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Minimum Information About a Simulation Experiment (MIASE)

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dc.contributorVirginia Techen
dc.contributor.authorWaltemath, Dagmaren
dc.contributor.authorAdams, Richarden
dc.contributor.authorBeard, Daniel A.en
dc.contributor.authorBergmann, Frank T.en
dc.contributor.authorBhalla, Upinder S.en
dc.contributor.authorBritten, Randallen
dc.contributor.authorChelliah, Vijayalakshmien
dc.contributor.authorCooling, Michael T.en
dc.contributor.authorCooper, Jonathanen
dc.contributor.authorCrampin, Edmund J.en
dc.contributor.authorGarny, Alanen
dc.contributor.authorHoops, Stefanen
dc.contributor.authorHucka, Michaelen
dc.contributor.authorHunger, Peteren
dc.contributor.authorKlipp, Eddaen
dc.contributor.authorLaibe, Camilleen
dc.contributor.authorMiller, Andrew K.en
dc.contributor.authorMoraru, Ionen
dc.contributor.authorNickerson, Daviden
dc.contributor.authorNielsen, Poulen
dc.contributor.authorNikolski, Machaen
dc.contributor.authorSahle, Svenen
dc.contributor.authorSauro, Herbert M.en
dc.contributor.authorSchmidt, Henningen
dc.contributor.authorSnoep, Jacky L.en
dc.contributor.authorTolle, Dominicen
dc.contributor.authorWolkenhauer, Olafen
dc.contributor.authorLe Novère, Nicolasen
dc.date.accessed2014-05-13en
dc.date.accessioned2014-06-17T20:12:10Zen
dc.date.available2014-06-17T20:12:10Zen
dc.date.issued2011-04-28en
dc.description.abstractReproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes.en
dc.description.sponsorshipThe discussions that led to the definition of MIASE benefited from the support of a Japan Partnering Award by the UK Biotechnology and Biological Sciences Research Council. DW was supported by the Marie Curie program and by the German Research Association (DFG Research Training School “dIEM oSiRiS” 1387/1). This publication is based on work (EJC) supported in part by Award No KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). FTB acknowledges support by the NIH (grant 1R01GM081070-01). JC is supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies, under the VPH NoE project (grant number 223920). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.identifier.citationWaltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, et al. (2011) Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol 7(4): e1001122en
dc.identifier.doihttps://doi.org/10.1371/journal.pcbi.1001122en
dc.identifier.issn1553-7358en
dc.identifier.urihttp://hdl.handle.net/10919/49011en
dc.identifier.urlhttp://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001122en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectAlgorithmsen
dc.subjectBiochemical simulationsen
dc.subjectComputational biologyen
dc.subjectComputerized simulationsen
dc.subjectMathematical modelingen
dc.subjectMathematical modelsen
dc.subjectSimulation and modelingen
dc.subjectSystems biologyen
dc.titleMinimum Information About a Simulation Experiment (MIASE)en
dc.title.serialPLoS Computational Biologyen
dc.typeArticle - Refereeden

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