Basic Cobra Methods

[Madhuri Belekar]

Hello,

I am Madhuri Belekar, as a new in CobraPy I am trying to solve basic cobra methods given in attached supplementary tutorial. In this tutorial all the example are executed in cobraToolbox and I am trying to execute it in CObraPy. But got stuck at Example 8,9 and 10 given in the attached tutorial. It would be very helpful if you will give some suggestion to write the code in CobraPy.

Thanks in advance. 

 

Regards,

Madhuri Belekar

C/O Dr. Anu Raghunathan

CEPD

[Moritz Beber]

Hi Madhuri,

Welcome to COBRApy! Since you are beginning on your journey, I highly recommend that you read through the online documentation (https://cobrapy.readthedocs.io/). It can be a bit daunting but just work through some of the topics that seem appealing to you.

Specifically, for example 8 you will need:

• https://cobrapy.readthedocs.io/en/latest/simulating.html#Running-FVA
• https://cobrapy.readthedocs.io/en/latest/deletions.html

For 9 there are two ways to solve the problem:

• Every metabolite has an attribute 'reactions' which is the set of reactions the metabolite participates in.
• You can also convert the model to a stoichiometric matrix with a helper function (https://cobrapy.readthedocs.io/en/latest/autoapi/cobra/util/index.html?highlight=stoichiometric_matrix#cobra.util.create_stoichiometric_matrix) and use numpy functions to create code very similar to the Matlab one.
• Essentiality is covered in above topic on deletions.

Regarding 10:

• Flux sampling is described in https://cobrapy.readthedocs.io/en/latest/sampling.html

All the best,

Moritz

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[Madhuri Belekar]

I will work on the above things. Thank You so much for your valuable suggestions.

Regards,

Madhuri Belekar

C/O Dr. Anu Raghunathan

CEPD

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