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

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.

[1]  Nicolas Le Novère,et al.  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project , 2014, BMC Bioinformatics.

[2]  Peter J. Hunter,et al.  An Overview of CellML 1.1, a Biological Model Description Language , 2003, Simul..

[3]  Jacky L. Snoep,et al.  Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language , 2011, BMC Systems Biology.

[4]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[5]  Melanie I. Stefan,et al.  BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models , 2010, BMC Systems Biology.

[6]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[7]  C. Ball,et al.  Repeatability of published microarray gene expression analyses , 2009, Nature Genetics.

[8]  C. Begley,et al.  Drug development: Raise standards for preclinical cancer research , 2012, Nature.

[9]  scharm martin,et al.  COMBINE Archive Show Case , 2016 .

[10]  Anton Nekrutenko,et al.  Ten Simple Rules for Reproducible Computational Research , 2013, PLoS Comput. Biol..

[11]  Herbert M. Sauro,et al.  Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology , 2016, bioRxiv.

[12]  Olaf Wolkenhauer,et al.  How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine , 2016, IEEE Transactions on Biomedical Engineering.

[13]  Oscar Corcho,et al.  Workflow-centric research objects: First class citizens in scholarly discourse. , 2012, ESWC 2012.

[14]  Dagmar Waltemath,et al.  Extracting reproducible simulation studies from model repositories using the combinearchive toolkit , 2015, BTW Workshops.

[15]  Datenbanksysteme für Business, Technologie und Web (BTW 2015) - Workshopband, 2.-3. März 2015, Hamburg, Germany , 2015, BTW Workshops.

[16]  Ulrik Brandes,et al.  GraphML Progress Report , 2001, GD.

[17]  Dagmar Waltemath,et al.  The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results , 2014, SWAT4LS.

[18]  Falk Schreiber,et al.  Editing, validating and translating of SBGN maps , 2010, Bioinform..

[19]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[20]  Norman W. Paton,et al.  SBRML: a markup language for associating systems biology data with models , 2010, Bioinform..

[21]  Yukiko Matsuoka,et al.  Software support for SBGN maps: SBGN-ML and LibSBGN , 2012, Bioinform..

[22]  Sean Bechhofer,et al.  Research Objects: Towards Exchange and Reuse of Digital Knowledge , 2010 .

[23]  Peter J. Hunter,et al.  Bioinformatics Applications Note Databases and Ontologies the Physiome Model Repository 2 , 2022 .

[24]  F. Prinz,et al.  Believe it or not: how much can we rely on published data on potential drug targets? , 2011, Nature Reviews Drug Discovery.

[25]  Matthias Klapperstück,et al.  VANTED v2: a framework for systems biology applications , 2012, BMC Systems Biology.

[26]  Denis Thieffry,et al.  Dynamical modeling of syncytial mitotic cycles in Drosophila embryos , 2007, Molecular systems biology.