default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBibTeX records: Frank T. Bergmann
@article{DBLP:journals/jib/SmithBGHKNSWK24,
author = {Lucian P. Smith and
Frank T. Bergmann and
Alan Garny and
Tom{\'{a}}s Helikar and
Jonathan R. Karr and
David P. Nickerson and
Herbert M. Sauro and
Dagmar Waltemath and
Matthias K{\"{o}}nig},
title = {The simulation experiment description markup language {(SED-ML):}
language specification for level 1 version 5},
journal = {J. Integr. Bioinform.},
volume = {21},
number = {1},
year = {2024},
url = {https://doi.org/10.1515/jib-2024-0008},
doi = {10.1515/JIB-2024-0008},
timestamp = {Sun, 08 Sep 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/SmithBGHKNSWK24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/SchaffLMBFSS23,
author = {James C. Schaff and
Anuradha Lakshminarayana and
Robert F. Murphy and
Frank T. Bergmann and
Akira Funahashi and
Devin P. Sullivan and
Lucian P. Smith},
title = {{SBML} level 3 package: spatial processes, version 1, release 1},
journal = {J. Integr. Bioinform.},
volume = {20},
number = {1},
year = {2023},
url = {https://doi.org/10.1515/jib-2022-0054},
doi = {10.1515/JIB-2022-0054},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/SchaffLMBFSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jossw/Bergmann23,
author = {Frank T. Bergmann},
title = {{BASICO:} {A} simplified Python interface to {COPASI}},
journal = {J. Open Source Softw.},
volume = {8},
number = {91},
pages = {5553},
year = {2023},
url = {https://doi.org/10.21105/joss.05553},
doi = {10.21105/JOSS.05553},
timestamp = {Tue, 28 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jossw/Bergmann23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShaikhSVMWAAAAB22,
author = {Bilal Shaikh and
Lucian P. Smith and
Dan Vasilescu and
Gnaneswara Marupilla and
Michael Wilson and
Eran Agmon and
Henry Agnew and
Steven S. Andrews and
Azraf Anwar and
Moritz E. Beber and
Frank T. Bergmann and
David Brooks and
Lutz Brusch and
Laurence Calzone and
Kiri Choi and
Joshua Cooper and
John Detloff and
Brian Drawert and
Michel Dumontier and
G. Bard Ermentrout and
James R. Faeder and
Andrew P. Freiburger and
Fabian Fr{\"{o}}hlich and
Akira Funahashi and
Alan Garny and
John H. Gennari and
Padraig Gleeson and
Anne Goelzer and
Zachary B. Haiman and
Jan Hasenauer and
Joseph L. Hellerstein and
Henning Hermjakob and
Stefan Hoops and
Jon C. Ison and
Diego Jahn and
Henry V. Jakubowski and
Ryann Jordan and
Mat{\'{u}}s Kalas and
Matthias K{\"{o}}nig and
Wolfram Liebermeister and
Rahuman S. Malik{-}Sheriff and
Synchon Mandal and
Robert A. McDougal and
J. Kyle Medley and
Pedro Mendes and
Robert M{\"{u}}ller and
Chris J. Myers and
Aur{\'{e}}lien Naldi and
Tung V. N. Nguyen and
David P. Nickerson and
Brett G. Olivier and
Drashti Patoliya and
Lo{\"{\i}}c Paulev{\'{e}} and
Linda R. Petzold and
Ankita Priya and
Anand K. Rampadarath and
Johann M. Rohwer and
Ali Sinan Saglam and
Dilawar Singh and
Ankur Sinha and
Jacky L. Snoep and
Hugh Sorby and
Ryan K. Spangler and
J{\"{o}}rn Starru{\ss} and
Payton J. Thomas and
David D. van Niekerk and
Daniel Weindl and
Fengkai Zhang and
Anna Zhukova and
Arthur P. Goldberg and
James C. Schaff and
Michael L. Blinov and
Herbert M. Sauro and
Ion I. Moraru and
Jonathan R. Karr},
title = {BioSimulators: a central registry of simulation engines and services
for recommending specific tools},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {108--114},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac331},
doi = {10.1093/NAR/GKAC331},
timestamp = {Mon, 08 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShaikhSVMWAAAAB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-06732,
author = {Bilal Shaikh and
Lucian P. Smith and
Dan Vasilescu and
Gnaneswara Marupilla and
Michael Wilson and
Eran Agmon and
Henry Agnew and
Steven S. Andrews and
