Question on GIMME

[Sudipta Dash]

Hi everyone!

I am new to COBRA toolbox and I have a very basic question.

While using GIMME, in the COBRA tutorial (https://opencobra.github.io/cobratoolbox/latest/tutorials/tutorialIO.html),:

load('dataEcoli');    This generates the Ecoli gene expression data.

But load(['options_methods' filesep options]) generates 'expressionRxns', 'threshold' and 'solver' fields.

How is this 'expressionRxns' data calculated?

1) I am working on a different model and I have the gene expression data for that. I can edit the 'expression' file in the workspace (having 'gene', 'rawValue' and 'value'). But I am stuck at ' expressionRxn'.

Attaching a screenshot of the line where I am stuck.

2) Also, is there a way to integrate protein expression data?

Thanks,

Sudipta

[Ronan M.T. Fleming]

[expressionRxns, parsedGPR, gene_used, signifRxns] = mapExpressionToReactions(model, expressionData, minSum)                                          
% Determines the expression data associated to each reaction present in
% the model

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[Sudipta Dash]

Thanks Ronan. It worked.

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Sudipta Dash

Student | M.Tech

Biotechnology & Biochemical Engineering

Indian Institute of Technology, Kharagpur

Email: sudipt...@gmail.com 

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