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BNMC Seminar - Dr. B.S. Manjunath: BISQUE and Bioimage Analysis, Friday Nov 20, 2009

Linda Taddeo — 2009-11-11T21:28:11-00:00

BISQUE AND BIOIMAGE ANALYSIS B.S.Manjunath Director, Center for Bio-image Informatics; Director, Interactive Digital Media Program; Professor, Electrical and Computer Engineering University of California, Santa Barbara Friday November 20, 2009 2:00 - 3:00 PM Refreshments 1:45 in the lobby Beckman Insitute Auditorium Recent advances in imaging technologies have resulted in large volumes of image and video data, with most of the analysis still done manually and in a qualitative manner. Manual analysis is not only time intensive but often is not reproducible as well. Further, there is little, if any, data base support to manage these image/video collections, to store, search and retrieve image related information within an integrated framework. In this talk, I will present recent progress at the UCSB Center for Bioimage Informatics in building an image informatics infrastructure. The UCSB's BISQUE database system tightly integrates image analysis with traditional database functionalities, and offers a rich set of tools for biologists to store, access, analyze, annotate, and share their image collections. The Bisque system is currently being deployed at several labs in the US and abroad. I will discuss some of the embedded tools including image segmentation, tracking and registration, that enable quantitative analysis of the bioimage data, as well as efforts on benchmarking/validating some of these image processing methods. This work is supported by NSF ITR, CISE and CDI awards. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar: Thurs, Oct 22: Reconstructing the Physiology of Extinct Plants using Mathematical Mod

Linda Taddeo — 2009-10-13T22:20:04-00:00

"Reconstructing the Physiology of Extinct Plants using Mathematical Modeling" Jonathan Wilson Postdoctoral Scholar Geological and Planetary Sciences Caltech Thursday Oct. 22, 2009 2:00 PM -3:00 PM Beckman Institute Auditorium Plants, unlike animals, have much of their function encoded in their anatomy: rate-limiting steps of several physiological processes are often determined by dimensions of anatomical structures. For example, plants move water great distances by exploiting the relative humidity difference between the soil and the atmosphere. Natural selection has fine-tuned the morphology of wood cells to minimize hydraulic resistance, and this resistance can be quantified using mathematical models, allowing plant function to be read from tissue-level anatomy. Furthermore, xylem-containing tissues are among the most likely to be preserved in the fossil record, opening up a 400-million-year window into the coevolution of plant function and the environment. In this talk, I will focus on the evolution of water transport in plants, and how mathematical models derived from analysis of anatomical structures allow for quantitative estimates of extinct plant function and physiology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar - Thursday, April 23 - "Quantitative imaging embryonic morphogenesis: left-right s

Linda Taddeo — 2009-04-17T22:43:15-00:00

*** Please note that this seminar will be held in the Hameetman Auditorium in the newly opened Cahill Center just south of California. *** ................................... "Quantitative imaging embryonic morphogenesis: left-right symmetry breaking and collective cell migration" Willy Supatto Postdoctoral Scholar in Biology Caltech Thursday, April 23, 2009 2:00 pm - 3:00 pm Hameetman Auditorium (refreshments at 1:45) An embryo is shaped by a fascinating and highly regulated choreography of morphogenetic events. The combination of (i) live microscopy, (ii) image analysis, and (iii) optical manipulation provides unique experimental approaches to study these processes in vivo. (i) We show how multiphoton microscopy is adapted for the 4D, long-term, deep-tissue imaging of scattering embryos in a manner that does not compromise their viability. (ii) The 3D-cell tracking of large cell populations and the computational analysis of their trajectories allow to investigate complex morphogenetic events and mutant phenotypes. (iii) Optical manipulation using femtosecond laser ablation provides a minimally invasive tool to disrupt or probe tissue morphogenesis. Finally, we illustrate these quantitative imaging approaches by studying left-right symmetry breaking in early zebrafish embryos and collective cell migration during Drosophila gastrulation. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar: Partial penetrance facilitates the evolution of discrete morphological changes - March

Linda Taddeo — 2009-03-12T20:43:47-00:00

Avigdor Eldar Postdoctoral Scholar Division of Biology, Caltech 2:00PM - 3:00PM March 19, 2009 (Thursday) Beckman Institute Auditorium Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fate of individual organisms differently. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve. Using B. subtilis sporulation as a model system, we identify a stochastic cell fate determination process in mutants, where multiple discrete cell fates are exposed, including a novel, potentially adaptive fate, where two spores are made by a single cell (twin sporulation). We experimentally analyze the underlying genetic network and show how fate discreteness and frequency depend on competition between the underlying cellular processes of differentiation, replication and division. Specifically, we show that the accumulation of consecutive mutations can gradually increase the penetrance of the new sporulation phenotype. Finally, we demonstrate the relevance of our mutational analysis to real evolutionary changes by analyzing wild species that show the alternative sporulation phenotype. Together our results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar: The impact of miRNAs on hematopoietic development, function and disease - Thursday, Fe

Linda Taddeo — 2009-02-12T20:11:45-00:00

Ryan O'Connell Post-doctoral Scholar Biology Caltech Thursday, February 19, 2009 2:00 PM to 3:00 PM (refreshments at 1:45) Noyes 153 Mammalian microRNAs (miRNAs) are emerging as key regulators of the development and function of the immune system, representing a novel layer of gene expression regulation. However, little is known regarding the role of miRNAs during inflammatory responses to infection. We have found that primary macrophages specifically upregulate miR-155 to high levels following exposure to a variety of microbial products and inflammatory cytokines. Strong but transient induction of miR-155 was also observed in mouse bone marrow after injection of bacterial LPS correlated with GM expansion. To test the functional consequences of miR-155 expression in the hematopoietic system, miR-155 expression was enforced in the bone marrow using retroviral-mediated gene transfer. Mir-155 expressing mice exhibited a profound myeloproliferative phenotype, characterized by granulocyte/monocyte (GM) expansion along with defects in several other cell lineages. Of note, the miR-155-induced GM populations displayed pathological features characteristic of myeloid neoplasia. Extending possible relevance to human disease, miR-155 was overexpressed in the bone marrow of patients with acute myeloid leukemia (AML). Finally, miR-155 repressed a subset of genes implicated in hematopoietic development and disease, suggesting a mechanistic basis for miR-155 function. These data implicate miR-155 as a contributor to physiological GM expansion during inflammation and to certain pathological features associated with AML, emphasizing the importance of proper miR-155 regulation in developing myeloid cells during times of inflammatory stress. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar: Mechanistic Study of The Mitochondrial Fission Complex

