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

Abstract

BackgroundWith 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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0369-z) contains supplementary material, which is available to authorized users.

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

“…CellML models [Cuellar et al, 2003] are run using CSim 3 . Developed simulation studies can be exported as (i) standalone SED-ML descriptions; (ii) SED-ML archives; COMBINE archives [Bergmann et al, 2014] (iii) with or (iv) without simulation results. COMBINE archives are zip-based containers to bundle all files relevant for a virtual experiment.…”

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

“…In systems biology, the reproducibility of results depends on two aspects [24]. Firstly, materials, methods and standard operating procedures used to generate experimental data should be provided.…”

“…Sometimes, however, it is useful to ship the complete set of model-related data to a different location, for example in large-scale projects. For this application, the COMBINE Archive [24] was developed. An archive is a single, zip-like file to exchange a model together with its associated simulation experiments and data, graphical representations, result plots, or any other files related to a modeling study.…”

The CombineArchiveWeb application – A web based tool to handle files associated with modelling results

“…To solve this issue, the COMBINE community [2] proposes the COMBINE archive format [3]. A COMBINE archive is a container that bundles all files related to a project into a single file.…”