Azraf Anwar and
Moritz E. Beber and
Frank T. Bergmann and
David Brooks and
Lutz Brusch and
Laurence Calzone and
Kiri Choi and
Joshua Cooper and
John Detloff and
Brian Drawert and
Michel Dumontier and
G. Bard Ermentrout and
James R. Faeder and
Andrew P. Freiburger and
Fabian Fr{\"{o}}hlich and
Akira Funahashi and
Alan Garny and
John H. Gennari and
Padraig Gleeson and
Anne Goelzer and
Zachary B. Haiman and
Joseph L. Hellerstein and
Stefan Hoops and
Jon C. Ison and
Diego Jahn and
Henry V. Jakubowski and
Ryann Jordan and
Mat{\'{u}}s Kalas and
Matthias K{\"{o}}nig and
Wolfram Liebermeister and
Synchon Mandal and
Robert A. McDougal and
J. Kyle Medley and
Pedro Mendes and
Robert M{\"{u}}ller and
Chris J. Myers and
Aur{\'{e}}lien Naldi and
Tung V. N. Nguyen and
David P. Nickerson and
Brett G. Olivier and
Drashti Patoliya and
Lo{\"{\i}}c Paulev{\'{e}} and
Linda R. Petzold and
Ankita Priya and
Anand K. Rampadarath and
Johann M. Rohwer and
Ali Sinan Saglam and
Dilawar Singh and
Ankur Sinha and
Jacky L. Snoep and
Hugh Sorby and
Ryan K. Spangler and
J{\"{o}}rn Starru{\ss} and
Payton J. Thomas and
David D. van Niekerk and
Daniel Weindl and
Fengkai Zhang and
Anna Zhukova and
Arthur P. Goldberg and
Michael L. Blinov and
Herbert M. Sauro and
Ion I. Moraru and
Jonathan R. Karr},
title = {BioSimulators: a central registry of simulation engines and services
for recommending specific tools},
journal = {CoRR},
volume = {abs/2203.06732},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.06732},
doi = {10.48550/ARXIV.2203.06732},
eprinttype = {arXiv},
eprint = {2203.06732},
timestamp = {Mon, 08 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-06732.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForsterBP21,
author = {Jonas F{\"{o}}rster and
Frank T. Bergmann and
J{\"{u}}rgen Pahle},
title = {CoRC: the {COPASI} {R} Connector},
journal = {Bioinform.},
volume = {37},
number = {17},
pages = {2778--2779},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab033},
doi = {10.1093/BIOINFORMATICS/BTAB033},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForsterBP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/SmithBGHKNSWK21,
author = {Lucian P. Smith and
Frank T. Bergmann and
Alan Garny and
Tom{\'{a}}s Helikar and
Jonathan R. Karr and
David P. Nickerson and
Herbert M. Sauro and
Dagmar Waltemath and
Matthias K{\"{o}}nig},
title = {The simulation experiment description markup language {(SED-ML):}
language specification for level 1 version 4},
journal = {J. Integr. Bioinform.},
volume = {18},
number = {3},
year = {2021},
url = {https://doi.org/10.1515/jib-2021-0021},
doi = {10.1515/JIB-2021-0021},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jib/SmithBGHKNSWK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SchmiesterSBCDE21,
author = {Leonard Schmiester and
Yannik Sch{\"{a}}lte and
Frank T. Bergmann and
Tacio Camba and
Erika Dudkin and
Janine Egert and
Fabian Fr{\"{o}}hlich and
Lara Fuhrmann and
Adrian L. Hauber and
Svenja Kemmer and
Polina A. Lakrisenko and
Carolin Loos and
Simon Merkt and
Wolfgang M{\"{u}}ller and
Dilan Pathirana and
Elba Raim{\'{u}}ndez{-}{\'{A}}lvarez and
Lukas Refisch and
Marcus Rosenblatt and
Paul Stapor and
Philipp St{\"{a}}dter and
Dantong Wang and
Franz{-}Georg Wieland and
Julio R. Banga and
Jens Timmer and
Alejandro F. Villaverde and
Sven Sahle and
Clemens Kreutz and
Jan Hasenauer and
Daniel Weindl},
title = {PEtab - Interoperable specification of parameter estimation problems
in systems biology},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {1},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1008646},
doi = {10.1371/JOURNAL.PCBI.1008646},
timestamp = {Wed, 07 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/SchmiesterSBCDE21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannCDRDTMB20,
author = {Frank T. Bergmann and
