computing Sciences and the School of Biological Sciences. This post offers a unique opportunity to work on a computational systems biology project within a truly interdisciplinary environment. You must have or be able to demonstrate: * A doctoral degree in biosciences or computing (or equivalent experience) * An interest in computational models of biological networks, * The ability to work with and develop models and modelling software in a Linux / Unix environment, including the ability to understand and work with large biological data sets and statistics. More information about the School of Computing Sciences can be found at <a href="http://www.cmp.uea.ac.uk/" target="_blank">http://www.cmp.uea.ac.uk/</a> Closing date: 25 April 2008. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

BioModels Database 10th release

Nicolas Le Novere — 2008-03-28T13:17:22-00:00

Hinxton, Friday 28th March 2008 Dear colleagues, We are pleased to announce the tenth release of BioModels Database. This new release sees the the addition of 52 models, 17 entering the curated branch. That brings the public version of BioModels Database to 244 models representing 25731 reactions. As usual, a significant portion of the annotation of existing models has also been updated. The database now features around 10000 cross-references. We are now focusing on developing BioModels Database software version 3, that will see pretty much everything rewritten. Therefore the current release is mainly a data-only one. However, we are still adding a few functionalities, such as new methods in the WebServices allowing more efficient retrieval of models For more details on this release, please consult: <a href="http://www.ebi.ac.uk/biomodels/release_28March2008.html" target="_blank">http://www.ebi.ac.uk/biomodels/release_28March2008.html</a> BioModels Database is developed by the teams of Nicolas Le NovÃ¨re (EMBL-EBI, United-Kingdom) and Michael Hucka (SBML Team, Caltech, USA) in collaboration with Upinder Bhalla (DOQCS, National Center for Biological Sciences, India), Ion Moraru (the Virtual Cell, USA), Herbert Sauro (Keck Graduate Institute, USA), Hiroaki Kitano (Systems Biology Institute, Japan), Hans Westerhoff and Jacky Snoep (JWS Online, Stellenbosch (ZA) and Manchester (UK) Universities), as part of the BioModels.net initiative. BioModels Database development has benefitted from funds of the European Molecular Biology Laboratory (Le NovÃ¨re team), the National Institute of General Medical Sciences (SBML team and Le NovÃ¨re team), the DARPA (Sauro team) and the National Center for Research Resources (Virtual Cell team). A big thank-you to all our collaborators and submitters! -- The BioModels Database team ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Workshop: Autonomous Decision Making in Planning and Control, May 29 2008

Maria — 2008-03-27T13:35:47-00:00

The Lean Engineering Research Group, Centre for Manufacturing at De Montfort University, Leicester, UK, and the Biological and Neural Computation Research Group, Science and Technology Research Institute at the University of Hertfordshire, Hatfield, UK, are organizing a workshop on: Autonomous Decision Making in Industrial Operations Planning and Control Date: Thursday, 29 May 2008 Venue: De Montfort University, Leicester, East Midlands, UK The aim of the workshop is to bring together researchers from a range of disciplines and potential users of research outcomes, to discuss the application of biological control processes to facilitate autonomous decision making in operations management. Biological control processes of interest include those that control gene transcription and translation processes, and the sequencing and synchronization required to produce individual organelles. The aim of the discussion is to develop a shared understanding of the problem domain, and defining the scope of research issues involved. For further details contact: Dr Riham Khalil, De Montfort University, Leicester - <a href="mailto:rkhalil@dmu.ac.uk" target="_blank">rkhalil@dmu.ac.uk</a> Dr Maria Schilstra, University of Hertfordshire, Hatfield - <a href="mailto:m.j.1.schilstra@herts.ac.uk" target="_blank">m.j.1.schilstra@herts.ac.uk</a> Preliminary programme: 9.30 Professor David Stockton, De Montfort University: Introduction and welcome 9.45 Dr Riham Khalil, De Montfort University and Dr Mark McAuley, University of Hertfordshire: Discrete event simulation of biological control processes, and its application to autonomous decision making in manufacturing systems 10.45 Break 11.00 Professor Herbert Kotzab, Copenhagen Business School: Autonomous cooperating logistic processes 11.40 Professor Edmund Burke, University of Nottingham: Next generation decision support: automating the heuristic design process 12.20 Lunch 13.20 Dr Ken Young, Warwick University: The future of autonomous systems in the UK 14.00 Lieven Demeester, Lieven, INSEAD, France: Organic production systems: what biological cells can teach us about manufacturing 14.40 Break 15.00 Panel discussion session 16.00 Professor David Stockton: Overview and future actions ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Post-doctoral position in computational methods for metabolic reprogramming, Genoscope - CEA, Paris

