Bifurcation discovery tool. - Vijay Chickarmane; Sri R. Paladugu; Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2005)

SBW - a modular framework for systems biology. - Frank T. Bergmann; Herbert M. Sauro (WSC, 2006)

Supporting the SBML layout extension. - Anastasia Deckard; Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2006)

Comparing simulation results of SBML capable simulators. - Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2008)

Antimony: a modular model definition language. - Lucian P. Smith; Frank T. Bergmann; Deepak Chandran; Herbert M. Sauro (Bioinform., 2009)

SBML2TikZ: supporting the SBML render extension in LaTeX. - Si Yuan Shen; Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2010)

A Profile of Today's SBML-Compatible Software. - Michael Hucka; Frank T. Bergmann; Sarah M. Keating; Lucian P. Smith (e-Science Workshops, 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)

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; et al. (PLoS Comput. Biol., 2011)

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; et al. (Bioinform., 2012)

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 001; et al. (BMC Bioinform., 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 001; et al. (CoRR, 2014)

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)

COMBINE Archive Specification Version 1. - Frank T. Bergmann; Nicolas Rodriguez 001; Nicolas Le Novère (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)

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; et al. (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)

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. - Brett G. Olivier; Frank T. Bergmann (J. Integr. Bioinform., 2015)

Piecewise parameter estimation for stochastic models in COPASI. - Frank T. Bergmann; Sven Sahle; Christoph Zimmer (Bioinform., 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)

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)

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 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

SED-ML web tools: generate, modify and export standard-compliant simulation studies. - Frank T. Bergmann; David P. Nickerson; Dagmar Waltemath; Martin Scharm (Bioinform., 2017)

A portable structural analysis library for reaction networks. - Yosef Bedaso; Frank T. Bergmann; Kiri Choi; Kyle Medley; Herbert M. Sauro (Biosyst., 2018)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). - Frank T. Bergmann; Jonathan Cooper; Matthias König 003; Ion I. Moraru; David P. Nickerson; Nicolas Le Novère; Brett G. Olivier; Sven Sahle; Lucian P. Smith; Dagmar Waltemath (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)

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; et al. (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; et al. (J. Integr. Bioinform., 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 Release 2. - Michael Hucka; Frank T. Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Matthias König 003; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; et al. (J. Integr. Bioinform., 2019)

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)

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 003; Chris J. Myers; Maciek J. Swat; Darren J. Wilkinson; Michael Hucka (J. Integr. Bioinform., 2020)

CoRC: the COPASI R Connector. - Jonas Förster; Frank T. Bergmann; Jürgen Pahle (Bioinform., 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 003 (J. Integr. Bioinform., 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; et al. (PLoS Comput. Biol., 2021)

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 006; et al. (CoRR, 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 006; et al. (Nucleic Acids Res., 2022)

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., 2023)

BASICO: A simplified Python interface to COPASI. - Frank T. Bergmann (J. Open Source Softw., 2023)

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 003 (J. Integr. Bioinform., 2024)