CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models
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...
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| Format: | Article |
| Language: | en_US |
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Springer-Verlag
2013
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| Online Access: | http://hdl.handle.net/1721.1/82621 https://orcid.org/0000-0001-7387-3572 |
| _version_ | 1826213996197314560 |
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| author | Ayyadurai, V. A. Shiva Dewey, C. Forbes |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Ayyadurai, V. A. Shiva Dewey, C. Forbes |
| author_sort | Ayyadurai, V. A. Shiva |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T15:58:09Z |
| format | Article |
| id | mit-1721.1/82621 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:58:09Z |
| publishDate | 2013 |
| publisher | Springer-Verlag |
| record_format | dspace |
| spelling | mit-1721.1/826212022-10-02T05:24:54Z CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models Ayyadurai, V. A. Shiva Dewey, C. Forbes Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Mechanical Engineering MIT Sociotechnical Systems Research Center Ayyadurai, V. A. Shiva Dewey, C. Forbes 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. EchoMail, Inc. International Center for Integrative Systems 2013-12-02T18:44:02Z 2013-12-02T18:44:02Z 2010-10 2010-05 Article http://purl.org/eprint/type/JournalArticle 1865-5025 1865-5033 http://hdl.handle.net/1721.1/82621 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. https://orcid.org/0000-0001-7387-3572 en_US http://dx.doi.org/10.1007/s12195-010-0143-x Cellular and Molecular Bioengineering http://creativecommons.org/licenses/by/3.0/ application/pdf Springer-Verlag PMC |
| spellingShingle | Ayyadurai, V. A. Shiva Dewey, C. Forbes CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models |
| title | CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models |
| title_full | CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models |
| title_fullStr | CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models |
| title_full_unstemmed | CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models |
| title_short | CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models |
| title_sort | cytosolve a scalable computational method for dynamic integration of multiple molecular pathway models |
| url | http://hdl.handle.net/1721.1/82621 https://orcid.org/0000-0001-7387-3572 |
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