CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models
Name
Ayyadurai_2010-CytoSolve.pdf
Size
1.08 MB
Format
Adobe PDF
Checksum (MD5)
e7a013f7097d44ab4c125f7171efbcff
Author(s)
Ayyadurai, V. A. Shiva
Dewey, C. Forbes
Date Issued
October 2010
Journal
Cellular and Molecular Bioengineering
Publisher
Springer-Verlag
Citation
Ayyadurai, V. A. Shiva, and C. Forbes Dewey. “CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models.” Cellular and Molecular Bioengineering 4, no. 1 (March 23, 2011): 28-45.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Mechanical Engineering
MIT Sociotechnical Systems Research Center
Terms of Use
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1007/s12195-010-0143-x
