Science Score: 13.0%
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○codemeta.json file
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✓DOI references
Found 2 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary
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Repository
A Qiime plugin for MICOM.
Basic Info
- Host: GitHub
- Owner: micom-dev
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://micom-dev.github.io/q2-micom
- Size: 67.6 MB
Statistics
- Stars: 10
- Watchers: 2
- Forks: 6
- Open Issues: 5
- Releases: 11
Topics
Metadata Files
README.md
A QIIME 2 plugin for MICOM.
Installation
You will need an existing QIIME 2 environment. Follow the instructions on (how to install QIIME 2) otherwise. q2-micom is compatible with all QIIME 2 distributions.
Let's assume that environment was called qiime2-2024.2 for all further steps.
Add q2-micom to the QIIME 2 environment
This will be the same step for any supported QIIME 2 version but will vary depending on your operating system (similar to the normal QIIME 2 installation).
```bash wget https://raw.githubusercontent.com/micom-dev/q2-micom/main/q2-micom.yml conda env update -n qiime2-2024.2 -f q2-micom.yml
OPTIONAL CLEANUP
rm q2-micom-*.yml ```
Finally, you activate your environment.
bash
conda activate qiime2-2024.2
q2-micom will now install an open source solver that can be used with MICOM. If you use MICOM
regularly we do recommend to obtain an academic license for CPLEX or Gurobi which will be faster.
Install a faster solver (recommended but optional)
CPLEX
QIIME 2 versions before 2021.4 are only compatible with CPLEX 12.10 or earlier (later version require at least Python 3.7).
After registering and downloading the CPLEX studio for your OS unpack it (by running the provided installer) to a directory of your choice (we will assume it's called ibm).
Now install the CPLEX python package into your activated environment:
bash
pip install ibm/cplex/python/3.8/x86-64_linux
Substitute 3.8 with the Python version in your QIIME 2 environment, 3.6 for QIIME 2 up to 2021.2 and 3.8 for QIIME 2 2021.4 and newer.
Substitute x86-64_linux with the folder corresponding to your system (there will only be one subfolder in that directory).
Gurobi
Gurobi can be installed with conda.
bash
conda install -c gurobi gurobi
You will now have to register the installation using your license key.
bash
grbgetkey YOUR-LICENSE-KEY
Finish your installation
If you installed q2-micom in an already existing QIIME 2 environment, update the plugin cache:
bash
conda activate qiime2-2024.2 # or whatever you called your environment
qiime dev refresh-cache
You are now ready to run q2-micom!
Usage
Here is a graphical overview of a q2-micom analysis.
The best way to get started is to work through the community tutorial.
Supported QIIME 2 versions
q2-micom is tested against:
- the current QIIME 2 version
- the previous version
It should also work with
- the development version
However, this may occasionally break. Check here for the current status.
References
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
mSystems 5:e00606-19
https://doi.org/10.1128/mSystems.00606-19
Owner
- Name: micom-dev
- Login: micom-dev
- Kind: organization
- Website: https://micom-dev.github.io/micom
- Repositories: 3
- Profile: https://github.com/micom-dev
Developers of the microbial community modeling package micom.
GitHub Events
Total
- Delete event: 7
- Issue comment event: 10
- Push event: 15
- Pull request review event: 1
- Pull request event: 15
- Fork event: 2
- Create event: 9
Last Year
- Delete event: 7
- Issue comment event: 10
- Push event: 15
- Pull request review event: 1
- Pull request event: 15
- Fork event: 2
- Create event: 9
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Christian Diener | c****r@g****m | 242 |
| dependabot[bot] | 4****] | 7 |
| Sean Gibbons | s****s@s****g | 6 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 21
- Total pull requests: 36
- Average time to close issues: 4 months
- Average time to close pull requests: 1 day
- Total issue authors: 11
- Total pull request authors: 4
- Average comments per issue: 5.24
- Average comments per pull request: 1.03
- Merged pull requests: 30
- Bot issues: 0
- Bot pull requests: 27
Past Year
- Issues: 0
- Pull requests: 19
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 0
- Pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 14
Top Authors
Issue Authors
- Mechah (8)
- kf-cuanschutz (2)
- afvrbanac (2)
- said3427 (2)
- Zhaoju-Deng (1)
- Hansol-cloud (1)
- mutantjoo0 (1)
- ghost (1)
- TKuehnast (1)
- dependabot[bot] (1)
- cdiener (1)
- cgj-tang (1)
Pull Request Authors
- dependabot[bot] (33)
- cdiener (5)
- Oddant1 (4)
- kf-cuanschutz (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 364 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 22
- Total maintainers: 1
pypi.org: q2-micom
QIIME 2 plugin for metabolic modeling of microbial communities.
- Homepage: https://github.com/micom-dev/q2-micom
- Documentation: https://q2-micom.readthedocs.io/
- License: Apache License 2.0
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Latest release: 0.16.0
published over 1 year ago