Ruprecht-Karls-Universität Heidelberg
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Modelling of Biological Processes

Dr. Frank T. Bergmann

Dr. Frank T. Bergmann
Dr. Frank T. Bergmann
INF 267
69120 Heidelberg
Fon +49 6221 54-51277
ed.grebledieh-inu.tnauqoib TEA nnamgreb.knarf

Current Research:

  • Spatial Simulations of biochemichemical networks with COPASI
  • Development of Model Exchange Standards & Infrastructure

Research Projects:

Teaching:

Selected Publications:

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. SauroComputational 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 HMSupporting 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.

Contact

Dr. Frank T. Bergmann
INF 267
69120 Heidelberg
Fon +49 6221 54-51277
ed.grebledieh-inu.tnauqoib TEA nnamgreb.knarf


/var/www/cos/ / http://www.cos.uni-heidelberg.de/ Dr. Frank T. Bergmann _e