Vincent Schachter — 2008-03-17T19:32:38-00:00

An 18 months post-doctoral position in computational systems and synthetic biology is available in the Computational Systems Biology Lab at Genoscope(Institute for Genomics, Life Sciences Department, CEA), Evry, France on the following topic : "Design and application of computational methods for metabolic reprogramming" The research of the Computational Systems Biology group at Genoscope (<a href="http://www.genoscope.cns.fr/bioinfo" target="_blank">http://www.genoscope.cns.fr/bioinfo</a> ) focuses on the study of microbial metabolism metabolism using constraint-based models and on the design of computational methods for synthetic biology. The successful candidate will participate in the development of a computational framework aimed at helping with the reprogramming of microbial metabolism to perform a well-specified metabolic function. Starting from a non-modified microbial cell, a high-level specification of the metabolic function to be performed and a set of elementary metabolic and regulatory components, the goal is to generate one or several experimental strategies for metabolic reprogramming that are likely to yield the metabolic function. An experimental strategy is typically a sequence of steps of the following types : genetic modifications ( such as the insertion of a "biobrick" or the deletion of a gene), adaptive evolution, and assembly of partially engineered systems. The computational framework will be tested for specific synthesis goals in collaboration with experimental groups. Applicants should have a PhD in Computer Science, Computational Biology, Bioinformatics, Biochemical Engineering, or Physics. Applicants with a background in computer science, physics or chemistry should document a strong interest for molecular biology at a research level. Previous exposure to synthetic biology, a working knowledge of biochemistry, experience with modelling metabolic networks, and/or experience in microbiology will be strong assets. The ability to work independently in an interdisciplinary environment will be essential. The successful candidate will start in September 2008. To apply, please email a CV, list of publications and addresses of at least two referees to : Dr Vincent Schachter Computational Systems Biology Group Genoscope, CEA/DSV/IG email : <a href="mailto:vs@genoscope.cns.fr" target="_blank">vs@genoscope.cns.fr</a> Hosting Group : The Computational Systems Biology Group (<a href="http://www.genoscope.cns.fr/bioinfo" target="_blank">http://www.genoscope.cns.fr/bioinfo</a>) at Genoscope focuses on developing and applying computational methods to analyze metabolic behavior, study metabolic evolution, and help with redesign of metabolic networks. The group is also involved in the design of software tools for metabolic networks representation and manipulation, and collaborates closely with experimental groups at Genoscope and in the Paris area. The group also participates in two EU FP6 Networks of Excellence (the BioSapiens bioinformatics NOE, and the ENFIN Systems Biology NOE) and in the TARPOL (synthetic biology for the environment) FP7 project. Genoscope is both the French National Genome Center (the second largest european sequencing center in terms of throughput) and a research institute dedicated to high-throughput biology, bioinformatics and systems biology. It was recently integrated into the CEA Life Sciences Division, forming (together with the National Genotyping Center) the new Institute for Genomics. Genoscope's main research focus is on prokaryote metabolism, including the study of bacterial communities (through metagenome sequencing and analysis projects), the search for novel enzymatic functions, metabolic reprogramming, and modeling. Application areas include the search for new bio-energies, bioremediation, and the search for cleaner and more efficient chemical processes. Hosting Institution : CEA, a.k.a the French Atomic Energy Commission (Commissariat Ã l'Ã©nergie atomique), is a large fundamental and applied research organization. It is active in three main fields : energy, information and health technologies, and defense. In each of these fields, the CEA maintains a cross-disciplinary culture of engineers and researchers, building on the synergies between fundamental and technological research. -- ---------------------------------- Vincent SchÃ¤chter Computational Systems Biology Group - Genoscope - CEA 2 rue Gaston Cremieux, 91057 Evry, France tel: (+33) 1 60 87 25 92 <a href="http://www.genoscope.cns.fr/bioinfo" target="_blank">http://www.genoscope.cns.fr/bioinfo</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Three research positions "Theoretical Systems Biology" in Dresden, Germany

