fbc_curation_matlab contains MATLAB/COBRA helpers for checking reproducibility of fbc models.
- The main file for running fbc_curation in MATLAB is present in
run_FROG.mfrom thesrc/curatordirectory - An additional function GetMD5 (Copyright (c) 2017-2019, Jan Simon). This is required to generate MD5 signature for model files.
- Clone the repository to your system.
- Extract the folders.
- Add the folders to you MATLAB path using
addpath(genpath(path to fbc_curation_matlab)) - Installation is complete!
Step 1: Initialize CobraToolBox using the command
initCobraToolbox
fbc_curation_matlab uses functions from CobraToolBox. So it has to be initialized every time MATLAB is started. Running this command once every session is enough.
Step 2: Running FBC-curation
run_FROG(path to model)
Step 2 with FBC Curator name
run_FROG(path to model, curator_name)
This command will start the fbc curation and FROG report files will be available in the current directory as COMBINE archive format. It is basically a zip file with all the report files in a specific file structure.
To make sure if the tool is installed properly, run the following command.
run_FROG(path to fbc_curation_matlab/src/fbc_curation/examples/models/e_coli_core.xml)
If the command runs and give the following output without any error. The installation is successfull.
Using gurobi solver.
Loading model from e_coli_core.xml... Elapsed time is 3.178258 seconds.
Created directory ./FROG successfully.
[00] Wrote Metadata details to FROG/metadata.json.
[01] Wrote FBA objective results to FROG/01_objective.tsv.
[02] Wrote FVA results (optPercentage = 100) to FROG/02_fva.tsv.
Single gene deletion analysis in progress ...
100% [........................................]
[03] Wrote gene deletion results to FROG/03_gene_deletion.tsv.
Single reaction deletion analysis in progress ...
100% [........................................]
[04] Wrote gene deletion results to FROG/04_reaction_deletion.tsv.
Total Elapsed time is 4.759139 seconds.
Created COMBINE archive file ./e_coli_core.zip successfully.
e_coli_core.zip file renamed to ./e_coli_core.omex successfully.
>> run_FROG('fbc_curation_matlab-main/src/fbc_curation/examples/models/iJR904.xml', 'Karthik Raman');
Using glpk solver.
Loading model from fbc_curation_matlab-main/src/fbc_curation/examples/models/iJR904.xml... Elapsed time is 39.618113 seconds.
Created directory ./FROG successfully.
FROG curator name:Karthik Raman
[00] Wrote Metadata details to FROG/00_metadata.json.
[01] Wrote FBA objective results to FROG/01_objective.tsv.
[02] Wrote FVA results (optPercentage = 100) to FROG/02_fva.tsv.
Single gene deletion analysis in progress ...
100% [........................................]
[03] Wrote gene deletion results to FROG/03_gene_deletion.tsv.
Single reaction deletion analysis in progress ...
100% [........................................]
[04] Wrote gene deletion results to FROG/04_reaction_deletion.tsv.
Total Elapsed time is 111.763478 seconds.
Created COMBINE archive file ./iJR904.zip successfully.
iJR904.zip file renamed to ./iJR904.omex successfully.
>>
See the files in fbc_curation/examples/results/ for how the output files look like.
- In macos systems, you might encounter some security prompts saying 'The system cannot open GetMD5.mexmaci64 file as the devoluper is unknown'. This can be solved by going into System preferences > Security & Privacy > General tab > allow the GetMD5.mexmaci64 file in 'allow apps downloaded from' section. Now, running the
run_FROGwill generate the output successfully.
fbc_curation_matlab source is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license you choose to use the software under.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
- The author thanks the entire SBML community, particularly the SBML Team, the SBML 2020 HARMONY & COMBINE participants for useful discussions. Specials thanks to Matthias König and his excellent
fbc-curationPython Package, Brett Olivier and Rahuman Sheriff. - Initiative for Biological Systems Engineering
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI)
© 2020 Karthik Raman