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I am trying to predict interactions between microbes using the simulatePairwiseInteractions function with my models created through CarveMe.
I modified the 'HighFiberDiet_Oxygen' condition provided …
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#### Problem description
> With the memote API it would be quite simple to integrate memote into a pipeline that automatically addresses erroneous test results. There is a plethora of tools availab…
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#### Problem description
> I don't believe this framework is general enough to be appropriate for the wide range of modeling tools that the community will develop. For example, Pathway Tools uses a…
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Quick question – are the models generated by this tool meant to be simulation ready? I am running multiple model reconstructions and all of them do not supply biomass requirements and hold no growth. …
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Problem: when using MATLAB 2019a with CPLEX 12.10 on Windows 10x64 [enterprise and professional SKUs], generateMexFastFVA.m produces the following warning and error:
```
>> generateMexFastFVA
> Th…
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>> sedUnix('CDT1.faa');
>> modelaceto = importModel('RehMBEL1391_sbml_L3V1.xml');
WARNING: The following metabolites are never used in a reaction:
fol_c
WARNING: The following genes are not a…
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Just found that a cobrapy model defines the property `boundaries` whereas the pathway predictor expects `exchanges`. We are thinking about implementing further methods/properties here (https://github.…
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This is a list of comments and suggestions on existing toolbox READMEs.
Related review issues:
#50 , #52
### Main
- indicate which tools are not octave compatible
- list required matlab/octate …
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Hello,
I have a problem running the following command : `m2m recon -g rocks -o rocks_m2m -c 16`
Here is the error message :
```
######### Running metabolic network reconstruction with Pathway T…
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@edkerk @BenjaSanchez , Dear both, in next phase, I want to focus on adding new GPRs into model. The followed is the detailed step:
1) Add new GPRs by merge of ise926, yeast7.6 and ito980;
2) Add ne…