Lutz Brusch — 2008-03-14T16:51:55-00:00

Three research positions "Theoretical Systems Biology" at Dresden University of Technology, Germany Applications from highly qualified candidates are invited for * two full postdoctoral fellow positions for up to three years and * one PhD position for three years in theoretical systems biology, mathematical biology and computational cell biology. The goal is to discover, in close collaboration with experimental and medical partners, novel biophysical and biochemical mechanisms of information and material transport between subcellular compartments such as the plasma membrane, Golgi and nucleus as well as the spatio-temporal regulation of such mechanisms. The new members of our group will coordinate and conduct the above research and complement running projects which utilise a broad spectrum of theoretical tools with a focus on multi-scale modelling of spatio-temporal pattern formation. The ideal postdoctoral candidate holds a Ph.D. in physics, applied mathematics or biology (or similar), has demonstrated expertise in systems biology, biophysics, nonlinear dynamics, stochastic methods or network analysis and has a strong interest in molecular cell biology. The Ph.D. candidate should possess a masters or diploma degree in physics or applied mathematics. A high level of motivation and commitment are required. Strong communication skills are important for the close collaborations with experimentalists and medical doctors. The envisaged research will be conducted at the interdisciplinary Center for Information Services and High Performance Computing (ZIH), Dresden University of Technology, Germany, which hosts a department focusing on the mathematical modelling of biological systems (head: Andreas Deutsch). The Dresden campus is characterized by a vibrant international community of researchers that performs cross-disciplinary research at the highest level in state-of-the-art research centers. The city of Dresden and its surroundings are also rich in culture and impressive scenery. ZIH is an equal opportunity employer and strives to increase the number of women in research. We also encourage and invite applications from disabled individuals, who will be given priority if suitably qualified. The positions are available from June 1, 2008. Deadline for applications (by email, including contact details of two references): April 10, 2008. Contact: Andreas Deutsch Center for Information Services and High Performance Computing (ZIH) Dresden University of Technology, Germany Tel.: +49 351 463-31943 Fax.: +49 351 463-38245 Email: <a href="mailto:andreas.deutsch@tu-dresden.de" target="_blank">andreas.deutsch@tu-dresden.de</a> WWW: <a href="http://theobio.mtbio.de/imc" target="_blank">http://theobio.mtbio.de/imc</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a>

