COMBINE archive

Examples


Publications


  • Dagmar Waltemath, Olaf Wolkenhauer: How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Transactions on Biomedical Engineering (2016) 63:10. doi:10.1109/TBME.2016.2555481
  • Martin Scharm, Dagmar Waltemath: A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research (2016) 5:2421. doi:f1000research.9379.1
  • Falk Schreiber, Gary D Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath: Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 Journal of Integrative Bioinformatics (2016) 13:3. doi:10.2390/biecoll-jib-2016-289
  • Martin Scharm, Dagmar Waltemath: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. Proceedings of the Workshop on Data management in Life Sciences, BTW (2015) link:btw-2015.de/res/proceedings/Workshops/DMS/Scharm-Extracting_reproducible_sim.pdf
  • Michael Hucka, David P Nickerson, Gary D Bader, Frank T Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J Myers, Falk Schreiber, Dagmar Waltemath, and Nicolas Le Novère: Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. Front Bioeng Biotechnol. (2015) 3:19. doi:10.3389/fbioe.2015.00019
  • Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom C Theile, Dagmar Waltemath: The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results. Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014). link:ceur-ws.org/Vol-1320/paper_19.pdf
  • Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics (2014) 15:1. doi:10.1186/s12859-014-0369-z
  • Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences 9.3 (2014) 9:3. doi:10.4056/sigs.5279417

Specifications


  • Frank T. Bergmann, Nicolas Rodriguez, Nicolas Le Novère. COMBINE archive specification.(2014)
    The Version 1 of the Open Modeling EXchange format (OMEX) specification was published on September 15, 2014 and can be found at the COMBINE website.