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