Modelling of Biological Processes Dr. Frank Bergmann
Im Neuenheimer Feld 267
69120 Heidelberg
Fon +49 6221 54-51277
Fax +49 6221 54-51483
frank.bergmann@bioquant.uni-heidelberg.de
Current Research
- Spatial Simulations of biochemichemical networks with COPASI
- Development of Model Exchange Standards & Infrastructure
Research Projects
- COPASI
- SysBioApps
- SBML
- Systems Biology Workbench
Teaching
- Python Course (SS 2017)
- Python Course (SS 2016)
- Python Course (SS 2015)
- C++ Course (WS 2014 / 2015)
- C++ Course (SS 2014)
- C++ Course (WS 2013 / 2014)
Selected Publications
- Bergmann, F. T., J. Cooper, M. König, I. Moraru, D. P. Nickerson, N. Le Novère, B. G. Olivier, S. Sahle, L. P. Smith, and D. Waltemath, Simulation experiment description markup language (SED-ML) level 1 version 3 (L1V3), Journal of integrative bioinformatics, 15 (1), 2018
- Bergmann, F. T., S. Hoops, B. Klahn, U. Kummer, P. Mendes, J. Pahle, S. Sahle, COPASI and its applications in biotechnology, Journal of biotechnology, 2017,
- Bergmann, F. T., D. P. Nickerson, D. Waltemath, and M. Scharm, SED-ML web tools: generate, modify and export standard-compliant simulation studies, Bioinformatics, 33(8), 2017
- Großeholz, R., C. Koh, N. Veith, T. Fiedler, M. Strauss, B. G. Olivier, B. C. Collins, O. T. Schubert, F. T. Bergmann, B. Kreikemeyer, R. Aebersold, and U. Kummer, Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis, NPJ systems biology and applications, 2, 2016
- Waltemath, D., J. R. Karr, F. T. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. J. Myers, P. Pir, B. Alaybeyoglu, N. K. Aranganathan, K. Baghalian, A. T. Bittig, P. E. P. Burke, M. Cantarelli, Y. H. Chew, R. S. Costa, J. Cursons, T. Czauderna, A. P. Goldberg, H. F. Gómez, J. Hahn, T. Hameri, D. F. H. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knüpfer, M. König, D. Lee, A. Lloret-Villas, N. Mandrik, J K. Medley, B. Moreau, H. Naderi-Meshkin, S. K. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. J. Stanford, J. Song, T. Theile, M. Tokic, N. Tomar, V. Toure, J. Uhlendorf, T. M. Varusai, L. H. Watanabe, F. Wendland, M. Wolfien, J. T. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, and F. Schreiber, Toward community standards and software for whole-cell modeling, IEEE Transactions on Biomedical Engineering, 63 (10), 2016
- Lubitz, T., J. Hahn, F. T. Bergmann, E. Noor, E. Klipp, and W. Liebermeister, SBtab: a flexible table format for data exchange in systems biology, Bioinformatics, 32(16), 2016
- Bergmann, F. T., S. Sahle, and C. Zimmer, Piecewise parameter estimation for stochastic models in COPASI, Bioinformatics, 32(10), 2016
- Olivier, B. G., and F. T. Bergmann, The systems biology markup language (SBML) level 3 package: Flux balance constraints, Journal of integrative bioinformatics, 12(2), 2015
- Gauges, R, U. Rost, S. Sahle, K. Wengler, and F. T. Bergmann, The systems biology markup language (SBML) level 3 package: layout, version 1, Journal of integrative bioinformatics, 12(2), 2015
- Hucka, M., D. P. Nickerson, G. D. Bader, F. T. Bergmann, J. Cooper, E. Demir, A. Garny, M. Golebiewski, C. J., and F. Schreiber, Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative, Frontiers in bioengineering and biotechnology, 3, 19, 2015
- Bergmann, F. T., J. Jonathan, N. Le Novere, D. P. Nickerson, and D. Waltemath, Simulation experiment description markup language (SED-ML) Level 1 Version 2, Journal of integrative bioinformatics, 12(2), 119-212, 2015
