Frank T. Bergmann

According to our database, Frank T. Bergmann authored at least 40 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2024

2023

BASICO: A simplified Python interface to COPASI.

Frank T. Bergmann

J. Open Source Softw., November, 2023

SBML level 3 package: spatial processes, version 1, release 1.

James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith

J. Integr. Bioinform., March, 2023

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

CoRR, 2022

2021

PEtab - Interoperable specification of parameter estimation problems in systems biology.

Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl

PLoS Comput. Biol., 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2021

CoRC: the COPASI R Connector.

Jonas Förster, Frank T. Bergmann, Jürgen Pahle

Bioinform., 2021

2020

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.

Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin S. Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka

J. Integr. Bioinform., 2020

Systems biology graphical notation markup language (SBGNML) version 0.3.

Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna

J. Integr. Bioinform., 2020

2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang

J. Integr. Bioinform., 2019

2018

SBML Level 3 Package: Flux Balance Constraints version 2.

Brett G. Olivier, Frank T. Bergmann

J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

J. Integr. Bioinform., 2018

SBML Level 3 package: Render, Version 1, Release 1.

Frank T. Bergmann, Sarah M. Keating, Ralph Gauges, Sven Sahle, Katja Wengler

J. Integr. Bioinform., 2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath

J. Integr. Bioinform., 2018

A portable structural analysis library for reaction networks.

Yosef Bedaso, Frank T. Bergmann, Kiri Choi, Kyle Medley, Herbert M. Sauro

Biosyst., 2018

2017

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm

Bioinform., 2017

2016

Toward Community Standards and Software for Whole-Cell Modeling.

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

IEEE Trans. Biomed. Eng., 2016

Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation.

Christoph Zimmer, Frank T. Bergmann, Sven Sahle

CoRR, 2016

SBtab: a flexible table format for data exchange in systems biology.

Timo Lubitz, Jens Hahn, Frank T. Bergmann, Elad Noor, Edda Klipp, Wolfram Liebermeister

Bioinform., 2016

Piecewise parameter estimation for stochastic models in COPASI.

Frank T. Bergmann, Sven Sahle, Christoph Zimmer

Bioinform., 2016

2015

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

Brett G. Olivier, Frank T. Bergmann

J. Integr. Bioinform., 2015

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson

J. Integr. Bioinform., 2015

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

J. Integr. Bioinform., 2015

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wengler, Frank Thomas Bergmann

J. Integr. Bioinform., 2015

COMBINE Archive Specification Version 1.

Frank T. Bergmann, Nicolas Rodriguez, Nicolas Le Novère

J. Integr. Bioinform., 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Frank T. Bergmann, Jonathan Cooper, Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2015

2014

COMBINE archive: One File To Share Them All.

Frank T. Bergmann, Richard Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

CoRR, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Frank T. Bergmann, Richard R. Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

BMC Bioinform., 2014

2012

Software support for SBGN maps: SBGN-ML and LibSBGN.

Martijn P. van Iersel, Alice Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly A. Sorokin, Ugur Dogrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber

Bioinform., 2012

2011

Minimum Information About a Simulation Experiment (MIASE).

Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère

PLoS Comput. Biol., 2011

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.

Dagmar Waltemath, Richard R. Adams, Frank T. Bergmann, Michael Hucka, Fedor A. Kolpakov, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Sven Sahle, Jacky L. Snoep, Nicolas Le Novère

BMC Syst. Biol., 2011

A Profile of Today's SBML-Compatible Software.

Michael Hucka, Frank T. Bergmann, Sarah M. Keating, Lucian P. Smith

Proceedings of the IEEE 7th International Conference on E-Science, 2011

2010

SBML2TikZ: supporting the SBML render extension in LaTeX.

Si Yuan Shen, Frank T. Bergmann, Herbert M. Sauro

Bioinform., 2010

2009

Antimony: a modular model definition language.

Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, Herbert M. Sauro

Bioinform., 2009

2008

Comparing simulation results of SBML capable simulators.

Frank T. Bergmann, Herbert M. Sauro

Bioinform., 2008

2006

Supporting the SBML layout extension.

Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro

Bioinform., 2006

SBW - a modular framework for systems biology.

Frank T. Bergmann, Herbert M. Sauro

Proceedings of the Winter Simulation Conference WSC 2006, 2006

2005

Bifurcation discovery tool.

Vijay Chickarmane, Sri R. Paladugu, Frank T. Bergmann, Herbert M. Sauro

Bioinform., 2005