Linda Taddeo — 2009-01-14T01:13:36-00:00

"Mechanistic Study of The Mitochondrial Fission Complex" Yan Zhang Postdoctoral scholar, Division of Biology Caltech Thursday, January 22, 2009 Noyes 153 2:00PM - 3:00PM (refreshments outside the room at 1:45) Mitochondria undergo frequent and regulated fusion and fission. The balance of these two opposite processes control mitochondrial morphology and function. Mutations in genes essential for mitochondrial fusion are responsible for two types of neuropathy, Charcot-Marie-Tooth type 2A and autosomal dominant optic atrophy. Mice lacking any one of the mitochondrial fusion genes die embryonically. On the other hand, mitochondrial fission is an essential process during human development and plays a crucial step in the execution of apoptosis in many cells. The research interest in our lab is to understand the role of mitochondrial dynamics in normal cell physiology and human diseases. In this presentation, I will focus on our new findings in the mechanism of the fission-complex recruitment to the mitochondria. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Postdoc opening in the BNMC @ Caltech

mhucka — 2008-12-06T01:39:37-00:00

The Beckman Institute' Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) has an immediate opening for a postdoctoral fellow to work jointly in two areas: computational morphodynamics, and software implementation for SBML (the Systems Biology Markup Language). The position is for one year, possibly longer (depending on funding circumstances). Here is more information about the specific topics: * Computational morphodynamics is a new research area, the study of the interaction between physical, informational, and geometrical processes that influences the changing form, shape, and structure of living cells, tissues and organisms. See <a href="http://computational-morphodynamics.net/" target="_blank">http://computational-morphodynamics.net/</a> for more information. The candidate will develop and implement predictive computational models to explore how the morphology of organisms is specified, and in particular, explore how mechanics, cell growth, and cell division affect morphology, and how do biochemical and informational processes determine the major changes in the morphology of living organisms. They will also work closely with experimenters to analyze existing data and suggest new experiments based on predictive simulations. * The Systems Biology Markup Language (SBML) is a standard format for representing computational models in systems biology. See <a href="http://sbml.org" target="_blank">http://sbml.org</a> for more information. We are working on the next generation of SBML, and as part of that, want to produce a new reference implementation of an SBML interpreter. The goal is to produce an open-source add-on to a mathematical environment, most probably R or Octave. Applicants should have a PhD in a relevant area such as computer science, computational biology, bioinformatics, plant biology, or similar. Knowledge of Mathematica, Malab, R and either C or C++ are crucial, as is experience in developing deterministic (ODE) and stochastic models of biological systems. Experience with modeling biological networks using ODE or stochastic frameworks, and/or experience in relevant areas of biology, will be strong assets. Please direct inquiries to <a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a> and/or <a href="mailto:bshapiro@caltech.edu." target="_blank">bshapiro@caltech.edu.</a> If sending an application, please include a CV and at least two references. Thanks, Mike -- 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 _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar: In vitro transcriptional circuits: design, dynamics, and robustness

Linda Taddeo — 2008-11-18T19:36:34-00:00

Biological Network Modeling Center Seminar: "In vitro transcriptional circuits: design, dynamics, and robustness" Erik Winfree Associate Professor of Computer Science and Computation and Neural Systems Caltech Thursday, November 20, 2008 2:00PM - 3:00PM Beckman Institute Auditorium (refreshments at 1:45 in the lobby) Synthetic biochemical circuits both provide an opportunity to embed control logic within chemical systems for technological applications and provide a platform for probing our understanding of general principles for biochemical circuits. We have developed a general approach to the construction of in vitro biochemical circuits based on the transcription and degradation of RNA molecules. Consisting of just DNA templates and two enzymes, in principle arbitrary circuits can be systematically constructed, displaying a rich variety of dynamical and computational behavior. We have experimentally demonstrated individual transcriptional switches, a bistable network, and several oscillating circuits. In doing so, we have encountered a number of unexpected difficulties -- deviations from ideal circuit behavior -- that help frame the critical questions of how to model and design robust biochemical systems. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar - Dissecting dynamics of shoot stem cells in Arabidopsis Thaliana

Linda Taddeo — 2008-09-11T23:14:06-00:00

Vijay Chickarmane Senior Postdoctoral Scholar in Biology Caltech BNMC seminar series: "Dissecting dynamics of shoot stem cells in Arabidopsis Thaliana" Thursday, September 18, 2008 2:00 PM to 3:00 PM (refreshments at 1:45 in the foyer) Broad #100 (Rock Auditorium) The above-ground tissues of many plants are generated from shoot stem cells. The shoot apical meristem, which houses these stem cells, provides a very dynamic environment. On the one hand it is a veritable fountain of youth, as it continuously provides differentiated cells which form the leaves and floral organs, while on the other hand, the number of stem cells is homeostatically maintained throughout development. Recent experiments have shown that such tight and robust regulation of stem cell maintenance is achieved through interactions with neighboring cell populations. Other data suggests that hormones are also involved in maintaining homeostasis. In this talk I will report on ongoing experiments and computational modeling which is aimed at unraveling these mechanisms, and provide a view of the fascinating dynamics which takes place in the shoot apical meristem. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

