Specifying a new growth medium in an AGORA model

[Laura Confalonieri]

Hi all,

I am a PhD student new to CobraPy. I am trying to specify a new growth medium (LB from carveme/media_db.tsv at master · cdanielmachado/carveme · GitHub) into Staph. epi ATCC 12228 AGORA model (AGORA/Staphylococcus_epidermidis_ATCC_12228.xml at master · VirtualMetabolicHuman/AGORA · GitHub).

I have read the docs and also got a table for LB in .ods format with metabolite names, exchange reactions and bounds from an experienced user; however, I have not yet figured out how to input it in the .xml file using CobraPy. 

Could you please send me some suggestions?

Many thanks and best wishes,

Laura

[Greg Medlock]

Hi Laura,

After you load the xml file into cobrapy as a model, you need to change find the exchange reaction in the model corresponding to each exchange reaction in your spreadsheet; then, set the lower bound of the reaction to -1*limit (where limit is the value from the "limit" column in the spreadsheet; exchange bounds are defined as negative for uptake and positive for secretion).

Alternatively, you can use the model.medium helper for this. See the documentation here: https://cobrapy.readthedocs.io/en/latest/media.html.

One caveat to think about: your model from AGORA might not have all of the exchange reactions defined in the LB.xlsm file.

Greg 

[Laura Confalonieri]

Hi Greg,

Thank you very much for your prompt reply. 

Given the complexity of the .xml file, it might be better for me not to edit it directly. 

I did try to re-specify the growth medium in CobraPy as indicated in the docs, using the model.medium helper. However, I might not have done this correctly.

It is clear to me how to drop a single reaction (e.g. oxygen exchange), but not how to replace the growth medium completely.

Shall I repeat the following steps for all the reactions which are included in the AGORA model:

medium = model.medium 

medium["EX_co2_e"] = 0.0

model.medium = medium 

model.medium

then redefine all the reactions and limits as listed in the LB.xls file:

medium = model.medium 

medium["EX_adn_e"] = 1000.0

model.medium = medium 

model.medium

Is there an online course or tutorial that you would recommend?

Thanks again and best wishes,

Laura