Tobias Czauderna and
Ugur Dogrusoz and
Adrien Rougny and
Andreas Dr{\"{a}}ger and
Vasundra Tour{\'{e}} and
Alexander Mazein and
Michael L. Blinov and
Augustin Luna},
title = {Systems biology graphical notation markup language {(SBGNML)} version
0.3},
journal = {J. Integr. Bioinform.},
volume = {17},
number = {2-3},
year = {2020},
url = {https://doi.org/10.1515/jib-2020-0016},
doi = {10.1515/JIB-2020-0016},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/BergmannCDRDTMB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/SmithMBGKKMSWH20,
author = {Lucian P. Smith and
Stuart L. Moodie and
Frank T. Bergmann and
Colin S. Gillespie and
Sarah M. Keating and
Matthias K{\"{o}}nig and
Chris J. Myers and
Maciek J. Swat and
Darren J. Wilkinson and
Michael Hucka},
title = {Systems Biology Markup Language {(SBML)} Level 3 Package: Distributions,
Version 1, Release 1},
journal = {J. Integr. Bioinform.},
volume = {17},
number = {2-3},
year = {2020},
url = {https://doi.org/10.1515/jib-2020-0018},
doi = {10.1515/JIB-2020-0018},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/SmithMBGKKMSWH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBCDHKKNMOS19,
author = {Michael Hucka and
Frank T. Bergmann and
Claudine Chaouiya and
Andreas Dr{\"{a}}ger and
Stefan Hoops and
Sarah M. Keating and
Matthias K{\"{o}}nig and
Nicolas Le Nov{\`{e}}re and
Chris J. Myers and
Brett G. Olivier and
Sven Sahle and
James C. Schaff and
Rahuman S. Malik{-}Sheriff and
Lucian P. Smith and
Dagmar Waltemath and
Darren J. Wilkinson and
Fengkai Zhang},
title = {The Systems Biology Markup Language {(SBML):} Language Specification
for Level 3 Version 2 Core Release 2},
journal = {J. Integr. Bioinform.},
volume = {16},
number = {2},
year = {2019},
url = {https://doi.org/10.1515/jib-2019-0021},
doi = {10.1515/JIB-2019-0021},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/HuckaBCDHKKNMOS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/BedasoBCMS18,
author = {Yosef Bedaso and
Frank T. Bergmann and
Kiri Choi and
Kyle Medley and
Herbert M. Sauro},
title = {A portable structural analysis library for reaction networks},
journal = {Biosyst.},
volume = {169-170},
pages = {20--25},
year = {2018},
url = {https://doi.org/10.1016/j.biosystems.2018.05.008},
doi = {10.1016/J.BIOSYSTEMS.2018.05.008},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/BedasoBCMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannCKMNNOS18,
author = {Frank T. Bergmann and
Jonathan Cooper and
Matthias K{\"{o}}nig and
Ion I. Moraru and
David P. Nickerson and
Nicolas Le Nov{\`{e}}re and
Brett G. Olivier and
Sven Sahle and
Lucian P. Smith and
Dagmar Waltemath},
title = {Simulation Experiment Description Markup Language {(SED-ML)} Level
1 Version 3 {(L1V3)}},
journal = {J. Integr. Bioinform.},
volume = {15},
number = {1},
year = {2018},
url = {https://doi.org/10.1515/jib-2017-0086},
doi = {10.1515/JIB-2017-0086},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/BergmannCKMNNOS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannKGSW18,
author = {Frank T. Bergmann and
Sarah M. Keating and
Ralph Gauges and
Sven Sahle and
Katja Wengler},
title = {{SBML} Level 3 package: Render, Version 1, Release 1},
journal = {J. Integr. Bioinform.},
volume = {15},
number = {1},
year = {2018},
url = {https://doi.org/10.1515/jib-2017-0078},
doi = {10.1515/JIB-2017-0078},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/BergmannKGSW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBDHKNMOSSS18,
author = {Michael Hucka and
Frank T. Bergmann and
Andreas Dr{\"{a}}ger and
Stefan Hoops and
Sarah M. Keating and
Nicolas Le Nov{\`{e}}re and
Chris J. Myers and
Brett G. Olivier and
Sven Sahle and
James C. Schaff and
Lucian P. Smith and
Dagmar Waltemath and
Darren J. Wilkinson},
title = {The Systems Biology Markup Language {(SBML):} Language Specification
