Frontiers in Computational Neuroscience (Nov 2014)

OpenWorm: an open-science approach to modelling Caenorhabditis elegans

  • Balazs eSzigeti,
  • Balazs eSzigeti,
  • Padraig eGleeson,
  • Padraig eGleeson,
  • Michael eVella,
  • Michael eVella,
  • Sergey eKhayrulin,
  • Sergey eKhayrulin,
  • Andrey ePalyanov,
  • Andrey ePalyanov,
  • Jim eHokanson,
  • Jim eHokanson,
  • Michael eCurrie,
  • Matteo eCantarelli,
  • Giovanni eIdili,
  • Stephen eLarson

DOI
https://doi.org/10.3389/fncom.2014.00137
Journal volume & issue
Vol. 8

Abstract

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OpenWorm is an international collaboration with the aim of understanding how the behaviour of Caenorhabditis elegans (C. elegans) emerges through the underlying biophysical processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modelling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modelling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.

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