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A Web Tool for Generating High Quality Machine-readable Biological Pathways

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

V A Shiva Ayyadurai, C Forbes Dewey

Cellular and Molecular Bioengineering

|March 23, 2011

Summary

Computational systems biology faces challenges in whole-cell modeling. CytoSolve dynamically integrates smaller models across machines, avoiding code merging and enabling scalable, maintainable whole-cell pathway models.

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Area of Science:

Computational systems biology
Bioinformatics
Molecular modeling

Background:

Creating comprehensive whole-cell molecular pathway models is a significant challenge.
Current methods merge individual model source codes into large, monolithic programs, hindering maintenance and scalability.
Updating these monolithic models is difficult due to the complexity of managing numerous integrated source codes.

Purpose of the Study:

To introduce CytoSolve, a novel system for dynamic integration of distributed molecular pathway models.
To demonstrate a scalable approach for whole-cell modeling without merging source codes.
To overcome the maintenance and scalability limitations of monolithic computational models.

Main Methods:

Developed CytoSolve, a system for dynamic integration of computations from smaller, independently running models.
Distributed components of the Epidermal Growth Factor Receptor (EGFR) model across multiple machines.
Dynamically integrated results from parallel computations to simulate the complete pathway.

Main Results:

CytoSolve successfully replicated the results of the monolithic EGFR model.
The dynamic integration of parallel computations yielded identical outcomes to single-machine execution.
The parallel and dynamic computation overhead was approximately double that of the monolithic model.

Conclusions:

CytoSolve offers a scalable solution for whole-cell modeling by enabling parallel computation of independently maintained models.
This approach facilitates easier updates and management of complex biological pathway models.
The system allows models to reside on different machines globally, promoting collaborative and distributed research.