for Level 3 Version 1 Core},
journal = {J. Integr. Bioinform.},
volume = {15},
number = {1},
year = {2018},
url = {https://doi.org/10.1515/jib-2017-0080},
doi = {10.1515/JIB-2017-0080},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/HuckaBDHKNMOSSS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBDHKNMOSSS18a,
author = {Michael Hucka and
Frank T. Bergmann and
Andreas Dr{\"{a}}ger and
Stefan Hoops and
Sarah M. Keating and
Nicolas Le Nov{\`{e}}re and
Chris J. Myers and
Brett G. Olivier and
Sven Sahle and
James C. Schaff and
Lucian P. Smith and
Dagmar Waltemath and
Darren J. Wilkinson},
title = {The Systems Biology Markup Language {(SBML):} Language Specification
for Level 3 Version 2 Core},
journal = {J. Integr. Bioinform.},
volume = {15},
number = {1},
year = {2018},
url = {https://doi.org/10.1515/jib-2017-0081},
doi = {10.1515/JIB-2017-0081},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/HuckaBDHKNMOSSS18a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/OlivierB18,
author = {Brett G. Olivier and
Frank T. Bergmann},
title = {{SBML} Level 3 Package: Flux Balance Constraints version 2},
journal = {J. Integr. Bioinform.},
volume = {15},
number = {1},
year = {2018},
url = {https://doi.org/10.1515/jib-2017-0082},
doi = {10.1515/JIB-2017-0082},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/OlivierB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergmannNWS17,
author = {Frank T. Bergmann and
David P. Nickerson and
Dagmar Waltemath and
Martin Scharm},
title = {{SED-ML} web tools: generate, modify and export standard-compliant
simulation studies},
journal = {Bioinform.},
volume = {33},
number = {8},
pages = {1253--1254},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw812},
doi = {10.1093/BIOINFORMATICS/BTW812},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BergmannNWS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergmannSZ16,
author = {Frank T. Bergmann and
Sven Sahle and
Christoph Zimmer},
title = {Piecewise parameter estimation for stochastic models in {COPASI}},
journal = {Bioinform.},
volume = {32},
number = {10},
pages = {1586--1588},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv759},
doi = {10.1093/BIOINFORMATICS/BTV759},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BergmannSZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LubitzHBNKL16,
author = {Timo Lubitz and
Jens Hahn and
Frank T. Bergmann and
Elad Noor and
Edda Klipp and
Wolfram Liebermeister},
title = {SBtab: a flexible table format for data exchange in systems biology},
journal = {Bioinform.},
volume = {32},
number = {16},
pages = {2559--2561},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw179},
doi = {10.1093/BIOINFORMATICS/BTW179},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LubitzHBNKL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tbe/WaltemathKBCHKL16,
author = {Dagmar Waltemath and
Jonathan R. Karr and
Frank T. Bergmann and
Vijayalakshmi Chelliah and
Michael Hucka and
Marcus Krantz and
Wolfram Liebermeister and
Pedro Mendes and
Chris J. Myers and
Pinar Pir and
Begum Alaybeyoglu and
Naveen K. Aranganathan and
Kambiz Baghalian and
Arne T. Bittig and
Paulo E. Pinto Burke and
Matteo Cantarelli and
Yin Hoon Chew and
Rafael S. Costa and
Joseph Cursons and
Tobias Czauderna and
Arthur P. Goldberg and
Harold F. G{\'{o}}mez and
Jens Hahn and
Tuure Hameri and
Daniel F. Hernandez Gardiol and
Denis Kazakiewicz and
Ilya Kiselev and
Vincent Knight{-}Schrijver and
Christian Kn{\"{u}}pfer and
Matthias K{\"{o}}nig and
Daewon Lee and
Audald Lloret{-}Villas and
Nikita Mandrik and
J. Kyle Medley and
Bertrand Moreau and
Hojjat Naderi{-}Meshkin and
Sucheendra K. Palaniappan and
Daniel Priego{-}Espinosa and
Martin Scharm and
Mahesh Sharma and
Kieran Smallbone and
Natalie J. Stanford and
Je{-}Hoon Song and
Tom Theile and
Milenko Tokic and
Namrata Tomar and
