Minimum information about a simulation experiment (MIASE)

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dc.contributor.authorWaltemath, Dagmar
dc.contributor.authorAdams, Richard
dc.contributor.authorBeard, Daniel A.
dc.contributor.authorBergmann, Frank T.
dc.contributor.authorBalla, Upinder S.
dc.contributor.authorBritten, Randall
dc.contributor.authorChelliah, Vijayalakshmi
dc.contributor.authorCooling, Michael T.
dc.contributor.authorCooper, Jonathan
dc.contributor.authorCrampin, Edmund J.
dc.contributor.authorGarny, Alan
dc.contributor.authorHoops, Stefan
dc.contributor.authorHucka, Michael
dc.contributor.authorHunter, Peter
dc.contributor.authorKlipp, Edda
dc.contributor.authorLaibe, Camille
dc.contributor.authorMiller, Andrew K.
dc.contributor.authorMoraru, Ion
dc.contributor.authorNickerson, David
dc.contributor.authorNielsen, Poul
dc.contributor.authorNikolski, Macha
dc.contributor.authorSahle, Sven
dc.contributor.authorSauro, Herbert M.
dc.contributor.authorSchmidt, Henning
dc.contributor.authorSnoep, Jacky L.
dc.contributor.authorTolle, Dominic
dc.contributor.authorWolkenhauer, Olaf
dc.contributor.authorLe Novere, Nicolas
dc.date.accessioned2013-02-25T13:55:18Z
dc.date.available2013-02-25T13:55:18Z
dc.date.issued2011-04
dc.descriptionThe original publication is available at www.ploscompbiol.orgen_ZA
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 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_ZA
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_ZA
dc.description.versionPublishers versionen_ZA
dc.format.extent4 p.
dc.identifier.citationWaltemath D., ... et al. 2011. Minimum information about a simulation experiment (MIASE). PLoS Computational Biology, 7(4): e1001122. doi:10.1371/journal.pcbi.1001122en_ZA
dc.identifier.issn1553-7358 (online)
dc.identifier.issn1553-734X (print)
dc.identifier.otherdoi:10.1371/journal.pcbi.1001122
dc.identifier.urihttp://hdl.handle.net/10019.1/79606
dc.language.isoen_ZAen_ZA
dc.publisherPLOSen_ZA
dc.rights.holderThe author holds the copyrighten_ZA
dc.subjectMIASEen_ZA
dc.subjectComputational biologyen_ZA
dc.subjectBiochemical computational modelsen_ZA
dc.titleMinimum information about a simulation experiment (MIASE)en_ZA
dc.typeArticleen_ZA
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