GEM Random Sampling
Input model1:
[?]
Input model2:
[?]
T scores for change in gene expression:
[?]
Degrees of Freedom (T-scores)
[?]
Fileformat
[?]
Email (Optional)
[?]

Run

Degrees of freedom

Number of reactions in the models.

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E-mail

Enter your E-mail Id for getting the result in your mail.

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File format

You can select between Excel, SBML in Raven or Cobra format or simply choose Autodetect and the tool will automatically detect the uploaded format.

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Input model 1

The input is a GEM in Excel or SBML format (Cobra or Raven format). To see some examples of the format go to Models/Download. This model should be simulating any condition, i.e. aerobic or anaerobic different to model 2.

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Input model 2

The input is a GEM in Excel or SBML format (Cobra or Raven format). To see some examples of the format go to Models/Download. This model should be simulating any condition, i.e. aerobic or anaerobic different to model 1.

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T scores

A text file with the T-scores describing the changes in gene expression.

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RANDOM SAMPLING

In this function, two models showing different conditions are compared returning a number of random solutions for the model. The solutions are generated by maximizing (with random weights) for a random set of three reactions. For reversible reactions it randomly chooses between maximizing and minimizing.

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General Instructions

Click "[?]" to display instructions here, or navigate through the links below.

Tool description
Input instructions
Output instructions

Example files to download

Model file1
Model file2
T-value file
In this example the degrees of freedom is 1632

Click Load Example files and hit Run

Input Instructions

For this function, two models showing different conditions should be uploaded along with the T-scores for change in gene expression.

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Output description

This tool returns a number of random solutions for the model. The solutions are generated by maximizing (with random weights) for a random set of three reactions.

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Online tools powered by RAVEN

Citations
1) Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013) The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum. PLoS Comput. Biol., 9, e1002980.
A * indicates that these authors contributed equally to the work.