Vasundra Tour{\'{e}} and
Jannis Uhlendorf and
Thawfeek M. Varusai and
Leandro H. Watanabe and
Florian Wendland and
Markus Wolfien and
James T. Yurkovich and
Yan Zhu and
Argyris Zardilis and
Anna Zhukova and
Falk Schreiber},
title = {Toward Community Standards and Software for Whole-Cell Modeling},
journal = {{IEEE} Trans. Biomed. Eng.},
volume = {63},
number = {10},
pages = {2007--2014},
year = {2016},
url = {https://doi.org/10.1109/TBME.2016.2560762},
doi = {10.1109/TBME.2016.2560762},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tbe/WaltemathKBCHKL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ZimmerBS16,
author = {Christoph Zimmer and
Frank T. Bergmann and
Sven Sahle},
title = {Reducing local minima in fitness landscapes of parameter estimation
by using piecewise evaluation and state estimation},
journal = {CoRR},
volume = {abs/1601.04458},
year = {2016},
url = {http://arxiv.org/abs/1601.04458},
eprinttype = {arXiv},
eprint = {1601.04458},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ZimmerBS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannCNNW15,
author = {Frank T. Bergmann and
Jonathan Cooper and
Nicolas Le Nov{\`{e}}re and
David P. Nickerson and
Dagmar Waltemath},
title = {Simulation Experiment Description Markup Language {(SED-ML)} Level
1 Version 2},
journal = {J. Integr. Bioinform.},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-262},
doi = {10.2390/BIECOLL-JIB-2015-262},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/BergmannCNNW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BergmannRN15,
author = {Frank T. Bergmann and
Nicolas Rodriguez and
Nicolas Le Nov{\`{e}}re},
title = {{COMBINE} Archive Specification Version 1},
journal = {J. Integr. Bioinform.},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-261},
doi = {10.2390/BIECOLL-JIB-2015-261},
timestamp = {Thu, 03 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/BergmannRN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/GaugesRSWB15,
author = {Ralph Gauges and
Ursula Rost and
Sven Sahle and
Katja Wengler and
Frank Thomas Bergmann},
title = {The Systems Biology Markup Language {(SBML)} Level 3 Package: Layout,
Version 1 Core},
journal = {J. Integr. Bioinform.},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-267},
doi = {10.2390/BIECOLL-JIB-2015-267},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/GaugesRSWB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBDHKNMOSSS15,
author = {Michael Hucka and
Frank T. Bergmann and
Andreas Dr{\"{a}}ger and
Stefan Hoops and
Sarah M. Keating and
Nicolas Le Nov{\`{e}}re and
Chris J. Myers and
Brett G. Olivier and
Sven Sahle and
James C. Schaff and
Lucian P. Smith and
Dagmar Waltemath and
Darren J. Wilkinson},
title = {Systems Biology Markup Language {(SBML)} Level 2 Version 5: Structures
and Facilities for Model Definitions},
journal = {J. Integr. Bioinform.},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-271},
doi = {10.2390/BIECOLL-JIB-2015-271},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/HuckaBDHKNMOSSS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/HuckaBHKSSSW15,
author = {Michael Hucka and
Frank T. Bergmann and
Stefan Hoops and
Sarah M. Keating and
Sven Sahle and
James C. Schaff and
Lucian P. Smith and
Darren J. Wilkinson},
title = {The Systems Biology Markup Language {(SBML):} Language Specification
for Level 3 Version 1 Core},
journal = {J. Integr. Bioinform.},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-266},
doi = {10.2390/BIECOLL-JIB-2015-266},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/HuckaBHKSSSW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/OlivierB15,
author = {Brett G. Olivier and
Frank T. Bergmann},
title = {The Systems Biology Markup Language {(SBML)} Level 3 Package: Flux
Balance Constraints},
journal = {J. Integr. Bioinform.},
