Frank T. Bergmann
Frank T. Bergmann
BioQUANT/COS, Heidelberg University, Heidelberg, Germany
Verified email at
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Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language
D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov, AK Miller, ...
BMC systems biology 5, 1-10, 2011
TinkerCell: modular CAD tool for synthetic biology
D Chandran, FT Bergmann, HM Sauro
Journal of biological engineering 3, 1-17, 2009
Minimum information about a simulation experiment (MIASE)
D Waltemath, R Adams, DA Beard, FT Bergmann, US Bhalla, R Britten, ...
PLoS computational biology 7 (4), e1001122, 2011
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
FT Bergmann, R Adams, S Moodie, J Cooper, M Glont, M Golebiewski, ...
BMC bioinformatics 15, 1-9, 2014
Antimony: a modular model definition language
LP Smith, FT Bergmann, D Chandran, HM Sauro
Bioinformatics 25 (18), 2452-2454, 2009
Software support for SBGN maps: SBGN-ML and LibSBGN
MP Van Iersel, AC Villéger, T Czauderna, SE Boyd, FT Bergmann, A Luna, ...
Bioinformatics 28 (15), 2016-2021, 2012
COPASI and its applications in biotechnology
FT Bergmann, S Hoops, B Klahn, U Kummer, P Mendes, J Pahle, S Sahle
Journal of biotechnology 261, 215-220, 2017
SBW-a modular framework for systems biology
FT Bergmann, HM Sauro
Proceedings of the 2006 Winter Simulation Conference, 1637-1645, 2006
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative
M Hucka, DP Nickerson, GD Bader, FT Bergmann, J Cooper, E Demir, ...
Frontiers in bioengineering and biotechnology 3, 19, 2015
Bifurcation discovery tool
V Chickarmane, SR Paladugu, F Bergmann, HM Sauro
Bioinformatics 21 (18), 3688-3690, 2005
The Systems Biology Markup Language (SBML): language specification for level 3 version 1 core
M Hucka, FT Bergmann, S Hoops, SM Keating, S Sahle, JC Schaff, ...
Journal of integrative bioinformatics 12 (2), 382-549, 2015
Toward community standards and software for whole-cell modeling
D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ...
IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016
Computer-aided design of biological circuits using TinkerCell
D Chandran, FT Bergmann, HM Sauro
Bioengineered bugs 1 (4), 276-283, 2010
Comparing simulation results of SBML capable simulators
FT Bergmann, HM Sauro
Bioinformatics 24 (17), 1963-1965, 2008
Supporting the SBML layout extension
A Deckard, FT Bergmann, HM Sauro
Bioinformatics 22 (23), 2966-2967, 2006
SBtab: a flexible table format for data exchange in systems biology
T Lubitz, J Hahn, FT Bergmann, E Noor, E Klipp, W Liebermeister
Bioinformatics 32 (16), 2559-2561, 2016
Standards and ontologies in computational systems biology
HM Sauro, FT Bergmann
Essays in biochemistry 45, 211-222, 2008
The systems biology markup language (SBML) level 3 package: flux balance constraints
BG Olivier, FT Bergmann
Journal of integrative bioinformatics 12 (2), 660-690, 2015
Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis
R Großeholz, CC Koh, N Veith, T Fiedler, M Strauss, B Olivier, BC Collins, ...
NPJ systems biology and applications 2 (1), 1-9, 2016
The systems biology markup language (SBML) level 3 package: layout, version 1 core
R Gauges, U Rost, S Sahle, K Wengler, FT Bergmann
Journal of Integrative Bioinformatics 12 (2), 550-602, 2015
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