Box 5.5BioSPICE

BioSPICE, the Biological Simulation Program for Intra-Cellular Evaluation, is in essence a modeling framework that provides users with model components, tools, databases, and infrastructure to develop predictive dynamical models of cellular function. BioSPICE seeks to promote a synergy between experiment and model, in which model predictions drive experiment and experimental results identify areas in which a given model needs to be improved, and the intent is that researchers go from data to models to analysis and hypothesis generation, iteratively refining their understanding of the biological processes.

An important component of BioSPICE is a library of experimentally validated (and hence trusted) model components that can be used as starting points in larger-scale simulations, as elements from this library are composed in new ways or adapted to investigate other biological systems. Many biological parts and processes are represented as components, including phosphorylization events, chemotaxis, and conserved elements of various pathways. Also, because BioSPICE is designed as an open-source environment, it is hoped that the user community itself will make available a repertoire of model components that span a wide range of spatial, temporal, and functional scales, including those that simulate a single chemical reaction with high fidelity, those that simulate entire pathways, and those that simulate more abstract higher-order motifs.

BioSPICE tools are intended to enable researchers to use public databases and local resources to formulate a qualitative description of the cellular process of interest (e.g., models of networks or pathways), to annotate the links between entities with biochemical interactions, and finally to convert this annotated qualitative description to a set of equations that can be analyzed and simulated. In addition, BioSPICE provides a number of simulation engines with the capability to simulate ordinary, stochastic, and partial differential equations and other tools that support stability and bifurcation analysis and qualitative reasoning that combines probabilistic and temporal logic.

SOURCE: Sri Kumar, Defense Advanced Research Projects Agency, June 30, 2003.

From: 5, Computational Modeling and Simulation as Enablers for Biological Discovery

Cover of Catalyzing Inquiry at the Interface of Computing and Biology
Catalyzing Inquiry at the Interface of Computing and Biology.
National Research Council (US) Committee on Frontiers at the Interface of Computing and Biology; Wooley JC, Lin HS, editors.
Washington (DC): National Academies Press (US); 2005.
Copyright © 2005, National Academy of Sciences.

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