volume = {12},
number = {2},
year = {2015},
url = {https://doi.org/10.2390/biecoll-jib-2015-269},
doi = {10.2390/BIECOLL-JIB-2015-269},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/OlivierB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BergmannAMCGGHLMNORSSSWYN14,
author = {Frank T. Bergmann and
Richard R. Adams and
Stuart L. Moodie and
Jonathan Cooper and
Mihai Glont and
Martin Golebiewski and
Michael Hucka and
Camille Laibe and
Andrew K. Miller and
David P. Nickerson and
Brett G. Olivier and
Nicolas Rodriguez and
Herbert M. Sauro and
Martin Scharm and
Stian Soiland{-}Reyes and
Dagmar Waltemath and
Florent Yvon and
Nicolas Le Nov{\`{e}}re},
title = {{COMBINE} archive and {OMEX} format: one file to share all information
to reproduce a modeling project},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {369},
year = {2014},
url = {https://doi.org/10.1186/s12859-014-0369-z},
doi = {10.1186/S12859-014-0369-Z},
timestamp = {Thu, 03 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BergmannAMCGGHLMNORSSSWYN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BergmannAMCGGHLMNORSSSWYN14,
author = {Frank T. Bergmann and
Richard Adams and
Stuart L. Moodie and
Jonathan Cooper and
Mihai Glont and
Martin Golebiewski and
Michael Hucka and
Camille Laibe and
Andrew K. Miller and
David P. Nickerson and
Brett G. Olivier and
Nicolas Rodriguez and
Herbert M. Sauro and
Martin Scharm and
Stian Soiland{-}Reyes and
Dagmar Waltemath and
Florent Yvon and
Nicolas Le Nov{\`{e}}re},
title = {{COMBINE} archive: One File To Share Them All},
journal = {CoRR},
volume = {abs/1407.4992},
year = {2014},
url = {http://arxiv.org/abs/1407.4992},
eprinttype = {arXiv},
eprint = {1407.4992},
timestamp = {Thu, 03 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BergmannAMCGGHLMNORSSSWYN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IerselVCBBLDSDMFAMMKNS12,
author = {Martijn P. van Iersel and
Alice Vill{\'{e}}ger and
Tobias Czauderna and
Sarah E. Boyd and
Frank T. Bergmann and
Augustin Luna and
Emek Demir and
Anatoly A. Sorokin and
Ugur Dogrus{\"{o}}z and
Yukiko Matsuoka and
Akira Funahashi and
Mirit I. Aladjem and
Huaiyu Mi and
Stuart L. Moodie and
Hiroaki Kitano and
Nicolas Le Nov{\`{e}}re and
Falk Schreiber},
title = {Software support for {SBGN} maps: {SBGN-ML} and LibSBGN},
journal = {Bioinform.},
volume = {28},
number = {15},
pages = {2016--2021},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts270},
doi = {10.1093/BIOINFORMATICS/BTS270},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/IerselVCBBLDSDMFAMMKNS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WaltemathABHKMMNSSN11,
author = {Dagmar Waltemath and
Richard R. Adams and
Frank T. Bergmann and
Michael Hucka and
Fedor A. Kolpakov and
Andrew K. Miller and
Ion I. Moraru and
David P. Nickerson and
Sven Sahle and
Jacky L. Snoep and
Nicolas Le Nov{\`{e}}re},
title = {Reproducible computational biology experiments with {SED-ML} - The
Simulation Experiment Description Markup Language},
journal = {{BMC} Syst. Biol.},
volume = {5},
pages = {198},
year = {2011},
url = {https://doi.org/10.1186/1752-0509-5-198},
doi = {10.1186/1752-0509-5-198},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/WaltemathABHKMMNSSN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WaltemathABBBBCCCCGHHHKLMMNNNSSSSTWN11,
author = {Dagmar Waltemath and
Richard R. Adams and
Daniel A. Beard and
Frank T. Bergmann and
Upinder S. Bhalla and
Randall Britten and
Vijayalakshmi Chelliah and
Mike T. Cooling and
Jonathan Cooper and
Edmund J. Crampin and
Alan Garny and
Stefan Hoops and
Michael Hucka and
Peter J. Hunter and
Edda Klipp and
Camille Laibe and
Andrew K. Miller and
Ion I. Moraru and
David P. Nickerson and
Poul M. F. Nielsen and
Macha Nikolski and
Sven Sahle and
Herbert M. Sauro and
Henning Schmidt and
Jacky L. Snoep and
Dominic P. Tolle and
