The Cell Collective: Toward an open and collaborative approach to systems biology
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The Cell Collective: Toward an open and collaborative approach to systems biology Tom´asˇ Helikar1* , Bryan Kowal2 , Sean McClenathan2 , Mitchell Bruckner1 , Thaine Rowley1 , Alex Madrahimov1 , Ben Wicks2 , Manish Shrestha2 , Kahani Limbu2 and Jim A Rogers1,3
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. Background The immense complexity in biological structures and processes such as intracellular signal transduction networks is one of the obstacles to fully understanding how these systems function. As understanding of these biochemical pathways increases, it is clear that they form networks of astonishing complexity and diversity. This means that the complex pathways involved in regulation of one area of the cell (so complex that a researcher could spend their entire career working in that area alone) are so interconnected to other, equally complex areas that all of the different pathway systems must be studied together, as a whole, if any of the individual components are to be understood. However, the large scale and minute intricacy of each of the individual networks makes it difficult for cell biologists or biochemists working in one area of a cell’s biochemistry to be aware of, let alone relate their results to, findings obtained from the various different areas. So how will all *Correspondence: [email protected] 1 Department of Mathematics, University of Nebraska at Omaha, Omaha, NE, USA Full list of author information is available at the end of the article
of these individually complex systems be possible to study in an integrated biochemical “mega-system?” In order to address this problem, the concept of systems biology study has emerged [1-8]. However, with i) data being generated by laboratory scientists at a staggering rate in the course of studying the individual systems, ii) the fact that these individual
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