Materials and installation#

Software#

The protocol runs in MATLAB, together with software to reconstruct and analyse GEMs. The published protocol states MATLAB R2013b or later, and RAVEN (MATLAB) describes the requirements of RAVEN 3. No extra MathWorks toolboxes are required. Most of the software is open source or available under an academic licence.

Software

Dependency

Source

MATLAB

Licence

https://mathworks.com/products/matlab.html

RAVEN

libSBML, solver

CompMetEng/RAVEN

COBRA

MATLAB

opencobra/cobratoolbox

Gurobi

Licence

https://www.gurobi.com/products/gurobi-optimizer/

libSBML

MATLAB

http://sbml.org/Software/libSBML

  • RAVEN drives the reconstruction.

  • libSBML imports and exports the community-standard SBML (.xml) format.

  • Simulation needs a linear-programming solver. The protocol uses Gurobi (free academic licence). RAVEN also runs on the open-source GLPK solver that it bundles.

Installation describes the complete setup.

Files#

Homology-based reconstruction needs files for the target organism and for the template organisms.

File type

Usage

Organism

Source

GEM (SBML)

Template network

S. cerevisiae

yeast-GEM v8.3.0

GEM (SBML)

Template network

R. toruloides

rhto-GEM v1.1.2

Protein FASTA

BLAST

S. cerevisiae

hanpo-GEM data/genomes/sce.faa

Protein FASTA

BLAST

R. toruloides

hanpo-GEM data/genomes/rhto.faa

Protein FASTA

BLAST

H. polymorpha

JGI Hanpo2

DNA FASTA

Biomass curation

H. polymorpha

NCBI GCF_001664045.1_Hanpo2

GenBank

Biomass curation

H. polymorpha

NCBI GCF_001664045.1_Hanpo2

The target organism needs a protein FASTA file of all proteins in its genome, a DNA FASTA file for the nucleotide ratios and a GenBank file for the ribonucleotide ratios. Each template needs a protein FASTA file and a model file in SBML format.

Matching identifiers

For automatic gene matching, the protein FASTA file and the model file of each template must use the same gene identifiers.

The hanpo-GEM repository provides all required files for H. polymorpha, and a clone of it gives a local copy.

Literature data#

Known metabolic behaviour of the target organism improves the quality of the model: the macromolecule fractions of the biomass, essential and non-essential genes, usable nutrient sources and the growth rate. A short literature search gives the total protein, lipid and carbohydrate content for H. polymorpha, which sets the stoichiometric coefficients of the biomass (Biomass composition). Values from related organisms can replace missing organism-specific data.

Installing RAVEN#

After obtaining the software and files, install RAVEN (Installing RAVEN). pathtool adds the RAVEN folder to the MATLAB path, and RAVEN bundles libSBML. Gurobi is added to the path by its own MATLAB integration (RAVEN (MATLAB)), and verify the installation with:

checkRaven

Installing RAVEN shows the output of a successful run.

Troubleshooting

  • Problem: checkRaven reports Fail for Export Excel format.

  • Possible reason: The Text Analytics Toolbox of MATLAB can conflict with Excel files.

  • Solution: Uninstall the Text Analytics Toolbox. Support is available through the RAVEN issues page.