Ph.D. student position - single molecule imaging in living bacteria

Johan Elf — 2008-03-06T07:51:58-00:00

Ph.D. student position in Molecular Biotechnology focused at single molecule imaging in living bacteria at the Department of Cell and Molecular Biology, Uppsala University. The project aims at studying the kinetics of gene regulation in individual living bacterial cells using single molecule imaging (Elf et al. Science 2007) in combination with mathematical and computational modelling. The single molecule approach makes it possible to study gene regulation in real-time such that it can be compared to quantitative dynamical models of intracellular biophysics. The research project is funded by the European Research Councils program for frontier research. The project includes continued development of our single molecule microscope, bacterial strain construction, and fabrication of micro fluidic devises for single cell manipulation. The project can also be combined with our ongoing effort in algorithm and software development for analysis of spatially resolved stochastic kinetics. You will be expected to teach in Swedish or English, for at most 20% of the time. The successful applicant is likely to have an interdisciplinary background including micro/molecular biology, physics, chemistry and scientific computing, with expertise in at least one of these fields. Previous research experience, and hand-on experience with optics, lasers, electronics or microbes will be considered advantageous. Information: More information can be obtained at <a href="http://www.personalavd.uu.se/ledigaplatser/" target="_blank">http://www.personalavd.uu.se/ledigaplatser/</a> or by contacting Docent Johan Elf, e-mail: <a href="mailto:johan.elf@icm.uu.se." target="_blank">johan.elf@icm.uu.se.</a> Please also check the group's website at <a href="http://www.icm.uu.se/molbio/elflab." target="_blank">http://www.icm.uu.se/molbio/elflab.</a> Union representatives are: Anders Grundström, SACO-rådet, tel +46 18-471 5380, Carin Söderhäll, OFR-S/ST, tel +46 18-471 1996, Stefan Djurström, SEKO, tel +46 18-471 3315. Application no later than April 28, 2008 to: Registrator, UFV-PA 2008/421, Uppsala universitet, Box 256, 751 05 UPPSALA, Sweden. Fax +46 18-471 2000 or e-mail: <a href="mailto:registrator@uu.se." target="_blank">registrator@uu.se.</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Opportunity: Postdoctoral Position in COMPUTATIONAL SYSTEMS BIOLOGY @ UT Southwestern in Dallas, TX

Christian Forst — 2008-03-05T19:49:22-00:00

The Department of Clinical Sciences at UT Southwestern Medical Center (Dallas, TX) is offering a postdoctoral position in computational systems biology. The successful candidate will have the opportunity to work on an exiting project analyzing host-pathogen interactions in collaborations with experimental labs. The project involves the development of algorithms for reconstructing biological networks, analyzing such networks by integration with genome-scale data and potentially develop predictive computer models. The ideal candidate would have an interdisciplinary background with a Ph.D. in Biochemistry, Computer Science, Mathematics, Molecular Biology, Physics or Statistics. Substantial training in computer science/theoretical biology with knowledge in molecular biology, as well as programming experience in C++, Java, Perl, Python is required. A basic understanding in graph theory and immunology is preferred. Interested applicants should send a CV/resume and three reference letters to Dr. Christian Forst, Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9072; Phone: 214-648-4012; E-mail: Christian_dot_Forst_at_utsouthwestern_dot_edu. The University of Texas Southwestern Medical Center is an Affirmative Action/Equal Opportunity Employer. Women and minority candidates are encouraged to apply. PS: I apologize for any duplicate postings. ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