CACR Seminar: "Two Open Computational Problems in Biology"

Linda Taddeo — 2008-01-15T21:09:14-00:00

CACR Seminar Friday January 25 3:00 pm Powell-Booth 100 "Two Open Computational Problems in Biology" Dr. C. Titus Brown, Caltech / Michigan State U The number and variety of large-scale biological data sets is ever increasing, bringing new computational questions and problems with them. An especially fruitful area of biological inquiry has been engendered by the massive amount of sequencing data being produced by several new technologies. I'll discuss two specific biological approaches fostered by new technology: the use of comparative genomics to find and understand functional parts of genomes, and the use of microbial community sequencing to understand microbial ecosystems. Both of these areas are important areas of research with many computational questions buried within them. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar - In Promptu Ponere: Removing Noise in Cryoimaging

Linda Taddeo — 2008-01-07T18:46:08-00:00

Alexandre Cunha The Center for Integrative Study of Cell Regulation and CACR Caltech Thursday, January 24, 2008 2:00 PM to 3:00 PM Beckman Institute Auditorium (refreshments at 1:45 in the lobby) "In Promptu Ponere: Removing Noise in Cryoimaging" Electron cryomicroscopy is a remarkable technology enabling new discoveries at sub-cellular scales making the cryoelectron scope one of the most valuable and advanced assets in the toolbox of the contemporary structural biologist. This technology is still young and there is much to do to improve the cryoimaging pipeline, including the development of suitable image processing algorithms. In this presentation I will describe my inroads into filtering typical, highly noisy cryoimages. I will review some recently proposed variational models for denoising, recall some classical filters which are still frequently used by practitioners, and talk about our new developments in nonlocal filters capable of producing significantly better results. I will illustrate with cases in Caulobacter crescentus tomograms, in large image sets used for single particle analysis, and in MRI. I will also comment on the computational aspects for efficiently processing large, high resolution images containing millions to billions of pixels/voxels, and how we are using parallelism and multicore computing to achieve ten to hundred fold speed ups. This is joint work with Grant Jensen. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar: "Life at Low Molecule Number" - Thursday, Nov 29, 3-4pm

Linda Taddeo — 2007-11-26T22:36:34-00:00

Terrence J. Sejnowski Professor of Computational Neurobiology Salk Institute for Biological Studies Thursday, November 29, 2007 3:00 PM to 4:00 PM Beckman Institute Auditorium (refreshments at 2:45 in the lobby) "Life at Low Molecule Number" Transient molecular signals occur in microdomains that are typically neither well mixed nor in equilibirum. The number of molecules is often so small that large fluctuations occur. As a consequence, knowing the spatial organization of the molecular components is essential in understanding cell signaling pathways. Monte Carlo computer simulations that incorporate realistic 3-D geometries can be used to explore the subcellular architecture and physiology of cells and synapses. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar: Regulatory Genomics of Sea Urchins - Thursday, June 21

Linda Taddeo — 2007-06-12T23:48:21-00:00

BNMC Seminar: Regulatory Genomics of Sea Urchins R. Andrew Cameron Director, Center for Computational Regulatory Genomics Beckman Institute Caltech Thursday, June 21, 2007 2:00 PM to 3:00 PM Broad #100 (Rock Auditorium) The developing sea urchin embryo can be thought of as a bunch of outwardly indistinguishable cells that are busy mounting different programs of gene expression which define the territories that will make up the larva. Thus, the study of development is the study of embryonic gene regulation. This point has been brought home in recent studies that have described the gene regulatory network that leads to the specification of the endomesoderm territory in the sea urchin blastula. Some 60 different regulatory genes are assembled into this network and they explain the intercellular signals and autonomous expression events known to occur in this embryo. The gene activities in this network are linked through the cis-regulatory modules of the genome, the hard-wired inherited information in the genome. With the advent of a draft genomic sequence for the sea urchin, opportunities are emerging for accelerating the discovery of network interactions and fully describing how development works in this outwardly simple embryo. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar - Thursday, May 10 - Anand R. Asthagiri

Linda Taddeo — 2007-05-02T17:32:55-00:00

FROM MOLECULAR NETWORKS TO MULTICELLAR STRUCTURES: PREDICTING PHENOTYPE DIVERSITY AND TRANSITIONS Anand R. Asthagiri Assistant Professor of Chemical Engineering Caltech Thursday, May 10, 2007 2:00 PM to 3:00 PM Beckman Institute Auditorium (refreshments at 1:45) Multicellular patterns and structures emerge as cells execute instructions received from cues in their microenvironment. Deciphering how cells integrate these cues to achieve an organized, functional structure is a fundamental question in biology with important biomedical implications in areas such as tissue engineering and regenerative medicine. An essential element in multicellular assembly involves direct cell-cell interactions. Cell-cell contacts are not only physical links between neighboring cells, but also sources of biochemical signals that instruct cellular behavior. Our lab has been focused on elucidating how direct cell-cell interactions crosstalk with other environmental cues to affect individual cell fate choices, and thereby, generate multicellular patterns. This talk will focus on our recent work in modeling multicellular patterning during the development of the organism, C. elegans. An intriguing aspect of this system is that patterning is guided by both a soluble signal and direct cell-cell interactions. Our computational analysis reveals that cell-cell coupling enhances cell perception of a gradient in the soluble signal [Giurumescu et. al. (2006) PNAS]. In addition, we have developed a parameter-unbiased, computational framework that accurately predicts wild-type and mutant phenotypes. This ability to predict phenotypes has opened the door to intriguing new questions such as: what new phenotypes are possible, and what perturbations (mutations) render such phenotypes? I will describe how answering these questions have offered a unique opportunity to explore both the molecular genetics of patterning and the evolutionary capacity of this signaling network for creating phenotypic diversity. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar, April 26 - Adrienne Roeder

