Literature DB >> 25433232

A call for virtual experiments: accelerating the scientific process.

Jonathan Cooper1, Jon Olav Vik2, Dagmar Waltemath3.   

Abstract

Experimentation is fundamental to the scientific method, whether for exploration, description or explanation. We argue that promoting the reuse of virtual experiments (the in silico analogues of wet-lab or field experiments) would vastly improve the usefulness and relevance of computational models, encouraging critical scrutiny of models and serving as a common language between modellers and experimentalists. We review the benefits of reusable virtual experiments: in specifying, assaying, and comparing the behavioural repertoires of models; as prerequisites for reproducible research; to guide model reuse and composition; and for quality assurance in the translational application of models. A key step towards achieving this is that models and experimental protocols should be represented separately, but annotated so as to facilitate the linking of models to experiments and data. Lastly, we outline how the rigorous, streamlined confrontation between experimental datasets and candidate models would enable a "continuous integration" of biological knowledge, transforming our approach to systems biology.
Copyright © 2014 Elsevier Ltd. All rights reserved.

Keywords:  Computational physiology; Functional curation; Model comparison; Reproducible research; Virtual experiments

Mesh:

Year:  2014        PMID: 25433232     DOI: 10.1016/j.pbiomolbio.2014.10.001

Source DB:  PubMed          Journal:  Prog Biophys Mol Biol        ISSN: 0079-6107            Impact factor:   3.667


  16 in total

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Authors:  David Nickerson; Koray Atalag; Bernard de Bono; Jörg Geiger; Carole Goble; Susanne Hollmann; Joachim Lonien; Wolfgang Müller; Babette Regierer; Natalie J Stanford; Martin Golebiewski; Peter Hunter
Journal:  Interface Focus       Date:  2016-04-06       Impact factor: 3.906

2.  Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Authors:  Natalie J Stanford; Martin Scharm; Paul D Dobson; Martin Golebiewski; Michael Hucka; Varun B Kothamachu; David Nickerson; Stuart Owen; Jürgen Pahle; Ulrike Wittig; Dagmar Waltemath; Carole Goble; Pedro Mendes; Jacky Snoep
Journal:  Methods Mol Biol       Date:  2019

3.  Reproducibility in Computational Neuroscience Models and Simulations.

Authors:  Robert A McDougal; Anna S Bulanova; William W Lytton
Journal:  IEEE Trans Biomed Eng       Date:  2016-03-08       Impact factor: 4.538

Review 4.  Calibration of ionic and cellular cardiac electrophysiology models.

Authors:  Dominic G Whittaker; Michael Clerx; Chon Lok Lei; David J Christini; Gary R Mirams
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2020-02-21

5.  Combining computational models, semantic annotations and simulation experiments in a graph database.

Authors:  Ron Henkel; Olaf Wolkenhauer; Dagmar Waltemath
Journal:  Database (Oxford)       Date:  2015-03-08       Impact factor: 3.451

6.  OpenCOR: a modular and interoperable approach to computational biology.

Authors:  Alan Garny; Peter J Hunter
Journal:  Front Physiol       Date:  2015-02-06       Impact factor: 4.566

7.  Cellular cardiac electrophysiology modeling with Chaste and CellML.

Authors:  Jonathan Cooper; Raymond J Spiteri; Gary R Mirams
Journal:  Front Physiol       Date:  2015-01-06       Impact factor: 4.566

8.  Hodgkin-Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods.

Authors:  Aidan C Daly; David J Gavaghan; Chris Holmes; Jonathan Cooper
Journal:  R Soc Open Sci       Date:  2015-12-23       Impact factor: 2.963

9.  The Cardiac Electrophysiology Web Lab.

Authors:  Jonathan Cooper; Martin Scharm; Gary R Mirams
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

10.  Where next for the reproducibility agenda in computational biology?

Authors:  Joanna Lewis; Charles E Breeze; Jane Charlesworth; Oliver J Maclaren; Jonathan Cooper
Journal:  BMC Syst Biol       Date:  2016-07-15
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