SENIOR SCIENTIFIC DATABASE CURATOR

Nicolas Le Novere — 2008-02-07T10:17:06-00:00

EMBL site: EMBL-EBI Hinxton Commencing date: ASAP Job description: A consequence of the progressive rise of Systems Biology as a new paradigm in life science, is a fast increase of the number of quantitative models. BioModels Database (<a href="http://www.ebi.ac.uk/biomodels/" target="_blank">http://www.ebi.ac.uk/biomodels/</a>) is the reference database for annotated computational models of biological processes published in the literature. BioModels Database is looking for a new curator to join its team. This person will verify the syntax and semantics of models submitted to the resource, check the results of their simulation, and thoroughly annotate them. In addition to the model verification, the curator will write documentation, user-manual and tutorials, and provide training to users and curators worldwide. It is anticipated that during the course of his activity, the curator will acquire an incomparable master of quantitative modelling in Biology. Qualifications and experience: Applicants should hold a PhD or a Masters in Biology, Physics or Mathematics. The curation of computational models necessitates an understanding of the biology, the mathematics and the computing methods used to generate them. It is therefore expected that applicants should have former experience in Computational Systems Biology, with a basic knowledge of chemical kinetics, differential calculus, and numerical analysis. An experience of software used to develop models and run simulations is necessary, as well as a former experience of Linux/Unix and at least one scripting language (Perl, Python, Shell etc). The post-holder will interact with other members of the team, model submitters, tool developers and the users of the resource, and is expected to have exceptional interpersonal skills. Because of the documentation and the training, an excellent master of English is mandatory. Contract: An initial contract of 3 years will be offered to the successful candidate. Closing date: 28 March 2008 Web page: <a href="http://www.ebi.ac.uk/" target="_blank">http://www.ebi.ac.uk/</a> EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. Please note that EMBL does not return CVs or attached documents to applicants. To apply, please send a CV (including names and addresses of referees) and covering letter, by email, quoting ref. no. W/08/014/EBI in the subject line, to: <a href="mailto:applications@ebi.ac.uk" target="_blank">applications@ebi.ac.uk</a> and <a href="mailto:lenov@ebi.ac.uk" target="_blank">lenov@ebi.ac.uk</a> Personnel, EMBL, Postfach 10.2209, 69012 Heidelberg, Germany. Fax: +49 6221 387555 E-mail: <a href="mailto:application@embl.de" target="_blank">application@embl.de</a> -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Tel:+441223494521, Mob:+447833147074 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:<a href="mailto:nlenovere@hotmail.com" target="_blank">nlenovere@hotmail.com</a> <a href="http://www.ebi.ac.uk/~lenov/," target="_blank">http://www.ebi.ac.uk/~lenov/,</a> <a href="http://www.ebi.ac.uk/compneur/" target="_blank">http://www.ebi.ac.uk/compneur/</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Taverna workshop after 'genomes to systems' meeting in Manchester

Douglas Bruce Kell — 2008-02-02T04:22:59-00:00

Many folk on this list are likely attending the Genomes to Systems conference in Manchester March 17-19, 2008 (www.genomestosystems.org). As you know, we are promoting the use of Taverna-based workflows for doing systems biology manipulations, one advantage being the ability to share and reuse such workflows. May I draw your attention to the advert and registration form for a *free* Taverna tutorial that will be held at the University of Manchester the following day after G2S? <a href="http://www.mygrid.org.uk/taverna-genomics-2008" target="_blank">http://www.mygrid.org.uk/taverna-genomics-2008</a> Further details from Katy Wolstencroft (<a href="mailto:katy.wolstencroft@manchester.ac.uk" target="_blank">katy.wolstencroft@manchester.ac.uk</a>). Please could you also forward this to colleagues not on this list who may also be attending G2S? I'll also take the opportunity to draw attention to our recent paper describing how Taverna can be configured to read and write SBML (Li, P., Oinn, T., Stoiland, S. & Kell, D. B. (2008). Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics 24, 287-289), available at <a href="http://dbkgroup.org/dbkPubs.htm." target="_blank">http://dbkgroup.org/dbkPubs.htm.</a> Kind regards, Douglas. -- **PLEASE NOTE NEW POSTAL ADDRESS** Douglas B. Kell EPSRC/RSC Research Chair in Bioanalytical Science, and Director, Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, MANCHESTER M1 7DN. Tel: 0161 306 4492 Fax: 0161 306 4556 <a href="mailto:dbk@manchester.ac.uk" target="_blank">dbk@manchester.ac.uk</a> <a href="http://dbkgroup.org/" target="_blank">http://dbkgroup.org/</a> <a href="http://www.mcisb.org/" target="_blank">http://www.mcisb.org/</a> <a href="http://www.mib.ac.uk/" target="_blank">http://www.mib.ac.uk/</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Posting of a Workshop/Conference