Linda Taddeo — 2007-04-10T22:30:27-00:00

** Please note that this seminar will be held in Broad #100. ** .......................................... BIOLOGICAL AND IMAGING APPROACHES TO UNDERSTANDING PLANT CELL GROWTH Adrienne Roeder Thursday, April 26, 2007 2:00 PM to 3:00 PM Broad #100 (Rock Auditorium) (refreshments at 1:45) With the increasing focus on biofuels derived from cellulose in the plant cell walls, understanding how plant cells regulate their growth and division becomes critical. Plant cells are locked into position by their cell walls, which essentially glue the cells together so that they cannot slide past one another. Consequently, the growth of neighboring cells must be closely coordinated. This raises the question of how cells of different sizes can form adjacent to one another. An extreme example occurs in the Arabidopsis sepal where giant cells that can stretch half the length of the sepal form next to much smaller cells. To determine how giant cells form, we are currently imaging living sepals over time and tracking the cells as they develop. To process the images, Michael C. Burl at JPL has developed a segmentation program that extracts the 3D surfaces of the nuclei. One of the first observations we have made is that the giant cells have enlarged nuclei suggesting that they have undergone endoreduplication, a specialized cell cycle in which the DNA is replicated, but the cell does not divide. Endoreduplication is common in plants and insects, and also occurs in a few mammalian cell types. The endoreduplication of giant cells suggests that these large cells can form next to their smaller neighbors because they stop dividing earlier and continue to expand at the same rate as their neighbors, which remain small by continuing to divide. Recent work suggests that a signaling pathway is involved in giant cell development. The function of the giant cells is currently unclear, but they are not present in a canola, broccoli, or Capsella, which are plants related to Arabidopsis, suggesting that they arose recently in evolution. About the speaker Adrienne Roeder is a Postdoctoral Scholar in Biology in the Meyerowitz lab at Caltech. She received a Helen Hay Whitney Postdoctoral Fellowship to investigate the development of giant cells. Adrienne has been involved in research on plant development since she was an undergraduate at Stanford where she investigated the first asymmetric division of the Arabidopsis zygote. Her interest in computational approaches also dates back to Stanford where she minored in Mathematical and Computational Sciences. Adrienne learned molecular genetic approaches to plant development in her graduate studies at UCSD where she studied the differentiation of the tissues in the Arabidopsis fruit. Her graduate work was funded by a Howard Hughes Medical Institute predoctoral fellowship. Currently she is bringing her biological and computational interests back together by participating in the Computable Plant project (<a href="http://www.computableplant.org/" target="_blank">http://www.computableplant.org/</a>). _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar: March 22, 2007 - Weiwei Zhong - Genome-wide exploration of C. elegans

Linda Taddeo — 2007-03-15T17:50:45-00:00

BNMC SEMINAR: GENOME-WIDE EXPLORATION OF C. ELEGANS Weiwei Zhong Postdoctoral Scholar in Biology Caltech Thursday, March 22, 2007 2:00 PM to 3:00 PM Beckman Institute Auditorium (refreshments at 1:45 in the lobby) Genetic interactions underlie how a genome specifies the properties of an organism. We propose two strategies to systematically map C. elegans genetic interactions, especially those involved in complex biological processes: 1. Probabilistic prediction of genetic interactions. By integrating various genomic data (such as phenotype, expression, and interactome data) from multiple species, we can reliably predict the probability of two genes being an interacting pair. Using such results to prioritize test candidates can greatly increase our efficiency in experimental testing. 2. Automated experimental testing of genetic interactions. We are developing an automated system to conduct high-throughput, quantitative analysis of C. elegans genetic interactions. Hypothesis-driven discovery is a process of two steps: hypothesis generation and experimental verification. By optimizing both steps, we expect our experimental pipeline to bring new insights into the understanding of the C. elegans genetic interaction network. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar - Lighting the Way in Biomedicine

Linda Taddeo — 2007-02-27T00:38:46-00:00

Changhuei Yang Assistant Professor of Electrical Engineering and Bioengineering California Institute of Technology Thursday, March 08, 2007 2:00 PM to 3:00 PM Beckman Institute Auditorium (refreshments 1:45 in the lobby) Biophotonics is a rapidly evolving research area aimed at providing new light-based imaging, diagnostic and therapeutic tools for biologists and clinicians. I will be talking about two areas of biophotonics research that are occurring in my lab: The Optofluidic Microscope -- A microscope the size of Washington's nose on a quarter, that does not contain any lenses and is yet able to image with better resolution than a typical microscope. The application range of this invention is wide: it can change the way biologists think about and use microscope, it enables clinical point-of-care blood and urine analysis, and it can improve Third World heathcare by providing cheap and rugged microscope units. Tissue Scattering Suppression by Time Reversal Phase Conjugation -- An approach for turning biological tissues transparent through the use of holography. Light scattering in tissues may look random but their trajectories are deterministic. As such, it is possible to create a situation where light scattered from a tissue will retrace their paths through the tissue. I will report on our initial findings and point out a few applications for such a phenomenon. .............................. Professor Yang graduated from MIT in 2002 and has steadily moved towards warmer climate thereafter. After short stints at ESPCI (Paris) and Duke University, he settled down in Caltech in Dec 2003. Professor Yang recently received the NSF CAREER award and the Coulter Foundation Early Career Award. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar: Sean Megason, Jan 25, 2007 - "In Toto Imaging of Vertebrate Development"

