| Enlightened Multiscale Simulation of Biochemical Networks |
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| Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio | |
| Feb 01 2008 | |
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Advertisement: An especially notable recent product of this continuing development effort is the Systems Biology Markup Language (SBML), which is a machine-readable language that provides a format, based on Extensible Markup Language (XML), for representing models in such a way that they can be executed within, and exchanged among, different software systems to communicate and exchange the models. By utilizing SBML to define their input and output formats, different software tools can all operate on an identical representation of a model, removing opportunities for errors in translation and assuring a common starting point for analyses and simulations. SBML can encode models representing biochemical entities (species) linked by reactions to form networks. An important principle is that a model is decomposed into explicitly labeled constituent elements, the set of which resembles a verbose rendition of chemical-reaction equations. The representation deliberately does not cast the model directly into a set of differential equations or other specific interpretation of the model. This explicit, modelingframework- agnostic decomposition makes it easier for a software tool to interpret the model and translate the SBML form into whatever internal form the tool uses. The formalisms in SBML enable modeling of a wide range of biological phenomena, including (and not limited to) metabolism, cell signaling, and gene regulation. SBML affords significant flexibility and power by making it possible to define arbitrary formulae for rates of change of variables and to express other constraints mathematically. The software infrastructure of SBML includes libSBML, which is an embedded software library that provides an application programming interface (API) for working with SBML in the C, C++, Java, PERL, MATLAB, Lisp, and Python programming languages. Programmers can embed libSBML in their application programs, saving themselves the work of implementing their own parsing, manipulation, and validation software. libSBML is open-source software written in C and C++ and is highly portable. It is currently supported on the Linux, Solaris, MacOS X, and Microsoft Windows operating systems. This work was done by John C. Doyle and Michael Hucka of California Institute of Technology for the Air Force Research Laboratory This Brief includes a Technical Support Package (TSP).
Enlightened Multiscale Simulation of Biochemical Networks (reference AFRL-0058) is currently available for download from the TSP library. Login first to download.
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