Table 1.
Resources for using community standards and software tools
| Resource | Description | Link/references |
|---|---|---|
| MIRIAM* | Minimum Information Required In the Annotation of biochemical Models | (Le Novère et al, 2005) |
| MIASE* | Minimum Information About a Simulation Experiment | (Waltemath et al, 2011) |
| MEMOTE | MEtabolic MOdel TEsts | https://memote.io/ |
| COBRA‐related Google groups | Help for users of COBRApy, the python implementation of COBRA software | https://groups.google.com/forum/#!forum/cobra-pie |
| Help for users of The COBRA Toolbox, the MATLAB implementation of COBRA software | https://groups.google.com/forum/#!forum/cobra-toolbox | |
| Discussion forum of the systems modeling community of the International Society for Computational Biology (ISCB) | https://groups.google.com/forum/#!forum/sysmod | |
| COBRA GitHub | Repository for COBRA software, includes issue and help pages | https://github.com/opencobra/ |
| COMBINE* | Community for coordinating standards for modeling in biology (umbrella organization for SBML, MIRIAM, MIASE, and more) | http://co.mbine.org |
| Kbase Help Board | Issue‐tracking system to aid users to utilize tools and datasets | https://kbase.us/help-board/ |
| SBML Validator* | Tests the syntax and internal consistency of an SBML file | http://sbml.org/Facilities/Validator/ |
| SBML Test Suite* | Conformance testing system to test the degree and correctness of the SBML support provided in a software package | http://sbml.org/Software/SBML_Test_Suite/ |
| BiGG Models | Freely accessible database of GEMs | http://bigg.ucsd.edu |
| BioModels* | Repository of mathematical models of biological and biomedical systems | https://www.ebi.ac.uk/biomodels/ |
| MetaNetX | Platform for accessing, analyzing and manipulating GEMs | https://www.metanetx.org |
| SBO terms* | Systems Biology Ontology terms are a nested classification scheme to group model components | http://www.ebi.ac.uk/sbo/ |
Resources developed for broad applications in computational systems biology are denoted with an asterisk; unmarked resources are specific to the COBRA field.