Linda Taddeo — 2006-12-13T23:37:34-00:00

BNMC SEMINAR: IN TOTO IMAGING OF VERTEBRATE DEVELOPMENT Sean G. Megason Postdoctoral Fellow Biological Imaging Center, Beckman Institute, Caltech Thursday, January 25, 2007 2:00 PM to 3:00 PM Beckman Institute Auditorium (refreshments at 1:45 in the lobby) We have recently been awarded a grant from the National Human Genome Research Institute for the establishment of a Center of Excellence in Genomic Science for the "In Toto Genomic Analysis of Vertebrate Development". The principle goal of this center is to create a "Digital Fish" using an integrated approach combining imaging, genetics, genomics, and information technology. Understanding how the genomic code is executed through development requires moving from the one-dimensional string of letters that has now been determined for the genome sequence towards understanding how the genome functions in the 4-dimensions of space and time of a developing embryo. The goal of this center is to perform a comprehensive, systems-based analysis of gene function across the space and time of the developing vertebrate embryo. The center has four aims: 1) The first aim is to develop a technology called "in toto imaging" that can digitize in vivo data in a systematic, high-throughput, and quantitative fashion. In toto imaging uses confocal/2-photon laser scanning microscopy to image whole developing embryos at single-cell resolution and special software to digitize and quantify this 4-dimensional data at the level of the cell. Acquiring data that is comprehensive (across the genome, space, and time), quantitative, cell-based, and centralized is essential for taking a system approach to biology. 2) The second aim is to develop a gene-trap-like technology called "flip trapping". In the initial conformation flip trap alleles produce a functional YFP fusion protein. After Cre mediated recombination, flip trap alleles produce a non-functional RFP gene trap. Each flip trap allele thus reveals: protein expression pattern, transcriptional expression pattern, protein subcellular localization; and a conditional mutant phenotype. Importantly, this information can be read out from the embryo in vivo and non-invasively. 3) The third aim is to develop a flexible, muliplex, fluorescent-based in situ hybridization technique using the Hybridization Chain Reaction (HCR) 4) In the fourth aim, we will integrate these technologies into a production phase. We will use in toto imaging to upload data fluorescently marked by flip traps and HCR on a genome-wide scale to create a "Digital Fish" that provides the foundation to model the execution of the genomic program that turns an egg into and embryo. Our data, software, and fish lines will be released rapidly to the community in the spirit of the Bermuda Principles. -------------- About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC seminar: Eric Mjolsness, Thursday, Nov 30, 2006

Linda Taddeo — 2006-11-21T19:00:28-00:00

BNMC SEMINAR: BIOCHEMICAL NETWORK MODELS WITH REALLY BIG MATRICES Eric Mjolsness Associate Professor, Department of Information and Computer Science UC, Irvine Thursday, November 30, 2006 2:00 PM to 3:00 PM Beckman Institute Auditorium (refreshments at 1:45 in the lobby) In this mostly theoretical talk, I will review how fully stochastic models of biochemical reaction networks can be expressed in terms of simple algebraic expressions built out of operators: infinite-dimensional matrices that move probability around between different possible states of the network. This formulation of the chemical master equation has several advantages. It allows some easy, small networks to be solved in an almost mechanical way. It allows solvable submodels to be used as subroutines inside of simulation algorithms for larger and more complicated networks. It admits a systematic approach to creating simulation algorithms based on the operator (matrix) exponential function. I will go on to show that there is a generalization of these ideas to parameter-bearing objects at multiple spatial scales, and not just molecules, which can serve as the foundation for a new general-purpose biological modeling language. -------------- About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar - Follow this Beat: Dynamic Imaging and Analysis of the Developing Embryonic Heart - Th

Linda Taddeo — 2006-10-20T18:00:04-00:00

Title: BNMC Seminar: Follow this Beat: Dynamic Imaging and Analysis of the Developing Embryonic Heart Speaker: Michael Liebling Date: Thursday, October 26, 2006 Time: 2:00 PM to 3:00 PM Location: Beckman Institute Auditorium (refreshments at 1:45 in the lobby) Studying the influence on embryonic development of fast biomechanical processes, such as those induced by blood flow in the embryonic heart, requires the ability to acquire dynamic, three-dimensional data with high temporal and spatial resolution. We devised novel strategies for collecting and synchronizing cyclic image sequences to build volumes over the entire depth of the beating embryonic zebrafish heart. Our data analysis and reduction protocols allow for the systematic extraction of quantitative information to describe phenotype and function. We have used this approach to characterize blood flow and heart efficiency by imaging fluorescent protein-expressing blood and cardiac cells as the heart develops from a tube to a multichambered organ. These (partly wavelet-based) methods are sufficiently robust to image tissues within the heart at cellular resolution over a wide range of ages and are generalizable to imaging and analyzing other fast moving structures at microscopic scales. This is joint work with Arian S. Forouhar, Mory Gharib, Mary E. Dickinson, and Scott E. Fraser. ............................. About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

