The BNMC's Activities
The BNMC has a secret tool in its efforts to build bridges between diverse research efforts and groups at Caltech: its members are directly involved in a wide variety of interdisciplinary projects, putting the BNMC at an exciting intersection of talent and activities in computation, biology, and theory.
| SBML | The Systems Biology Markup Language, the international de facto standard machine-readable format for exchanging computational models of biological reaction networks. |
| SBGN | The Systems Biology Graphical Notation, SBML’s new sister project aimed at standardizing graphical network diagrams of computational models. |
| BioModels Database | A free, centralized, publicly-accessible database of annotated, computational models in SBML and other structured formats. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, and more. |
| MIRIAM | Our effort to standardize “Minimal Information Requested In the Annotation of biochemical Models” (MIRIAM), so that different groups can collaborate on annotating and curating computational models in biology for database projects such as BioModels Database. |
| Stochastic Simulation | The BNMC’s staff include Dan Gillespie, the creator of the widely-used Gillespie stochastic simulation algorithm. Dr. Gillespie and several other BNMC researchers are actively involved in research on advanced multiscale adaptive algorithms for stochastic stimulation. |
| Computable Plant | A project to provide a quantitative and cellular description of plant development in Arabidopsis thaliana. |
| Sigmoid | A database of cellular signaling pathways and models thereof, to marshall the major forms of data and knowledge required as input to cellular modeling software and also to organize the outputs. |
| Cellerator | A free, full-featured, computational environment for describing and simulating cellular models using Mathematica. It supports single and multiple compartment systems with a wide variety of interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or exported for use in other programs. |
| SOSTOOLS | A free MATLAB toolbox for formulating and solving advanced nonlinear optimization problems. SOSTOOLS can be used to specify and solve multivariate sum of squares polynomial problems using a very simple, flexible, and intuitive high-level notation. |
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