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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Published in:
BMC Systems Biology, 2013, v. 7, n. 1, p. 3, doi. 10.1186/1752-0509-7-135
By:
- Chaouiya, Claudine;
- Berenguier, Duncan;
- Keating, Sarah M.;
- Naldi, Aurelien;
- Van Iersel, Martijn P.;
- Rodriguez, Nicolas;
- Dräger, Andreas;
- Büchel, Finja;
- Cokelaer, Thomas;
- Kowal, Bryan;
- Wicks, Benjamin;
- Gonçalves, Emanuel;
- Dorier, Julien;
- Page, Michel;
- Monteiro, Pedro T.;
- Kamp, Axel von;
- Xenarios, Ioannis;
- Jong, Hidde de;
- Hucka, Michael;
- Klamt, Steffen
Publication type:
Article
Wikidata as a knowledge graph for the life sciences.
Published in:
eLife, 2020, p. 1, doi. 10.7554/eLife.52614
By:
- WAAGMEESTER, ANDRA;
- STUPP, GREGORY;
- BURGSTALLER-MUEHLBACHER, SEBASTIAN;
- GOOD, BENJAMIN M.;
- GRIFFITH, MALACHI;
- GRIFFITH, OBI L.;
- HANSPERS, KRISTINA;
- HERMJAKOB, HENNING;
- HUDSON, TOBY S.;
- HYBISKE, KEVIN;
- KEATING, SARAH M.;
- MANSKE, MAGNUS;
- MAYERS, MICHAEL;
- MIETCHEN, DANIEL;
- MITRAKA, ELVIRA;
- PICO, ALEXANDER R.;
- PUTMAN, TIMOTHY;
- RIUTTA, ANDERS;
- QUERALT-ROSINACH, NURIA;
- SCHRIML, LYNN M.
Publication type:
Article
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.
Published in:
2024
By:
- Golebiewski, Martin;
- Bader, Gary;
- Gleeson, Padraig;
- Gorochowski, Thomas E.;
- Keating, Sarah M.;
- König, Matthias;
- Myers, Chris J.;
- Nickerson, David P.;
- Sommer, Björn;
- Waltemath, Dagmar;
- Schreiber, Falk
Publication type:
Editorial
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.
Published in:
Journal of Integrative Bioinformatics, 2023, v. 20, n. 1, p. 1, doi. 10.1515/jib-2023-0004
By:
- König, Matthias;
- Gleeson, Padraig;
- Golebiewski, Martin;
- Gorochowski, Thomas E.;
- Hucka, Michael;
- Keating, Sarah M.;
- Myers, Chris J.;
- Nickerson, David P.;
- Sommer, Björn;
- Waltemath, Dagmar;
- Schreiber, Falk
Publication type:
Article
Specifications of standards in systems and synthetic biology: status and developments in 2021.
Published in:
2021
By:
- Schreiber, Falk;
- Gleeson, Padraig;
- Golebiewski, Martin;
- Gorochowski, Thomas E.;
- Hucka, Michael;
- Keating, Sarah M.;
- König, Matthias;
- Myers, Chris J.;
- Nickerson, David P.;
- Sommer, Björn;
- Waltemath, Dagmar
Publication type:
Editorial
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).
Published in:
Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0005
By:
- Waltemath, Dagmar;
- Golebiewski, Martin;
- Blinov, Michael L;
- Gleeson, Padraig;
- Hermjakob, Henning;
- Hucka, Michael;
- Inau, Esther Thea;
- Keating, Sarah M;
- König, Matthias;
- Krebs, Olga;
- Malik-Sheriff, Rahuman S;
- Nickerson, David;
- Oberortner, Ernst;
- Sauro, Herbert M;
- Schreiber, Falk;
- Smith, Lucian;
- Stefan, Melanie I;
- Wittig, Ulrike;
- Myers, Chris J
Publication type:
Article
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Published in:
Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0015
By:
- Zhang, Fengkai;
- Smith, Lucian P.;
- Blinov, Michael L.;
- Faeder, James;
- Hlavacek, William S.;
- Juan Tapia, Jose;
- Keating, Sarah M.;
- Rodriguez, Nicolas;
- Dräger, Andreas;
- Harris, Leonard A.;
- Finney, Andrew;
- Hu, Bin;
- Hucka, Michael;
- Meier-Schellersheim, Martin
Publication type:
Article
Specifications of standards in systems and synthetic biology: status and developments in 2020.
Published in:
Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0022
By:
- Schreiber, Falk;
- Sommer, Björn;
- Czauderna, Tobias;
- Golebiewski, Martin;
- Gorochowski, Thomas E.;
- Hucka, Michael;
- Keating, Sarah M.;
- König, Matthias;
- Myers, Chris;
- Nickerson, David;
- Waltemath, Dagmar
Publication type:
Article
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.
Published in:
Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0018
By:
- 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
Publication type:
Article
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.