- Hucka, M, F. T. Bergmann, S. Hoops, S. M. Keating, S. Sahle, J. Schaff, L. P. Smith, and D. J. Wilkinson, The Systems Biology Markup Language (SBML): language specification for level 3 version 1 core, Journal of integrative bioinformatics, 12 (2), 3820549, 2015
- Bergmann, F. T., R. Adams, S. Moodie, J. Cooper, M. Glont, M. Golebiewski, M. Hucka, C. Laibe, A. K. Miller, and D. P. Nickerson, COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project, BMC bioinformatics, 15(1), 369, 2014
- Van Iersel, M. P., A. C. Villéger, T. Czauderna, S. E. Boyd, F. T. Bergmann, A. Luna, E. Demir, A. Sorokin, U. Dogrusoz and Y. Matsuoka, Software support for SBGN maps: SBGN-ML and LibSBGN, Bioinformatics, 28 (15), 2016-2021, 2012
- Waltemath, D., R. Adams, F. T. Bergmann, M. Hucka, F. Kolpakov, A. K. Miller, I. Moraru, D. Nickerson, S. Sahle, and J. L. Snoep, Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language, BMC systems biology, 5 (1), 198, 2011/12
- Hucka, M, F. T. Bergmann, S. M. Keating, and L. P. Smith, A profile of today's SBML-compatible software, 2011 IEEE Seventh International Conference on e-Science Workshops, 143-150, 2011
- Waltemath, D., Adams, R., Beard, D. A., Bergmann, F. T., Bhalla, U.S. , Britten, R., Chelliah, V., Cooling, M. T. , Cooper, J., Crampin, E.J., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C.,Miller, A.K., Moraru, I., Nickerson, D., Nielsen, P., Nikolski, M., Sahle, S., Sauro, H.M.,Schmidt, H., Snoep, J.L., Tolle, D., Wolkenhauer, O. & Le Novère, N (2011). Minimum information about a simulation experiment (MIASE). PLoS computational biology, 7(4), e1001122.
- Hucka, M., Bergmann, F. T., Keating, S. M., Schaff, J. C., & Smith, L. P. (2010). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version.
- Chandran, Deepak, Frank T. Bergmann, and Herbert M. Sauro. “TinkerCell: modular CAD tool for synthetic biology.” J Biol Eng 3.1 (2009): 19.
- Smith, L. P., Bergmann, F. T., Chandran, D., & Sauro, H. M. (2009). Antimony: a modular model definition language. Bioinformatics, 25(18), 2452-2454.
- Le Novère, N, Hucka, M, Mi, H, Moodie, S, Schreiber, F, Sorokin, A, Demir, E, Wegner, K, Aladjem, MI, Wimalaratne, SM, Bergmann, F.T., Gauges, R, Ghazal, P, Kawaji, H, Li, L, Matsuoka, Y, Villéger, A, Boyd, SE, Calzone, L, Courtot M, Dogrusoz, U, Freeman, TC, Funahashi, A, Ghosh, S, Jouraku, A, Kim, S, Kolpakov, F, Luna, A, Sahle, S, Schmidt, E, Watterson, S, Wu, G, Goryanin, I, Kell, DB, Sander, C, Sauro, H, Snoep, JL, Kohn, K & Kitano, H. (2009). The systems biology graphical notation. Nature biotechnology, 27(8), 735-741.
- Bergmann, F. T., & Sauro, H. M. (2008). Comparing simulation results of SBML capable simulators. Bioinformatics, 24(17), 1963-1965.
- Bergmann,F.T., Vallabhajosyula, R.R. & H.M. Sauro. Computational Tools for Modeling Protein Networks. Current Proteomics Pp. 181-197 Volume 3(3),(2006)
- Bergmann, F.T., Sauro, H.M. Computational systems biology: modularity and composition: SBW - a modular framework for systems biology. Proceedings of the 37th conference on Winter simulation WSC ‘06 Publisher: Winter Simulation Conference Pages: 1637 – 1645
- Deckard A, Bergmann FT, Sauro HM. Supporting the SBML layout extension. Bioinformatics. 2006 Oct 11;
- Chickarmane V, Paladugu SR, Bergmann FT, Sauro HM. Bifurcation discovery tool. Bioinformatics. 2005 Sep 15;21(18):3688-90.
