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.
- BiGMeC: Biosynthetic Gene cluster Metabolic pathway constructor
- The BiGMeC pipeline makes a draft reconstruction of the metabolic pathway associated with a non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) biosynthetic gene cluster. The output can be readily incorporporated into a genome-scale metabolic model.
- Written as Jupyter notebook.
- Available for download on GitHub: [BigMeC]
- Publication: Sulheim S, Fossheim FA, Wentzel A, Almaas E. BMC Bioinformatics 22, 81 (2021).
- Adjustable algal chloroplast plug-and-play for genome-scale modeling
- A standardized chloroplast model, iGR774, that consists of 788 reactions, 764 metabolites, and 774 genes. The model can (separately) mimick the chloroplast metabolism of three photosynthetic microalgae–Nannochloropsis gaditana, Chlamydomonas reinhardtii and Phaeodactylum tricornutum.
- We have developed multiple software tools for working with this plug-and-play model in the COBRA Toolbox for MATLAB. This includes tools for connecting the chloroplast model to a genome-scale metabolic reconstruction in need of a chloroplast, for switching the model between running in different organism modes, and for expanding it by introducing more reactions either related to one of the current organisms included in the model, or to a new organism.
- Publication: Røkke GB, Hohmann-Marriott MF, Almaas E. PLoS ONE 15(2): e0229408 (2020).
- Complete and updated file package on GitHub: [Link]
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