Towards systematic, data-driven validation of a collaborative, multi-scale model of Caenorhabditis elegans. (10th September 2018)

• Record Type: Journal Article
• Authors: Gerkin, Richard C.; Jarvis, Russell J.; Crook, Sharon M.
• Is Part Of: Philosophical transactions. Volume 373:Number 1758(2018)
• Publication Date: 2018-09-10
• Subjects: modelling -- informatics -- unit-testing -- Python; Biology -- Periodicals; Science -- Periodicals; 570
• DOI: 10.1098/rstb.2017.0381
• Languages: English
• ISSNs: 0962-8436

Abstract

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'.