BNMC Seminar September 28 - Michael Hucka

Linda Taddeo — 2006-09-19T19:18:49-00:00

Title: BNMC Seminar: SBML, SBGN, and BioModels.net Speaker: Michael Hucka Date: Thursday, September 28, 2006 Time: 2:00 PM to 3:00 PM Location: Beckman Institute Auditorium (refreshments at 1:45 in the lobby) Systems biology by its nature requires collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics, and physics. Successful integration of these disciplines depends on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, software tools that permit analysis of vast and complex data, and agreed-upon standards that enable researchers to communicate and reuse each other's results in practical and unambiguous ways. In this presentation, I will discuss several international projects (SBML, SBGN, and BioModels.net) aimed at addressing the last issue. An important prerequisite for effective sharing of computational models is reaching agreement on how to communicate them, both between software and between humans. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models at the biochemical reaction level. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chance for errors in translation and assuring a common starting point for analyses and simulations. SBML has become the most successful effort in this direction so far, with over 100 software tools supporting it today. A recently-created sister project is the Systems Biology Graphical Notation (SBGN) project. It addresses the issue of consistent human communication, by attempting to add more rigor and consistency to the graphical network diagrams that often accompany published research on models of biological reaction systems. The real payoff will come when more people and software adopt such a common visual notation and it becomes as familiar to them as circuit schematics are to electronics engineers. Finally, when developing and publishing computational models, it is only natural to want to put them into a database. The BioModels.net project is an effort to (1) provide a free, centralized, publicly-accessible database of human-curated computational models in SBML and other structured formats; (2) define agreed-upon standards for model curation; and (2) define agreed-upon vocabularies for annotating models with connections to biological data resources. ................................ About the speaker: Dr. Michael Hucka is a Senior Research Fellow at Caltech. He is currently the co-director of the Biological Network Modeling Center, an initiative to bring together a number of efforts at Caltech in the area of computational systems biology. He is also one of the principal developers of the Systems Biology Markup Language (SBML), an international standard format for representing computational models in a way that can be used by different software systems to communicate and exchange those models. More recently, he has been involved in starting the SBGN effort, the BioModels Database, and the BioModels.net consortium. Dr. Hucka was previously a postdoctoral scholar in the Division of Biology at Caltech, where he worked on the GENESIS neural simulation package. He is also one of the creators of NeuroML. His formal training is in computer science and engineering. ............................. About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Meyerowitz and Lange Receive Balzan Prize

mhucka — 2006-09-08T20:52:45-00:00

<a href="http://pr.caltech.edu/media/Press_Releases/PR12891.html" target="_blank">http://pr.caltech.edu/media/Press_Releases/PR12891.html</a> Elliot Meyerowitz and fellow Caltech faculty Andrew Lange have been named Balzan Prizewinners for 2006 by the International Balzan Foundation. Meyerowitz, Beadle Professor of Biology and biology division chair, and co-principal investigator of the Biological Network Modeling Center (BNMC), will share his award for plant molecular genetics with Chris R. Somerville of Stanford University "...for their joint efforts in establishing Arabidopsis as a model organism for plant molecular genetics. This has far-reaching implications for plant science, both on a fundamental level and in potential applications." Lange, Goldberger Professor of Physics, will share his award for observational astronomy and astrophysics with Paolo de Bernardis of Universita di Roma La Sapienza in Italy "...for their contributions to cosmology, in particular the "BOOMERanG" Antarctic balloon experiment." Congratulations Elliot and Andrew! -- Mike Hucka, Ph.D. <<a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a>> tel +1.626.395.8128 Senior Research Fellow, Control and Dynamical Systems Co-director, Biological Network Modeling Center (BNMC) The Beckman Institute @ The California Institute of Technology _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Please spread the word: ICSB 2006 registration deadline

