SBML Level 3: an extensible format for the exchange and reuse of biological models

Autor: Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

Publikováno v: Molecular Systems Biology, Vol 16, Iss 8, Pp 1-21 (2020)

Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edi

Externí odkaz: https://doaj.org/article/86e517962df24b21af078b7f951f7487

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022

Autor: Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber

This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.1, SBML Level 3 Package:

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::97fba20e0e6970cbc6551463bc3e1711
https://resolver.caltech.edu/CaltechAUTHORS:20230420-698969800.9

Controlled vocabularies and semantics in systems biology

Autor: Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère

Publikováno v: Molecular Systems Biology, Vol 7, Iss 1, Pp 1-12 (2011)

Abstract The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing

Externí odkaz: https://doaj.org/article/9aeba1a5da7445ac90bb3d07cf5f7374

Nine best practices for research software registries and repositories

Autor: Daniel, Garijo, Hervé, Ménager, Lorraine, Hwang, Ana, Trisovic, Michael, Hucka, Thomas, Morrell, Alice, Allen

Publikováno v: PeerJ. Computer science. 8

Scientific software registries and repositories improve software findability and research transparency, provide information for software citations, and foster preservation of computational methods in a wide range of disciplines. Registries and reposi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::839f9aaf1c8c27303b125723d9a3ebd9
https://pubmed.ncbi.nlm.nih.gov/36092012

The Systems Biology Markup Language (SBML)

Autor: Sarah M. Keating, Claudine Chaouiya, Fengkai Zhang, Darren J. Wilkinson, Brett G. Olivier, Rahumann Sheriff, James C. Schaff, Frank Bergmann, Lucian P. Smith, Dagmar Waltemath, Stefan Hoops, Sven Sahle, Andreas Dräger, Michael Hucka, Chris J. Myers, Matthias König, Nicolas Le Novère

Publikováno v: Journal of Integrative Bioinformatics
Journal of Integrative Bioinformatics, 2019, 16 (2), ⟨10.1515/jib-2019-0021⟩
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP
Hucka, M, Bergmann, F T, Chaouiya, C, Dräger, A, Hoops, S, Keating, S M, König, M, Novère, N L, Myers, C J, Olivier, B G, Sahle, S, Schaff, J C, Sheriff, R, Smith, L P, Waltemath, D, Wilkinson, D J & Zhang, F 2019, ' The Systems Biology Markup Language (SBML) : Language Specification for Level 3 Version 2 Core Release 2 ', Journal of Integrative Bioinformatics, vol. 16, no. 2, pp. 1-183 . https://doi.org/10.1515/jib-2019-0021
Journal of Integrative Bioinformatics, Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2019, 16 (2), ⟨10.1515/jib-2019-0021⟩
Journal of Integrative Bioinformatics, Vol 16, Iss 2 (2019)
Journal of Integrative Bioinformatics, 16(2), 1-183. Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.)

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::54b02cdc918e9881621fb69d8250a015
https://hdl.handle.net/1871.1/e275d6d3-5821-4d80-adcd-4beffae06285