Many of the programs or data files are intended to be used together with the freely available COBRA toolbox for Matlab or COBRApy for python. On this page, we host the latest updated / tested version of the code, which may differ from versions accessible elsewhere.
ModelExplorer – software for visual inspection and testing of GEMs
- ModelExplorer2.0 also contains the fast ErrorTracer algorithm for consistency checking and identification of inconsistency origins.
- Executable for the software, written in C++:
- Tested on Linux – Ubuntu 16.04 LTS, 17.04, 17.10, 18.04 LTS and Manjaro 17.1.1. ModelExplorer2.1 with user manual: [ModelExplorer2.1_Linux.zip]
- Tested on Windows 8.1 and 10, 64bit, ModelExplorer2.1 with user manual: [ModelExplorer2.1_win64.zip]
- The software is also available on [GitHub].
- Practical demonstrations of the software are also available on [YouTube].
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
- Function for the Matlab COBRA Toolbox v3.0, written in Matlab and tested on Matlab 2017a, 2017b, 2018a.
- Publication: Karlsen E, Schulz C, Almaas E, BMC Bioinformatics (2018).
Robust optimization of Metabolic Pathways (RAMP)
- Matlab scripts used to make RAMP calculations. Results produced on the following platform: Ubuntu 14.04LTS with Matlab R2015b and Gurobi versions 6.0.5 and 7.0.1 (linux64).
- Publication: MacGillivray, Ko, Gruber et. al. Scientific Reports (2017).
Combination of gene-expression data and metabolic modeling – gxFBA
Yersinia genome-scale metabolic reconstructions
- SBML-formatted genome-scale manually curated reconstructions. Tested on the COBRA toolbox.
- Y. pestis strain Mediaevalis 91001: [Yp_iAN840m.xml]
- Publication: Navid, Almaas. Mol. BioSyst. (2009)
- (To be available) :
- Y. pestis strain Kim: Yp_iAN821.xml
- Y. pestis strain Orientalis: Yp_iAN825o.xml
- Y. pestis strain Antiqua: Yp_iAN873a.xml
- Y. pseudotuberculosis: Yps_iAN859.xml