Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022
- Matthias König, Padraig Gleeson, Martin Golebiewski, …, Björn Sommer, Dagmar Waltemath, Falk Schreiber
- J Integr Bioinform, 10.1515/jib-2023-0004
Nine best practices for research software registries and repositories
- Daniel Garijo, Hervé Ménager, Lorraine Hwang, …, Michael Hucka, Thomas Morrell, Alice Allen
- None, 10.7717/peerj-cs.1023
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1
- Lucian P Smith, Stuart L Moodie, Frank T Bergmann, …, Maciek J Swat, Darren J Wilkinson, Michael Hucka
- J Integr Bioinform, 10.1515/jib-2020-0018
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2
- Fengkai Zhang, Lucian P Smith, Michael L Blinov, …, Bin Hu, Michael Hucka, Martin Meier-Schellersheim
- J Integr Bioinform, 10.1515/jib-2020-0015
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
- Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, …, Melanie I Stefan, Ulrike Wittig, Chris J Myers
- J Integr Bioinform, 10.1515/jib-2020-0005
Specifications of standards in systems and synthetic biology: status and developments in 2020
- Falk Schreiber, Björn Sommer, Tobias Czauderna, …, Chris Myers, David Nickerson, Dagmar Waltemath
- J Integr Bioinform, 10.1515/jib-2020-0022
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
- Natalie J Stanford, Martin Scharm, Paul D Dobson, …, Carole Goble, Pedro Mendes, Jacky Snoep
- Methods Mol Biol, 10.1007/978-1-4939-9736-7_17
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
- Michael Hucka, Frank T Bergmann, Claudine Chaouiya, …, Dagmar Waltemath, Darren J Wilkinson, Fengkai Zhang
- J Integr Bioinform, 10.1515/jib-2019-0021
FAIRsharing as a community approach to standards, repositories and policies
- Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, …, Massimiliano Izzo, Allyson L Lister, Milo Thurston
- Nat Biotechnol, 10.1038/s41587-019-0080-8
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
- Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, …, Bernhard Ø Palsson, Ines Thiele, Ronan M T Fleming
- Nat Protoc, 10.1038/s41596-018-0098-2
Harmonizing semantic annotations for computational models in biology
- Maxwell Lewis Neal, Matthias König, David Nickerson, …, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
- Brief Bioinform, 10.1093/bib/bby087