mhucka — 2006-08-22T21:56:14-00:00

(Sorry if you receive duplicates of this from other mailing lists. --MH) CALL FOR ATTENDANCE ------------------------------------------------------- *** ICSB 2006 *** The Seventh International Conference on Systems Biology ------------------------------------------------------- Pacifico Yokohama Yokohama, Japan October 8-13, 2006 Late registration deadline: August 31 <a href="http://www.icsb-2006.org" target="_blank">http://www.icsb-2006.org</a> TIP: This week, some airlines made significant discounts (in some cases by 50%) on flights to Tokyo. You may wish to act quickly. Systems Biology is the synergistic application of experiment, theory and modeling towards understanding biological processes as whole systems instead of isolated parts. Understanding biological processes from the systems perspective is an essential cornerstone of a true understanding of biological function. The Seventh International Conference on Systems Biology (ICSB) continues an annual series of conferences initiated by Hiroaki Kitano in Tokyo in 2000. This year's conference will begin with tutorials on the morning of Sunday, October 8. The formal scientific sessions will begin on Monday, October 9 and end on Wednesday, October 11. Workshops will follow on October 12-13. The scientific sessions will feature plenary speeches and invited presentations by world-renowned researchers, along with afternoon poster sessions and evening social activities. PLENARY SPEAKERS ---------------- * Stephen Quake (Stanford University / HHMI) "Biological Large Scale Integration" * Atsushi Miyawaki (Riken Brian Science Institute) "Spatio-temporal Patterns of Intracellular Signaling" * Luis Serrano (European Molecular Biology Laboratory) "Noise Regulation by Negative Feedback Loops" * Steve Oliver (University of Manchester) "Dealing with the Complexity of a 'simple' Eukaryotic Cell" * Upinder S. Bhalla (National Centre of Biological Science, Bangalore) "Electricity meets Chemistry: Fast and Slow Signaling in Memory" PROGRAM COMMITTEE ----------------- (alphabetical order per region) Asia: * Uri Alon (Weitzman Institute of Science, Israel) * Upi Bhalla (National Centre for Biological Science, India) * Kwang-Hyun Cho (Seoul National Univ., Korea) * Hsuan-Cheng Huang(National Yang-Ming University, Taiwan) * Akira Funahashi (SBI & JST ERATO-SORST Kitano Project, Japan) * Mariko Hatakeyama (RIKEN GSC, Japan) * Yoshihide Hayashizaki (RIKEN GSC, Japan) * Do Han Kim (Gwangju Institute of Science and Technology, Korea) * Hiroaki Kitano (SBI & Sony CSL, Japan) * Shinya Kuroda (Univ. of Tokyo, Japan) * Sang Yup Lee (Korea Advanced Institute of Science and Technology) * Edison Liu (Genome Institute of Singapore, Singapore) * Douglas Murray (SBI & JST ERATO-SORST Kitano Project, Japan) * Shuichi Onami (Keio Univ., Japan) * Reiko Tanaka (RIKEN BioMimetic Center, Japan) * Masaru Tomita (Keio Univ., Japan) * Hiroki Ueda (RIKEN Center for Developmental Biology, Japan) Europe: * Lilla Alberghina (Univ. of Milano-Bicocca, Italy) * Marta Cascante (Univ. of Barcelona, Spain) * Roland Eils (DFKI, Germany) * Peter Ghazal (GTI, UK) * Igor Goryanin (Univ. of Edinburgh, UK) * Stefan Hohmann (Goteborg Univ., Sweden) * Douglas Kell (Univ. of Manchester, UK) * Edda Klipp (Max-Planck Institute for Molecular Genetics, Germany) * Pierre De Meyts (Hagedorn Research Institute, Denmark / Novo Nordisk) * Jens Nielsen (DTU (=Technical Univ. of Denmark), Denmark) * Staffan Normark (Karolinska Institute, Sweden) * Nicolas Le Novere (EMBL-EBI, UK) * Klaus Prank (GlaxoSmithKline) * Hans Westerhoff (Univ. of Amsterdam, the Netherlands) North America: * Adam Arkin (Lawrence Berkeley National Lab., USA) * Frederick Cross (Rockefeller Univ., USA) * Marie Csete (Emory Univ. USA) * Francis Doyle (UCSB, USA) * John Doyle (Caltech, USA) * Michael Hucka (Caltech, USA) * Trey Ideker (UCSD, USA) * Boris Kholodenko (Thomas Jefferson Univ., USA ) * Douglas Lauffenburger (MIT, USA) * Pedro Mendes (Virginia Tech., USA) * Bernhard Palsson (UCSD, USA) * John Tyson (Virginia Tech., USA) * Marc Vidal (Dana-Harber Cancer Institute, USA) * Tau-Mu Yi (UCI, USA) Student Session Organizer: * Satya Arjunan (Keio Univ. Japan) * John Cumbers (Brown Univ. USA) Advisory Committee * Sydney Brenner (Founding President, Okinawa Institute of Science and Technology & The Salk Institute) * Kiyoshi Kurokawa (President, The Science Council of Japan) * Koichi Kitazawa (Senior Executive-Director, Japan Science and Technology Agency) * Yoshiyuki Sakaki (Director, Riken Genomic Science Center) * Sin-ichi Nishikawa (Deputy Director, Laboratory for Stem Cell Biology, Center for Developmental Biology, Riken) * Yoshiki Hotta (President, Research Organization of Information and Systems) * Shigetada Nakanishi (Director, Osaka Bioscience Institute) Executive Committee * Kazuyuki Aihara (Univ. of Tokyo and ERATO Aihara Project) * Akiyasu Fujii (SBI) * Ken Fukuda (AIST) * Akira Funahashi (SBI & JST ERATO-SORST Kitano Project) * Mariko Hatakeyama (RIKEN GSC) * Hiroaki Kitano (SBI & Sony CSL) * Tatsuhiko Kodama (Univ. of Tokyo) * Shinya Kuroda (Univ. of Tokyo) * Yukiko Matsuoka (SBI & JST ERATO-SORST Kitano Project) * Satoru Miyano (Univ. of Tokyo) * Masahiko Noda (Japan Science and Technology Agency) * Makoto Suematsu (Keio Univ. School of Medicine) * Hiroki Ueda (RIKEN Center for Developmental Biology) * Toru Yao (RIKEN GSC) --------------------------- Please join us at ICSB 2006 --------------------------- <a href="http://icsb-2006.org" target="_blank">http://icsb-2006.org</a> mailto:<a href="mailto:info@icsb-2006.org" target="_blank">info@icsb-2006.org</a> _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

ICSB 2007 website

mhucka — 2006-08-11T05:54:43-00:00

As many of you know, the BNMC is co-organizing the Eighth International Conference on Systems Biology in 2007. It will be held Oct. 1-6 at Long Beach in California. We would like to bring your attention to the website for the event: <a href="http://www.icsb-2007.org" target="_blank">http://www.icsb-2007.org</a> It has just been put online, and although it is only a front page at the moment, in the months ahead it will be expanded greatly with information about the conference. Join us for ICSB 2007! Mike -- Mike Hucka, Ph.D. <<a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a>> tel +1.626.395.8128 Senior Research Fellow, Control and Dynamical Systems Co-director, Biological Network Modeling Center The Beckman Institute @ The California Institute of Technology _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Seminar July 14: Tau-Mu Yi

Linda Taddeo — 2006-06-29T01:01:31-00:00

BNMC Seminar: Modeling Pheromone-Induced Cell Polarization in Yeast Tau-Mu Yi Department of Developmental and Cell Biology UCI Friday, July 14, 2006 2:00 PM to 3:00 PM Beckman Institute auditorium (refreshments at 1:45 in the lobby) G-protein signal transduction pathways are the primary sensors of eukaryotic organisms. Haploid yeast cells use this system to sense and project up spatial gradients of mating pheromone leading to cell fusion. We have employed a systems biology approach to obtain a higher-resolution understanding of this process. .... About the speaker: Tau-Mu Yi learned about systems biology at Caltech, which was a wonderful experience. He is now at UCI where he investigates G-protein signaling, chemotaxis and cell polarization, and the robustness of biological systems. About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Seminar June 2: Herbert Sauro

mhucka — 2006-05-25T01:54:39-00:00

BNMC SEMINAR: MODULAR SOFTWARE AND MODULAR BIOLOGY Herbert Sauro Keck Graduate Institute Friday, June 2, 2006 2:00 PM to 3:00 PM Refreshments served at 1:45 PM Beckman Institute auditorium Abstract: Modularity is a key concept that pervades both software engineering and biological systems. In this talk I will discuss two things: the Systems Biology Workbench (SBW), which is an extensible and modular software framework for systems biology, and modularity in biological networks. I will discuss strategies for searching for functional motifs in networks, including work we have done in the evolution of in silico functional motifs. --- About Dr. Sauro: Herbert Sauro was originally educated as a biochemist/microbiologist but became interested in the use of simulation and theory to understand cellular networks after accidently coming across a paper by David Garkfinkel on the simulation of glycolysis. He wrote one of the first biochemical simulators for the PC (SCAMP) in the 1980s in order to assist work on extending metabolic control analysis (A theory closely related to biochemical systems theory). However, with the lack of community interest in systems biology during the late 80s and early 90s, he left science to start a software company and offer consultancy work to finance firms in the UK. With the surge in interest in systems biology in the US in the late 90s, he secured a position at Caltech to assist in the devleopment of the Systems Biology Markup Language. Since then he moved to a faculty position at the Keck Graduate Institute where he continues to do research on network motifs, theory and software. About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is an interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC holds a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Upcoming BNMC seminars

