Towards systematic, data-driven validation of a collaborative, multi-scale model of Caenorhabditis elegans

Richard Gerkin, Russell J. Jarvis, Sharon Crook

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The OpenWorm Project is an international open-source collaboration to create a multi-scale model of the organism Caenorhabditis elegans. At each scale, including subcellular, cellular, network and behaviour, this project employs one or more computational models that aim to recapitulate the corresponding biological system at that scale. This requires that the simulated behaviour of each model be compared with experimental data both as the model is continuously refined and as new experimental data become available. Here we report the use of SciUnit, a software framework for model validation, to attempt to achieve these goals. During project development, each model is continuously subjected to data-driven 'unit tests' that quantitatively summarize model-data agreement, identifying modelling progress and highlighting particular aspects of each model that fail to adequately reproduce known features of the biological organism and its components. This workflow is publicly visible via both GitHub and a web application and accepts community contributions to ensure that modelling goals are transparent and well-informed. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. Elegans at cellular resolution'.

Original languageEnglish (US)
Article number20170381
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Volume373
Issue number1758
DOIs
StatePublished - Jan 1 2018

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Caenorhabditis elegans
Connectome
Workflow
Software
modeling
model validation
development projects
Biological systems
organisms
software
project

Keywords

  • Informatics
  • Modelling
  • Python
  • Unit-testing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

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