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The Cell Collective: Toward an open and collaborative approach to systems biology

Tomáš Helikar1*, Bryan Kowal2, Sean McClenathan2, Mitchell Bruckner1, Thaine Rowley1, Alex Madrahimov1, Ben Wicks2, Manish Shrestha2, Kahani Limbu2 and Jim A Rogers13

Author Affiliations

1 Department of Mathematics, University of Nebraska at Omaha, Omaha, NE, USA

2 College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA

3 Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA

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BMC Systems Biology 2012, 6:96  doi:10.1186/1752-0509-6-96

Published: 7 August 2012

Abstract

Background

Despite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic study of biochemical pathways requires computer modeling. Due to the complexity of cells, it is not feasible for one person or group to model the cell in its entirety.

Results

The Cell Collective is a platform that allows the world-wide scientific community to create these models collectively. Its interface enables users to build and use models without specifying any mathematical equations or computer code - addressing one of the major hurdles with computational research. In addition, this platform allows scientists to simulate and analyze the models in real-time on the web, including the ability to simulate loss/gain of function and test what-if scenarios in real time.

Conclusions

The Cell Collective is a web-based platform that enables laboratory scientists from across the globe to collaboratively build large-scale models of various biological processes, and simulate/analyze them in real time. In this manuscript, we show examples of its application to a large-scale model of signal transduction.