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2020 – today
- 2024
[j35]Lucian P. Smith
, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. J. Integr. Bioinform. 21(1) (2024)- 2023
- [j34]James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith:
SBML level 3 package: spatial processes, version 1, release 1. J. Integr. Bioinform. 20(1) (2023) - [j33]Frank T. Bergmann:
BASICO: A simplified Python interface to COPASI. J. Open Source Softw. 8(91): 5553 (2023) - 2022
- [j32]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i3]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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j31]Jonas Förster, Frank T. Bergmann, Jürgen Pahle:
CoRC: the COPASI R Connector. Bioinform. 37(17): 2778-2779 (2021) - [j30]Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. J. Integr. Bioinform. 18(3) (2021) - [j29]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:
PEtab - Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17(1) (2021) - 2020
- [j28]Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna:
Systems biology graphical notation markup language (SBGNML) version 0.3. J. Integr. Bioinform. 17(2-3) (2020) - [j27]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:
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. J. Integr. Bioinform. 17(2-3) (2020)
2010 – 2019
- 2019
- [j26]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:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j25]Yosef Bedaso, Frank T. Bergmann, Kiri Choi, Kyle Medley, Herbert M. Sauro:
A portable structural analysis library for reaction networks. Biosyst. 169-170: 20-25 (2018) - [j24]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:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J. Integr. Bioinform. 15(1) (2018) - [j23]Frank T. Bergmann, Sarah M. Keating, Ralph Gauges, Sven Sahle, Katja Wengler:
SBML Level 3 package: Render, Version 1, Release 1. J. Integr. Bioinform. 15(1) (2018) - [j22]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:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018) - [j21]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:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018) - [j20]Brett G. Olivier, Frank T. Bergmann:
SBML Level 3 Package: Flux Balance Constraints version 2. J. Integr. Bioinform. 15(1) (2018) - 2017
- [j19]Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm:
SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinform. 33(8): 1253-1254 (2017) - 2016
- [j18]Frank T. Bergmann, Sven Sahle, Christoph Zimmer:
Piecewise parameter estimation for stochastic models in COPASI. Bioinform. 32(10): 1586-1588 (2016) - [j17]Timo Lubitz, Jens Hahn, Frank T. Bergmann, Elad Noor, Edda Klipp, Wolfram Liebermeister:
SBtab: a flexible table format for data exchange in systems biology. Bioinform. 32(16): 2559-2561 (2016) - [j16]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:
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63(10): 2007-2014 (2016) - [i2]Christoph Zimmer, Frank T. Bergmann, Sven Sahle:
Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. CoRR abs/1601.04458 (2016) - 2015
- [j15]Frank T. Bergmann, Jonathan Cooper, Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. J. Integr. Bioinform. 12(2) (2015) - [j14]Frank T. Bergmann, Nicolas Rodriguez, Nicolas Le Novère:
COMBINE Archive Specification Version 1. J. Integr. Bioinform. 12(2) (2015) - [j13]Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wengler, Frank Thomas Bergmann:
The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - [j12]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:
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015) - [j11]Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - [j10]Brett G. Olivier, Frank T. Bergmann:
The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J. Integr. Bioinform. 12(2) (2015) - 2014
- [j9]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:
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinform. 15: 369 (2014) - [i1]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:
COMBINE archive: One File To Share Them All. CoRR abs/1407.4992 (2014) - 2012
- [j8]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:
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinform. 28(15): 2016-2021 (2012) - 2011
- [j7]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:
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5: 198 (2011) - [j6]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:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011) - [c2]Michael Hucka, Frank T. Bergmann, Sarah M. Keating, Lucian P. Smith:
A Profile of Today's SBML-Compatible Software. e-Science Workshops 2011: 143-150 - 2010
- [j5]Si Yuan Shen, Frank T. Bergmann, Herbert M. Sauro:
SBML2TikZ: supporting the SBML render extension in LaTeX. Bioinform. 26(21): 2794-2795 (2010)
2000 – 2009
- 2009
- [j4]Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, Herbert M. Sauro:
Antimony: a modular model definition language. Bioinform. 25(18): 2452-2454 (2009) - 2008
- [j3]Frank T. Bergmann, Herbert M. Sauro:
Comparing simulation results of SBML capable simulators. Bioinform. 24(17): 1963-1965 (2008) - 2006
- [j2]Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro:
Supporting the SBML layout extension. Bioinform. 22(23): 2966-2967 (2006) - [c1]Frank T. Bergmann, Herbert M. Sauro:
SBW - a modular framework for systems biology. WSC 2006: 1637-1645 - 2005
- [j1]Vijay Chickarmane, Sri R. Paladugu, Frank T. Bergmann, Herbert M. Sauro:
Bifurcation discovery tool. Bioinform. 21(18): 3688-3690 (2005)
Coauthor Index
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