Published in:
Journal of Integrative Bioinformatics, 2019, v. 16, n. 2, p. 1, doi. 10.1515/jib-2019-0035
By:
- Schreiber, Falk;
- Sommer, Björn;
- Bader, Gary D.;
- Gleeson, Padraig;
- Golebiewski, Martin;
- Hucka, Michael;
- Keating, Sarah M.;
- König, Matthias;
- Myers, Chris;
- Nickerson, David;
- Waltemath, Dagmar
Publication type:
Article
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
Published in:
Journal of Integrative Bioinformatics, 2019, v. 16, n. 2, p. 1, doi. 10.1515/jib-2019-0021
By:
- Hucka, Michael;
- Bergmann, Frank T.;
- Chaouiya, Claudine;
- Dräger, Andreas;
- Hoops, Stefan;
- Keating, Sarah M.;
- König, Matthias;
- Le Novère, Nicolas;
- Myers, Chris J.;
- Olivier, Brett G.;
- Sahle, Sven;
- Schaff, James C.;
- Sheriff, Rahuman;
- Smith, Lucian P.;
- Waltemath, Dagmar;
- Wilkinson, Darren J.;
- Zhang, Fengkai
Publication type:
Article
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Published in:
Molecular Systems Biology, 2020, v. 16, n. 8, p. 1, doi. 10.15252/msb.20199110
By:
- Keating, Sarah M;
- Waltemath, Dagmar;
- König, Matthias;
- Zhang, Fengkai;
- Dräger, Andreas;
- Chaouiya, Claudine;
- Bergmann, Frank T;
- Finney, Andrew;
- Gillespie, Colin S;
- Helikar, Tomáš;
- Hoops, Stefan;
- Malik‐Sheriff, Rahuman S;
- Moodie, Stuart L;
- Moraru, Ion I;
- Myers, Chris J;
- Naldi, Aurélien;
- Olivier, Brett G;
- Sahle, Sven;
- Schaff, James C;
- Smith, Lucian P
Publication type:
Article
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.
Published in:
Briefings in Bioinformatics, 2022, v. 23, n. 4, p. 1, doi. 10.1093/bib/bbac212
By:
- Niarakis, Anna;
- Waltemath, Dagmar;
- Glazier, James;
- Schreiber, Falk;
- Keating, Sarah M;
- Nickerson, David;
- Chaouiya, Claudine;
- Siegel, Anne;
- Noël, Vincent;
- Hermjakob, Henning;
- Helikar, Tomáš;
- Soliman, Sylvain;
- Calzone, Laurence
Publication type:
Article
LibSBML: an API Library for SBML.
Published in:
Bioinformatics, 2008, v. 24, n. 6, p. 880
By:
- Benjamin J. Bornstein;
- Sarah M. Keating;
- Akiya Jouraku;
- Michael Hucka
Publication type:
Article
SBMLToolbox: an SBML toolbox for MATLAB users.
Published in:
Bioinformatics, 2006, v. 22, n. 10, p. 1275, doi. 10.1093/bioinformatics/btl111
By:
- Sarah M. Keating;
- Benjamin J. Bornstein;
- Andrew Finney;
- Michael Hucka
Publication type:
Article
BioModels—15 years of sharing computational models in life science.
Published in:
Nucleic Acids Research, 2020, v. 48, n. D1, p. D407, doi. 10.1093/nar/gkz1055
By:
- Malik-Sheriff, Rahuman S;
- Glont, Mihai;
- Nguyen, Tung V N;
- Tiwari, Krishna;
- Roberts, Matthew G;
- Xavier, Ashley;
- Vu, Manh T;
- Men, Jinghao;
- Maire, Matthieu;
- Kananathan, Sarubini;
- Fairbanks, Emma L;
- Meyer, Johannes P;
- Arankalle, Chinmay;
- Varusai, Thawfeek M;
- Knight-Schrijver, Vincent;
- Li, Lu;
- Dueñas-Roca, Corina;
- Dass, Gaurhari;
- Keating, Sarah M;
- Park, Young M
Publication type:
Article
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Published in:
Nature Protocols, 2019, v. 14, n. 3, p. 639, doi. 10.1038/s41596-018-0098-2
By:
- Heirendt, Laurent;
- Arreckx, Sylvain;
- Pfau, Thomas;
- Mendoza, Sebastián N.;
- Richelle, Anne;
- Heinken, Almut;
- Haraldsdóttir, Hulda S.;
- Wachowiak, Jacek;
- Keating, Sarah M.;
- Vlasov, Vanja;
- Magnusdóttir, Stefania;
- Ng, Chiam Yu;
- Preciat, German;
- Žagare, Alise;
- Chan, Siu H. J.;
- Aurich, Maike K.;
- Clancy, Catherine M.;
- Modamio, Jennifer;
- Sauls, John T.;
- Noronha, Alberto
Publication type:
Article
MOCCASIN: converting MATLAB ODE models to SBML.
Published in:
Bioinformatics, 2016, v. 32, n. 12, p. 1905, doi. 10.1093/bioinformatics/btw056
By:
- Gómez, Harold F.;
- Hucka, Michael;
- Keating, Sarah M.;
- Nudelman, German;
- Iber, Dagmar;
- Sealfon, Stuart C.
Publication type:
Article

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