Project duration: March 2015 – February 2018

The German Network for Bioinformatics Infrastructure (denbi) is a national infrastructure project that provides high-quality services, training events, courses, and tool support for bioinformatics research.

NBI-SysBio is one of the denbi nodes of expertise, providing standards-based management solutions for data and models in systems biology.

Visit the official project homepage at our partner institute HITS.

Our most favorite publications…

  1. Dagmar Waltemath and Olaf Wolkenhauer (2016) How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine. IEEE Transactions on Biomedical Engineering.doi:10.1109/TBME.2016.2555481 (open access)
  2. Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath (2015) Combining computational models, semantic annotations and simulation experiments in a graph database. Oxford DATABASE 2015 bau130 (open access)
  3. Martin Scharm, Olaf Wolkenhauer and Dagmar Waltemath (2015) An algorithm to detect and communicate the differences in computational models describing biological systems. Open Access article at Oxford Journals BIOINFORMATICS. doi: 10.1093/bioinformatics/btv484
  4. Frank T Bergmann, Jonathan Cooper, Nicolas Le Novère, David Nickerson, Dagmar Waltemath (2015) Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of Integrative Bioinformatics 12:2 (open access)
  5. Mike Hucka, Frank T Bergmann, Andreas Dräger, Stefan Hoops, Sarah M Keating, Le Novère N, Chris J Myers, Brett G Olivier, Sven Sahle, Jim C Schaff, Lucian P Smith, Dagmar Waltemath, Darren J Wilkinson (2015) Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics 12:2 (open access)


  1. DCite workshop (Warnemünde 2015)
  2. Kinetics on the move workshop (Heidelberg 2016)


  1. SED-ML simulation database for JWS Online Database (developed by Martin Peters, running at the University of Stellenbosch)
  2. MaSyMoS — a graph database to store models and model-related data
  3. MORRE — a ranked retrieval engine to search for models and model-related data
  4. BiVeS — for difference detection in XML-encoded models (developed by Martin Scharm, running in SEEK4SCIENCE and in PMR2)