Olaf Wolkenhauer and
Nicolas Le Nov{\`{e}}re},
title = {Minimum Information About a Simulation Experiment {(MIASE)}},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {4},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001122},
doi = {10.1371/JOURNAL.PCBI.1001122},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WaltemathABBBBCCCCGHHHKLMMNNNSSSSTWN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eScience/HuckaBKS11,
author = {Michael Hucka and
Frank T. Bergmann and
Sarah M. Keating and
Lucian P. Smith},
title = {A Profile of Today's SBML-Compatible Software},
booktitle = {{IEEE} 7th International Conference on E-Science, e-Science 2011,
Workshop Proceedings, Stockholm, Sweden, December 5-8, 2011},
pages = {143--150},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/eScienceW.2011.28},
doi = {10.1109/ESCIENCEW.2011.28},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eScience/HuckaBKS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShenBS10,
author = {Si Yuan Shen and
Frank T. Bergmann and
Herbert M. Sauro},
title = {SBML2TikZ: supporting the {SBML} render extension in LaTeX},
journal = {Bioinform.},
volume = {26},
number = {21},
pages = {2794--2795},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq512},
doi = {10.1093/BIOINFORMATICS/BTQ512},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ShenBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmithBCS09,
author = {Lucian P. Smith and
Frank T. Bergmann and
Deepak Chandran and
Herbert M. Sauro},
title = {Antimony: a modular model definition language},
journal = {Bioinform.},
volume = {25},
number = {18},
pages = {2452--2454},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp401},
doi = {10.1093/BIOINFORMATICS/BTP401},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmithBCS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergmannS08,
author = {Frank T. Bergmann and
Herbert M. Sauro},
title = {Comparing simulation results of {SBML} capable simulators},
journal = {Bioinform.},
volume = {24},
number = {17},
pages = {1963--1965},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn319},
doi = {10.1093/BIOINFORMATICS/BTN319},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BergmannS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DeckardBS06,
author = {Anastasia Deckard and
Frank T. Bergmann and
Herbert M. Sauro},
title = {Supporting the {SBML} layout extension},
journal = {Bioinform.},
volume = {22},
number = {23},
pages = {2966--2967},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl520},
doi = {10.1093/BIOINFORMATICS/BTL520},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DeckardBS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wsc/BergmannS06,
author = {Frank T. Bergmann and
Herbert M. Sauro},
editor = {L. Felipe Perrone and
Barry Lawson and
Jason Liu and
Frederick P. Wieland},
title = {{SBW} - a modular framework for systems biology},
booktitle = {Proceedings of the Winter Simulation Conference {WSC} 2006, Monterey,
California, USA, December 3-6, 2006},
pages = {1637--1645},
publisher = {{IEEE} Computer Society},
year = {2006},
url = {https://doi.org/10.1109/WSC.2006.322938},
doi = {10.1109/WSC.2006.322938},
timestamp = {Mon, 29 Apr 2024 16:19:40 +0200},
biburl = {https://dblp.org/rec/conf/wsc/BergmannS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChickarmanePBS05,
author = {Vijay Chickarmane and
Sri R. Paladugu and
Frank T. Bergmann and
Herbert M. Sauro},
title = {Bifurcation discovery tool},
journal = {Bioinform.},
volume = {21},
number = {18},
pages = {3688--3690},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti603},
doi = {10.1093/BIOINFORMATICS/BTI603},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChickarmanePBS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-09-10 02:11 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
