COPASI and its applications in biotechnology von Bergmann, Frank T., Hoops, Stefan, Klahn, Brian, Kummer, Ursula, Mendes, Pedro, Pahle, Jürgen, Sahle, Sven

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SBML Level 3 Package: Flux Balance Constraints version 2 von Olivier, Brett G., Bergmann, Frank T.

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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 von Hucka, Michael, Bergmann, Frank T, Chaouiya, Claudine, Dräger, Andreas, Hoops, Stefan, Keating, Sarah M, König, Matthias, Novère, Nicolas Le, Myers, Chris J, Olivier, Brett G, Sahle, Sven, Schaff, James C, Sheriff, Rahuman, Smith, Lucian P, Waltemath, Dagmar, Wilkinson, Darren J, Zhang, Fengkai

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TinkerCell: modular CAD tool for synthetic biology von Chandran, Deepak, Bergmann, Frank T, Sauro, Herbert M

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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core von Hucka, Michael, Bergmann, Frank T., Dräger, Andreas, Hoops, Stefan, Keating, Sarah M., Le Novère, Nicolas, Myers, Chris J., Olivier, Brett G., Sahle, Sven, Schaff, James C., Smith, Lucian P., Waltemath, Dagmar, Wilkinson, Darren J.

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

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The simulation experiment description markup language (SED-ML): language specification for level 1 version 5 von Smith, Lucian P., Bergmann, Frank T., Garny, Alan, Helikar, Tomáš, Karr, Jonathan, Nickerson, David, Sauro, Herbert, Waltemath, Dagmar, König, Matthias

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Software support for SBGN maps: SBGN-ML and LibSBGN von van Iersel, Martijn P, Villéger, Alice C, Czauderna, Tobias, Boyd, Sarah E, Bergmann, Frank T, Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I, Mi, Huaiyu, Moodie, Stuart L, Kitano, Hiroaki, Le Novère, Nicolas, Schreiber, Falk

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Systems biology graphical notation markup language (SBGNML) version 0.3 von Bergmann, Frank T., Czauderna, Tobias, Dogrusoz, Ugur, Rougny, Adrien, Dräger, Andreas, Touré, Vasundra, Mazein, Alexander, Blinov, Michael L., Luna, Augustin

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SBML Level 3 package: Render, Version 1, Release 1 von Bergmann, Frank T., Keating, Sarah M., Gauges, Ralph, Sahle, Sven, Wengler, Katja

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Inspecting the Solution Space of Genome-Scale Metabolic Models von Loghmani, Seyed Babak, Veith, Nadine, Sahle, Sven, Bergmann, Frank T, Olivier, Brett G, Kummer, Ursula

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The simulation experiment description markup language (SED-ML): language specification for level 1 version 4 von Smith, Lucian P., Bergmann, Frank T., Garny, Alan, Helikar, Tomáš, Karr, Jonathan, Nickerson, David, Sauro, Herbert, Waltemath, Dagmar, König, Matthias

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Comparing simulation results of SBML capable simulators von Bergmann, Frank T., Sauro, Herbert M.

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Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative von Hucka, Michael, Nickerson, David P, Bader, Gary D, Bergmann, Frank T, Cooper, Jonathan, Demir, Emek, Garny, Alan, Golebiewski, Martin, Myers, Chris J, Schreiber, Falk, Waltemath, Dagmar, Le Novère, Nicolas

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Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1 von Smith, Lucian P., Moodie, Stuart L., Bergmann, Frank T., Gillespie, Colin, Keating, Sarah M., König, Matthias, Myers, Chris J., Swat, Maciek J., Wilkinson, Darren J., Hucka, Michael

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CoRC: the COPASI R Connector von Förster, Jonas, Bergmann, Frank T., Pahle, Jürgen

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EnzymeML—a data exchange format for biocatalysis and enzymology von Range, Jan, Halupczok, Colin, Lohmann, Jens, Swainston, Neil, Kettner, Carsten, Bergmann, Frank T., Weidemann, Andreas, Wittig, Ulrike, Schnell, Santiago, Pleiss, Jürgen

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

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SBtab: a flexible table format for data exchange in systems biology von Lubitz, Timo, Hahn, Jens, Bergmann, Frank T, Noor, Elad, Klipp, Edda, Liebermeister, Wolfram

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

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