mhucka — 2006-05-12T01:33:47-00:00

Just to let people know about upcoming BNMC seminars: May 12, 2 PM: Marcus Heisler "Developmental Dynamics of Arabidopsis Primordium Formation" <a href="http://bnmc.caltech.edu/Events/10/marcus-heisler" target="_blank">http://bnmc.caltech.edu/Events/10/marcus-heisler</a> June 2, 2 PM: Herbert Sauro (Keck Graduate Institute) Title TBA July 14, 2 PM: Tau-Mu Yi (UCI) Title TBA All will be on Fridays, in the BI Auditorium, 2 PM, with coffee & tea served prior at 1:45. MH -- Mike Hucka, Ph.D. <<a href="mailto:mhucka@caltech.edu" target="_blank">mhucka@caltech.edu</a>> tel +1.626.395.8128 Senior Research Fellow, Control and Dynamical Systems Co-director, Biological Network Modeling Center (BNMC) The Beckman Institute @ The California Institute of Technology _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Seminar by Marcus Heisler, Friday May 12, 2 PM

mhucka — 2006-05-10T18:13:57-00:00

BNMC Seminar: Developmental Dynamics of Arabidopsis Primordium Formation Marcus Heisler 2 PM Friday May 12 Beckman Institute Auditorium Primordium formation is a fundamental developmental process in plants and animals. It involves a positioning mechanism that defines where the tissue or organ will arise as well as changes to growth and differentiation that result in outgrowth and the correct patterning of cell types. By real-time analysis of protein expression coupled with cell tracking and mathematical modeling we have started to investigate plant organ development. The picture that emerges is that of a largely self-regulating system involving polar transport of the plant morphogen auxin to position organ primordia, mediate organ growth and influence gene expression domains. Auxin transport appears to be coordinated by local cell-cell signaling and pre-existing differentiation patterns. This leads to a dynamic system in which global pattern results from local decisions by individual cells. --- About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is a new interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC has begun a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

CIMMS seminar: Eric Vanden-Eijnden

mhucka — 2006-04-29T02:39:44-00:00

This audience might be interested in finding out about the following seminar: <a href="http://www.cimms.caltech.edu" target="_blank">http://www.cimms.caltech.edu</a> CDS/CIMMS Seminar: Nested Stochastic Simulation Algorithm for Kinetic Monte Carlo Systems with Disparate Rates Dr. Eric Vanden-Eijnden, Courant Institute of Mathematical Sciences. New York The talk will present a new numerical algorithm for simulating continuous-time Markov chains with multiple time-scales. This algorithm is an improvement of the traditional stochastic simulation algorithm (SSA), also known as Gillespie's algorithm. It is in the form of a nested SSA and uses an outer SSA to simulate the slow reactions with rates computed from realizations of inner SSAs that simulate the fast reactions. The algorithm itself is quite general and seamless, and it amounts to a small modification of the original SSA. It can be justified using averaging theorems to multi-scale continuous-time Markov chains which allow one to identify the slow variables in the system, derive effective dynamics on the slow time scale, and give error estimates for the nested SSA. The efficiency of the nested SSA will be discussed using these error estimates, and illustrated through several numerical examples. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>

Seminar by Dan Gillespie, 2 PM, Wed. March 15

mhucka — 2006-03-15T08:06:51-00:00

BNMC Seminar: Stochastic Chemical Kinetics Dan Gillespie 2 PM Wednesday March 15 Beckman Institute Auditorium Abstract: The time evolution of a well-stirred chemically reacting system is traditionally modeled by a set of coupled ordinary differential equations called the reaction rate equation (RRE). The resulting picture of continuous deterministic evolution is, however, valid only for infinitely large systems. That condition is usually well approximated in laboratory test tube systems. But in biological systems formed by single living cells, the small population numbers of some reactant species can result in dynamical behavior that is noticeably discrete rather than continuous, and stochastic rather than deterministic. In that case, a more physically accurate mathematical modeling is obtained by using the machinery of Markov process theory, specifically, the chemical master equation (CME) and the stochastic simulation algorithm (SSA). This talk will review the theoretical foundations of stochastic chemical kinetics, and then discuss some recent efforts to (1) approximate the SSA by a faster simulation procedure, and (2) establish the formal connection between the CME/SSA description and the RRE description. --- About Dr. Gillespie: In the 1970's, Dan Gillespie developed an exact stochastic simulation approach for chemical kinetics that has since become the gold-standard algorithm for the field. This work has also been the starting point for a variety of modern efforts by many groups worldwide to accelerate stochastic simulation beyond what is possible using the basic Gillespie algorithm. Recent joint work involving Caltech and UCSB has been producing a steady stream of leading-edge results. About the BNMC: The Beckman Institute Biological Network Modeling Center (BNMC; <a href="http://bnmc.caltech.edu" target="_blank">http://bnmc.caltech.edu</a>) is a new interdisciplinary effort whose goal it is to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems. Its key members come from multiple Caltech divisions and groups, including Biology, Control and Dynamical Systems, and CACR (the Center for Advanced Computing Research). As part of its mission, the BNMC has begun a regular seminar series on topics relevant to computational modeling in biology. _______________________________________________ bnmc-announce mailing list <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a>