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.

Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface

“…Most of the conversions are performed using GINsim [10], enabling the support for SBML-qual, GINsim, as well as various text formats. Models can be directly imported from URLs and from CellCollective database [13]. Biocham reaction networks are also supported, following their Boolean semantics [4].…”

A framework for understanding the characteristics of complexity in biology

“…For example, Wilensky, colleagues, and other contributors (Jacobson & Wilensky, 2006;Resnick & Wilensky, 1998;Wilensky & Resnick, 1999) have developed models using a multi-agent simulator called NetLogo, that allows users to simulate systems through simple rules governing the agents and the environment (the extensive reference list is available at: http:// ccl.northwestern.edu/netlogo/references.shtml). The Cell Collective (http://cellcollective.org), while focused currently on cellular scale systems, allows computational biologists and students to create models of biological systems with or without the underlying mathematical expression (Helikar et al, 2012(Helikar et al, , 2015. These software platforms may allow researchers to develop learning modules related to specific dimensions of complexity and test the efficacy of instructional materials related to these dimensions.…”

Systems‐based understanding of pharmacological responses with combinations of multidisciplinary methodologies

“…Another approach to analysing the dynamic behavior of a system is to use rule-based formalism [32,60,61]. Let us analyse the situation depicted in Figure 6a.…”

“…Helikar et al are currently developing the 'Cell Collective' platform, which is based on this very theory. Indeed, they recently reported the dynamic analysis of a comprehensive, multi-scale model of EGFR family receptor signal transduction [61].…”