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

Scharm, Martin; Wendland, Florian; Peters, Martin; Wolfien, Markus; Theile, Tom; Waltemath, Dagmar

doi:10.7287/peerj.preprints.639v1

Cited by 7 publications

(5 citation statements)

References 6 publications

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“…Our graph database rather offers a solution for the management of those files. For example, the CombineArchive Toolkit ( 62 ) may query our database, collect all necessary information and automatically create an Open Modeling EXchange format file ( http://co.mbine.org/specifications/omex.version-1 ).…”

Section: Discussionmentioning

confidence: 99%

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

2015

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Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models’ structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried.Database URL: https://sems.uni-rostock.de/projects/masymos/

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Section: Discussionmentioning

confidence: 99%

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

2015

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“…For example, the CombineArchive Web application (WebCAT, [Scharm et al, 2014]), an online application to work on COMBINE archives, uses the API of the SED-ML Web Tools. WebCAT provides links to the SED-ML Web Tools to realise instantaneous simulation of studies.…”

Section: Resultsmentioning

confidence: 99%

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

Bergmann

Nickerson

Waltemath

et al. 2016

Preprint

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The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats. Availability and Implementation: sysbioapps.dyndns.org/SED-ML Web Tools. Further information: sysbioapps.dyndns.org/SED-ML Web Tools/Services/SedMLService.asmx.

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“…The initial archive was therefor imported into the CombineArchiveWeb application (WebCAT, 9 ) Version 0.4.13 ( webcat.sems.uni-rostock.de). WebCAT is a web interface to display and modify the files contained in an archive, together with metadata and file structures.…”

Section: Methodsmentioning

confidence: 99%

“…Repeated mentions of problems with replication and reproducibility 2– 4 led to new standards, tools, and methods for the transfer of reproducible simulation studies 5– 9 . Several projects and initiatives already deal with reproducibility issues, such as COMBINE ( co.mbine.org), FAIRDOM ( fair-dom.org), and the Reproducibility Initiative ( reproducibilityinitiative.org).…”

Section: Introductionmentioning

confidence: 99%

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

Scharm

Waltemath

2016

F1000Res

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COMBINE archives are standardised containers for data files related to a simulation study in computational biology. This manuscript describes a fully featured archive of a previously published simulation study, including (i) the original publication, (ii) the model, (iii) the analyses, and (iv) metadata describing the files and their origin. With the archived data at hand, it is possible to reproduce the results of the original work. The archive can be used for both, educational and research purposes. Anyone may reuse, extend and update the archive to make it a valuable resource for the scientific community.

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

Cited by 7 publications

References 6 publications

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

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

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

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

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