David MacIntyre — 2008-01-30T08:54:02-00:00

The CCAM Summer Undergraduate Research Internships in Quantitative Cell Biology

huber — 2008-01-15T21:58:12-00:00

CCAM Summer Undergraduate Research Internships in Quantitative Cell Biology Initiated in 1999, the Center for Cell Analysis and Modeling (CCAM) annually sponsors a summer undergraduate research program that brings undergraduate students with strong backgrounds in the physical sciences, engineering and mathematics into our laboratories for 10 weeks. As an NIH-funded National Technology Center for Networks and Pathways, research at CCAM encompasses a range of programs including: . Biophotonics research to develop optical methods for quantitative measurement of molecular events inside living cells . Coupling cell biology and biophotonics to develop methods for molecular level manipulation in living cells . Imaging methods for understanding macromolecular dynamics in living cells . Computational modeling of cellular physiology and intracellular transport using the Virtual Cell software . Computational modeling and simulation of cell motility . Computational biology and bioinformatics efforts in continued development of the Virtual Cell software. Internships will be awarded at a stipend level of $4000 for 10 weeks from June through mid August. Applicants should be finishing their junior year and should submit a letter of application describing their past experience, what kind of research interests them and why they are interested in CCAM. Applicants should also arrange to have their undergraduate transcript, and 2 reference letters sent to: Prof. Greg Huber The Richard Berlin Center for Cell Analysis & Modeling 263 Farmington Avenue University of Connecticut Health Center Farmington, CT 06030-1507 email: <a href="mailto:huber@uchc.edu" target="_blank">huber@uchc.edu</a> Applications will be considered as they are received through February 2008 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Research Fellow in Statistical Computation of Biological Networks (UK)

David Wild — 2008-01-15T15:24:22-00:00

Research Fellow in Statistical Computation of Biological Networks Warwick Systems Biology Centre, UK Fixed Term Contract for 3 years You will work on Bayesian statistical analysis of biological data to infer gene regulatory networks involved in plant response to external stresses as part of a 5M research award to the Universities of Warwick, Exeter and Essex. This BBSRC Systems Approach to Biological Research (SABR) Initiative will develop models of how plants cope with environmental stress. You will develop and apply statistical algorithms (eg Markov chain Monte Carlo, particle filtering and approximation methods such as Variational Bayes techniques) for network inference from a variety of data types (such as gene expression time series, ChIP-chip and bioinformatics data). You will work closely with a team of plant biologists to aid in experimental design and data analysis. The project is interdisciplinary, working with a large consortium of biologists, bioinformaticians, mathematicians and statisticians. You will have a PhD or equivalent in computational biology or a relevant quantitative field such as statistics, computer science, theoretical physics, applied mathematics, or engineering and a strong interest in molecular biology. Experience in statistical computation and the ability to programme in a high level language such as Matlab. R, and/or C/C++ is also essential. As is the ability to present and publish the research findings to a high level. If you wish to discuss the post prior to application, please contact Prof. David Wild (<a href="mailto:D.L.Wild@warwick.ac.uk" target="_blank">D.L.Wild@warwick.ac.uk</a>). Further details and application form at <a href="https://secure.admin.warwick.ac.uk/webjobs/jobs/research/job6771.html" target="_blank">https://secure.admin.warwick.ac.uk/webjobs/jobs/research/job6771.html</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Genomes to Systems Conference 2008

L.M.Parsons — 2008-01-15T12:55:33-00:00

Section on Computational Developmental Biology, 6th BGRS conference, Novosibirsk, Russia, June 22 -

