Metabolic 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].
• Publications:
  • Martyushenko N, Almaas E. BMC Bioinformatics 20:56 (2019)
  • Martyushenko N, Almaas E. Bioinformatics, btz761 (2019).

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.
  • Matlab function: [AutoKEGGREc.m]
  • Manual (PDF) for the function: [AutoKEGGREc Manual]
• 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).
  • Analysis of permissible uncertainty in growth coefficients (executed from shell): [RAMP_coefficients.tar.gz]
  • RAMP calculation of gene knockouts: [RAMP_GeneKO.tar.gz]
  • RAMP vs. FBA flux comparisons with experimental data: [RAMP_FBA_fluxcomparison.tar.gz]
• Publication: MacGillivray, Ko, Gruber et. al. Scientific Reports (2017).

Combination of gene-expression data and metabolic modeling – gxFBA

• COBRA toolbox function for analyzing gene-expression data on a genome-scale metabolic model.
• Download (v.1.3; 29/9/2014): [gxFBA.m]
• Download: [gxFBA_example.xml]
• Publication: Navid, Almaas. BMC Syst. Bio. (2012)

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

CryptFind – a method for identifying cryptic/pseudo genes using FBA

• perl script for identifying cryptic / pseudo genes in a genome-scale metabolic model.
• Download: [CryptFind.tar.gz]
• Publication: Navid, Almaas. Mol. BioSyst. (2009)
• python script by Snorre Sulheim: [cryptFind.py]