COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

BMC Bioinformatics

Frank T Bergmann⁶  Richard Adams⁵  Stuart Moodie⁴  Jonathan Cooper¹¹  Mihai Glont¹⁰  Martin Golebiewski⁸  Michael Hucka¹  Camille Laibe¹⁰  Andrew K Miller²  David P Nickerson²  Brett G Olivier⁷  Nicolas Rodriguez⁹  Herbert M Sauro³  Martin Scharm¹³  Stian Soiland-Reyes¹²  Dagmar Waltemath¹³  Florent Yvon¹⁰  Nicolas Le Novère¹⁰ 

[1] Computing and Mathematical sciences, California Institute of Technology, Pasadena 91125, CA, USA

[2] Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand

[3] Department of Bioengineering, University of Washington, Seattle 98195, WA, USA

[4] Current affiliation: Eight Pillars Ltd, 19 Redford Walk, Edinburgh EH13 0AG, UK

[5] ResearchSpace, 24 Fountainhall Road, Edinburgh EH9 2LW, UK

[6] Modelling of Biological Processes, BioQUANT/COS, University of Heidelberg, INF 267, Heidelberg 69120, Germany

[7] Systems Bioinformatics, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands

[8] HITS gGmbH, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany

[9] Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK

[10] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

[11] Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, UK

[12] School of Computer Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK

[13] Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock 18057, Germany

关键词: Reproducible science;    Reproducible research;    Computational modeling;    Archive;    Data format;   

Others  :  1084359
DOI  :  10.1186/s12859-014-0369-z

 received in 2014-07-04, accepted in 2014-10-30,  发布年份 2014

【 摘 要 】

Background

With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result.

Results

We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.

Conclusions

The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.

【 授权许可】

   
2014 Bergmann et al.; licensee BioMed Central Ltd.

【 图 表 】

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