Maria Samsonova — 2008-01-13T20:50:21-00:00

Computational Developmental Biology 6th BGRS Conference June 22- 28, 2008 | Akademgorodok | Novosibirsk, Russia Abstract submission deadline March 1st Registration deadline May 1st Dear Colleague, We kindly invite you to consider the participation in the Computational Developmental Biology section of the next BGRS conference. BGRS is a bi-annual conference on bioinformatics organized by the Institute of Cytology and Genetics of the SB RAS. The aim of the Computational Developmental Biology section is to foster fruitful and creative dialogs between experimental developmental biologists, mathematicians, computer scientists and scientists working in the field of systems biology of development. Special emphasis will be made on areas of greatest current interest and importance, such as pattern formation, cell fate determination, transcriptional and signaling networks, cell movements, morphomechanics, cell-cell communication, proliferation and death. The session will also be devoted to new experimental technologies and software design. The participants will be offered a social program for recreation and sightseeing. Those interested in the cultural traditions and wild-life of Siberia will be offered a post-conference tour to Altai mountains. For updated information please visit the BGRS web site <a href="http://www.bionet.nsc.ru/meeting/bgrs2008/index.html" target="_blank">http://www.bionet.nsc.ru/meeting/bgrs2008/index.html</a> Section conveners Maria Samsonova St.Petersburg State Polytechnical University, Russia Eric Mjolsness University of California , Irvine, USA ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

VIII Spanish Jornadas de Bioinform�tica =?iso-8859-1?q?=3A_long_abstracts_submission_December_15th?=

jvilla — 2007-12-11T08:00:28-00:00

Post-doc and PhD positions

James Schwaber — 2007-12-03T17:55:13-00:00

Hi All, We have several Post-doc positions <a href="http://www.dbi.tju.edu/dbi/staticpages.php?page=jobs&menu=36" target="_blank">http://www.dbi.tju.edu/dbi/staticpages.php?page=jobs&menu=36</a> <<a href="http://www.dbi.tju.edu/dbi/staticpages.php?page=jobs&menu=36" target="_blank">http://www.dbi.tju.edu/dbi/staticpages.php?page=jobs&menu=36</a>> currently available, that may be of interest to you or your colleagues. Candidates should have interest in performing and analyzing experimental data as well as computational modeling. Please distribute this email as you see fit. Regards, Jim Schwaber ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

PhD and Post-doc positions

Mark Poolman — 2007-11-29T17:37:41-00:00

Dear All, We have a Post-doc position <a href="https://edm.brookes.ac.uk/hr/hr/vacancies.do?id=4888674" target="_blank">https://edm.brookes.ac.uk/hr/hr/vacancies.do?id=4888674</a> and a PhD studenship <a href="http://www.jobs.ac.uk/jobs/RK576/PhD_Industrial_Studentship/" target="_blank">http://www.jobs.ac.uk/jobs/RK576/PhD_Industrial_Studentship/</a> currently available, that may be of interest to you or your colleagus. We are keen to hear from potential candidates with prior experience of metabolic modelling. Feel free to distribute this email as you see fit. Regards, Mark Poolman -- Dr. Mark Poolman Senior Research Fellow Cell Systems Modelling Group School of Life Science Oxford Brookes University ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Postdoc in Multi-Level Modelling of Mitochondrial Metabolism

