CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems

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Abstract

We present CMBSlib, a library of Computational Models of Biological Systems. It is aimed at providing a list of test problems for formalisms, modeling issues and implementation issues in systems biology.

The main motivation for CMBSlib is to stimulate research on the formal modeling of biological systems, by facilitating the exchange of formal models between researchers, and by providing a forum of comparison and validation of not only models, but also modeling formalisms and implementations.

Unlike a standardization effort, CMBSlib welcomes the most exotic formalisms and models provided they attack the modeling of well documented biological systems. Models of biological systems written in any referenced formalism can be submitted to CMBSlib. No special format or standard is required.

We discuss the advantages of and problems encountered in building such a library, give an example of typical entry in the library, and most of all we invite the community to become active contributors to CMBSlib.