Article

Cellular and Molecular Bioengineering

, Volume 4, Issue 1, pp 28-45

Open Access This content is freely available online to anyone, anywhere at any time.

CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models

  • V. A. Shiva AyyaduraiAffiliated withDepartment of Biological Engineering, Massachusetts Institute of TechnologyInternational Center for Integrative Systems Email author 
  • , C. Forbes DeweyJr.Affiliated withDepartment of Biological Engineering, Massachusetts Institute of TechnologyDepartment of Mechanical Engineering, Massachusetts Institute of Technology

Abstract

A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models’ source codes to create a large monolithic model (computer program) that runs on a single computer. Such a larger model is difficult, if not impossible, to maintain given ongoing updates to the source codes of the smaller models. This paper describes a new system called CytoSolve that dynamically integrates computations of smaller models that can run in parallel across different machines without the need to merge the source codes of the individual models. This approach is demonstrated on the classic Epidermal Growth Factor Receptor (EGFR) model of Kholodenko. The EGFR model is split into four smaller models and each smaller model is distributed on a different machine. Results from four smaller models are dynamically integrated to generate identical results to the monolithic EGFR model running on a single machine. The overhead for parallel and dynamic computation is approximately twice that of a monolithic model running on a single machine. The CytoSolve approach provides a scalable method since smaller models may reside on any computer worldwide, where the source code of each model can be independently maintained and updated.

Keywords

Systems biology SBML Model composition Biochemical simulation Distributed computing Molecular pathways Kinetic modeling Parallel simulation Collaboratory Systems architecture Software