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GonghuaLi / FastMM

FastMM: an ultra-efficient toolbox for constraint-based metabolic modeling
GNU General Public License v3.0
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can FastMM be installed on MacOs system? #4

Open DingTin opened 1 year ago

DingTin commented 1 year ago

Sorry to interrupt, but I got a problem when I try to install FastMM. The problem was that the installation requires Simulink Real-Time which only supports the platforms of Windows and Linux. So I want to ask whether FastMM could be used on MacOS. If not, is there a possible way to avoid using FastMM in GPMM since FastMM is optimal for GPMM.

GonghuaLi commented 1 year ago

Thank you for your interest in GPMM and FastMM. Unfortunately, FastMM is not compatible with MacOS in its current version. However, you can easily disable FastMM in GPMM by changing the GPMM option in “pars.txt” file.

In “pars.txt” file, set:

isFastMM = ‘no’;

Please note that GPMM will run much slower without FastMM."

DingTin commented 1 year ago

Thanks for this valuable suggestion. I set isFastMM = ‘no’ but it still could not work. With the errors below:

image

I saw that there was an issue in GPMM mentioned something similar so I followed the instructions you gave under that issue, I found the problem occurred in the last step "optimizeCbModel(Recon3)" (since I would not use FastMM so I skip step 3), and the error occurred as below. Would there be a possible way to solve that?

image
GonghuaLi commented 1 year ago

This issue is because of your the wrong install of COBRA 3.0 but not because of GPMM.

->

  1. Please use our pre-compiled version of cobra: https://github.com/GonghuaLi/extern_tools/blob/main/cobratoolbox-3.0.4_precompiled.rar.

  2. Please install cplex solver and add cplex to matlab path

  3. In FastMM directory: Install FastMM in matlab and run "Insatall", add FastMM to the matlab path, add the . /bin file into env-Path, export PATH="~~your fastamm path/bin:$PATH"

    1. If you are running in linux, set following env: export PATH="your matlab path/R20??/bin:$PATH" export PATH="your cplex path/Cplex/cplex/bin/x86-64_linux:$PATH" export PATH="your matlab path/R20??/bin/glnxa64:$PATH" export PATH="your FastMM path/bin:$PATH"

  4. Test in GPMM directory: load('./data/Recon3_v1.mat') changeCobraSolver('cplex') fluxes = FastMM_FVA(Recon3) optimizeCbModel(Recon3)

DingTin commented 1 year ago

Thanks a lot, it turned out to be that I didn't install cobra successfully. Right now it works well. But sorry for another question, I have used the "exchange_rxns_white_blood_final_recentmodel.txt" as nutrition uptake file but all the results of the out files are "0". So I'm wondering if I want to use GPMM on certain tissues or tumors of certain tissues, do I need to get the tissue-metabolite file of certain types？Sorry for taking up your time.