Microbial community modeling based on cobrapy.
Project description
micom is a Python package for metabolic modeling of microbial communities developed in the Human Systems Biology Group of Prof. Osbaldo Resendis Antonio at the National Institute of Genomic Medicine Mexico and the Gibbons Lab at the Institute for Systems Biology.
micom allows you to construct a community model from a list on input COBRA models and manages exchange fluxes between individuals and individuals with the environment. It explicitly accounts for different abundances of individuals in the community and can thus incorporate data from 16S rRNA sequencing experiments. It allows optimization with a variety of algorithms modeling the trade-off between egoistic growth rate maximization and cooperative objectives.
Attribution
Micom is described in a recent preprint that you can cite. If you have any questions contact us at oresendis (at) inmegen.gob.mx. Thanks :smile:
Installation
micom is available on PyPi and can be installed via
pip install micomGetting started
Documentation can be found at https://micom-dev.github.io/micom .
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file micom-0.9.9.tar.gz.
File metadata
- Download URL: micom-0.9.9.tar.gz
- Upload date:
- Size: 105.4 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.2 CPython/3.6.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
fb0384f9f85d6bca4750fbe3699333826d4d09ead70887d50e387c56bc3cf1cd
|
|
| MD5 |
8786f29b4df429eaf7a74e6052bd58b3
|
|
| BLAKE2b-256 |
08684ae3ae6c772489075393f217cd30302502c3f5866256d8f67697c29143f8
|
File details
Details for the file micom-0.9.9-py2.py3-none-any.whl.
File metadata
- Download URL: micom-0.9.9-py2.py3-none-any.whl
- Upload date:
- Size: 112.7 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.0.1 requests-toolbelt/0.9.1 tqdm/4.32.2 CPython/3.6.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
c63c359ba090d1d4bd10cc0cc15de11a44efded9a5a490f09b0d12736124ea0f
|
|
| MD5 |
cf25daf703f577f78e109fb92d53bff1
|
|
| BLAKE2b-256 |
8e52999511713c00a8baafa27b2ae932c77e74fde34c91a7629c63cb9eaf97f8
|
