Micom input file

[Satyajitbeura]

Sir, I have three manually curated models. I want to make community modeling through micom but fails to import my models to micom. please help me out.

Thank you

[cdiener]

Hi, welcome to MICOM. What does your input DataFrame look like and what errors are you getting?

[Satyajitbeura]

Respected sir, I'm new in this field. I have 3 models with me. I just made one .xls file and now I want to lord that file to the micom for community modeling. What are command lines I should use? Thanking you, Satyajit Beura

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On Tue, Oct 5, 2021, 09:56 Christian Diener ***@***.***> wrote: Hi, welcome to MICOM. What does your input DataFrame look like and what errors are you getting? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#62 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AV3MPMEUGGNXQ2ZVA5C6TMDUFJ453ANCNFSM5FGVP6EA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[cdiener]

Understood. For your Excel file make sure that you have the following column names in your table: id, file, abundance, sample_id. There should be 3 rows (excluding headers) that contain the following information:

• id: A name for the model that should not contain spaces.
• file: The path to the model file (*.xml file)
• abundance: The abundance of that organism in the sample. If you want each organism in the same abundance enter 1 here for each row.
• sample_id: It sounds you are only simulating a single sample so but the same name here for each row, for instance, "sample 1".

Now open a python session or a notebook and run the following:

import pandas as pd

table = pd.read_excel("[MY EXCEL FILE].xlsx")

You can have a look at the table afterwards to check everything was read correctly. You might get errors from pandas that ask you to install additional packages so just install those. After that you can use the table to run through the high-level MICOM analyses as described in the documentation, for instance by starting with:

from micom.workflows import build

manifest = build(table, out_folder="models", model_db=None, threads=2)

If you want a more thorough introduction to running through a MICOM analysis you can also look at our tutorials.

[Satyajitbeura]

Thank you sir for your help. sir, I want to design a diet (medium) instead of taking the western diet as a medium for my community model. How can I do that?

[cdiener]

You would have to identify which metabolites are present in the diet and how much of them is there. Then you need to map them to the respective ID system. For instance, if you use the AGORA database you can use https://www.vmh.life/#microbes/metabolites to map metabolite names to IDs.