title: The Cell Collective: toward an open and collaborative approach to systems biology.
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.
authors.affiliation: Department of Mathematics, University of Nebraska at Omaha, Omaha, NE, USA. thelikar@unomaha.edu
authors.forename: Tomáš
authors.initials: T
authors.lastname: Helikar
authors.forename: Bryan
authors.initials: B
authors.lastname: Kowal
authors.forename: Sean
authors.initials: S
authors.lastname: McClenathan
authors.forename: Mitchell
authors.initials: M
authors.lastname: Bruckner
authors.forename: Thaine
authors.initials: T
authors.lastname: Rowley
authors.forename: Alex
authors.initials: A
authors.lastname: Madrahimov
authors.forename: Ben
authors.initials: B
authors.lastname: Wicks
authors.forename: Manish
authors.initials: M
authors.lastname: Shrestha
authors.forename: Kahani
authors.initials: K
authors.lastname: Limbu
authors.forename: Jim A
authors.initials: JA
authors.lastname: Rogers
mesh_terms: D002477:Cells / Q000166:cytology / Q000378:metabolism; D003299:Cooperative Behavior; D038622:Internationality; D020407:Internet; D059232:Laboratory Personnel; D008954:Models, Biological; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors