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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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WholeCellKB: model organism databases for comprehensive whole-cell models.

Jonathan R Karr¹, Jayodita C Sanghvi, Derek N Macklin

¹Graduate Program in Biophysics, Stanford University, 318 Campus Drive West, Stanford, CA 94305, USA.

Nucleic Acids Research

|November 24, 2012

Summary

Whole-cell models aid biological analysis. WholeCellKB software enables comprehensive model organism databases, exemplified by WholeCellKB-MG for Mycoplasma genitalium, facilitating research.

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Area of Science:

Computational biology
Systems biology
Bioinformatics

Background:

Whole-cell models offer powerful tools for dissecting complex biological systems.
Developing these models necessitates robust and comprehensive model organism databases.
Existing resources may lack the detailed, integrated data required for whole-cell modeling.

Purpose of the Study:

To introduce WholeCellKB, an open-source, web-based software for constructing detailed model organism databases.
To present WholeCellKB-MG, a comprehensive database for Mycoplasma genitalium, built using WholeCellKB.
To provide accessible data for whole-cell model development and biological research.

Main Methods:

Developed WholeCellKB, a customizable, web-based platform for database construction.
Designed an extensive data model encompassing genes, proteins, reactions, and pathways.
Integrated data from over 900 sources to create the WholeCellKB-MG database for Mycoplasma genitalium.

Main Results:

WholeCellKB provides a flexible framework for creating detailed biological databases.
WholeCellKB-MG offers a comprehensive, cross-referenced dataset for Mycoplasma genitalium.
The database is accessible via a web interface and a RESTful web service.

Conclusions:

WholeCellKB is a valuable tool for building comprehensive model organism databases.
WholeCellKB-MG serves as a significant resource for Mycoplasma genitalium research and whole-cell modeling.
The open-source nature and accessibility of these resources promote wider scientific collaboration and discovery.