Enlightened Multiscale Simulation of Biochemical Networks. Core Theory, Validating Experiments, and Implementation in Open Software

摘要

The objective of the research is to develop mathematical and software infrastructure in support of post-genomics research in systems biology. One objective articulated in this effort centers on a deeper understanding of the organizational principles of biological networks. A distinguishing theme of this work is its focus on scalable methods of robustness and model validation and invalidation with data, as opposed to relying purely on simulation. The Systems Biology Markup Language (SBML) project is a machine-readable exchange language for computational models of biochemical networks. LibSBML, an embedded software library for SBML, was developed, providing an application programming interface for working with SBML. The LibSBML library provides an interface for working with SBML in a number of programming languages: C, C++, Java, Perl, MATLAB, Lisp, and Python. It is free, open-source, and portable to Linux, Windows, MacOS and Solaris. The effort led to (1) continued development of LibSBML, (increased support of SBML features and added functionality); and (2) supported SBML use and evolution (direct support for DARPA Bio-SPICE).