David Fell — 2007-11-26T00:49:03-00:00

I am currently seeking a Postdoc in Multi-Level Modelling of Mitochondrial Metabolism to join my Cell Systems Modelling Group (<a href="http://www.brookes.ac.uk/lifesci/cell_systems.html!" target="_blank">http://www.brookes.ac.uk/lifesci/cell_systems.html!</a>). This three year research position is funded by a BBSRC grant to Professor David Fell and Professor Mike Pidcock as part of a joint BBSRC-ANR initiative in Systems Biology. The ANR is funding in parallel a French team led by Prof Jean-Pierre Mazat (Bordeaux) who is also the overall coordinator of the project. For this position, we are seeking someone with previous post-doctoral level experience in computational or Systems Biology, preferably involving building stochastic, ODE or PDE-based models of biological systems, such as metabolism or signal transduction. Ideally you would have studied two out of three from biochemistry, computing and maths beyond first-year university-level. Experience of programming in a high-level language such as Python would be an advantage. Although we will use ScrumPy as a tool where appropriate, it is likely that some simulations may be ported to, or developed in MatLab, so experience in use of this or an equivalent package could be an advantage. Project meetings in Bordeaux quarterly, and short stays in Bordeaux (up to two weeks at a time) may be necessary to examine the experimental data and coordinate the UK and French modelling efforts. Although knowledge of French is not essential, it would be advantageous, if only to the level of being able to read scientific French. Further details of the project are available by emailing me. Closing date for applications is Dec 7th. Make applications by following instructions at: <a href="https://edm.brookes.ac.uk/hr/hr/vacancies.do" target="_blank">https://edm.brookes.ac.uk/hr/hr/vacancies.do</a> David Fell =================================================== Prof David A Fell, School of Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, UK Tel: +44 (0)1865 483247 Fax: +44 (0)1865 483242 Mob: +44 (0)7786 515729 <a href="http://mudshark.brookes.ac.uk/" target="_blank">http://mudshark.brookes.ac.uk/</a> -- No virus found in this outgoing message. Checked by AVG. Version: 7.5.503 / Virus Database: 269.16.7/1151 - Release Date: 25/11/2007 16:24 ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Call for papers VIII Jornadas de Bioinformatica

jvilla — 2007-11-21T23:30:23-00:00

We apologize for cross postings Call for papers to the "VIII Jornadas de Bioinformática" is now open! we are pleased to announce that the official short and long abstracts submission for the VIII Jornadas de Bioinformática to be held at the Centro de Investigación Príncipe Felipe in València on February 13-15th is now fully operative at the web of the Spanish Bioinformatics network: <a href="http://www.redbioinfo.es" target="_blank">http://www.redbioinfo.es</a> Information on the "jornadas" and detailed instructions on the abstract preparation and submission will be found in this page. Even if you did not send a short expression of interest before November 11th deadline you are still invited to submit a final short/long abstract before December 7th. IMPORTANT: Note that those who have already sent an EoI should resubmit their contribution in the form of a long abstract (oral contributions) or a short abstract (posters) to the EasyChair system following the instructions in <a href="http://cbbl.imim.es:8080/RNB/jornadas/abstract-submission" target="_blank">http://cbbl.imim.es:8080/RNB/jornadas/abstract-submission</a> Please, do not miss the important deadlines <a href="http://cbbl.imim.es:8080/RNB/jornadas/important-deadlines" target="_blank">http://cbbl.imim.es:8080/RNB/jornadas/important-deadlines</a> * Short Abstract Submission: Expression of interest (All Categories) 11th November (EXPIRED!) * Long Abstracts (All sections) 7th December * Acceptance of Oral & Poster presentation 3th January * Early Registration 10th January * VIII Jornadas de Bioinformática, Valencia 13th February We hope seeing you in València!! Ximo Dopazo, Ana Conesa, Hugo Gutiérrez de Terán and Jordi Villà -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biomèdica de Barcelon C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: <a href="mailto:jvilla@imim.es" target="_blank">jvilla@imim.es</a> <a href="http://cbbl.imim.es" target="_blank">http://cbbl.imim.es</a> // <a href="http://www.ps3grid.net" target="_blank">http://www.ps3grid.net</a> // <a href="http://www.redbioinfo.es" target="_blank">http://www.redbioinfo.es</a> MSc on Bioinformatics for Health Sciences <a href="http://diana.imim.es/Bioinformatics" target="_blank">http://diana.imim.es/Bioinformatics</a> ____________________________________________________________ To manage your sysbio list subscription, visit <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a> For a web interface to the sysbio mailing list, visit <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a> For questions or feedback about the sysbio list, contact <a href="mailto:bnmc-help@caltech.edu." target="_blank">bnmc-help@caltech.edu.</a>

Taverna workshop at Genomes to Systems Meeting, March 20th 2008

Douglas Bruce Kell — 2007-11-20T09:52:38-00:00