pyfba
A python implementation of flux balance analysis to model microbial metabolism
Science Score: 28.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Repository
A python implementation of flux balance analysis to model microbial metabolism
Basic Info
- Host: GitHub
- Owner: linsalrob
- License: mit
- Language: Python
- Default Branch: master
- Homepage: http://linsalrob.github.io/PyFBA/
- Size: 11.3 MB
Statistics
- Stars: 27
- Watchers: 5
- Forks: 13
- Open Issues: 9
- Releases: 2
Metadata Files
README.md
PyFBA
A python implementation of flux balance analysis to model microbial metabolism. Read more ...
About PyFBA
PyFBA is a Python flux-balance-analysis package that allows you to build models from genomes, gapfill models, and run flux-balance-analysis on that model. The aim of PyFBA is to provide an extensible, python-based platform for FBA work.
PyFBA is being developed by Daniel Cuevas, Taylor O'Connell, and Rob Edwards in Rob's bioinformatics group initially at San Diego State University and now at Flinders University. Amazing help was also provided by the developers of the ModelSEED, in particular Janaka Edirisinghe, Chris Henry, Ross Overbeek and others at Argonne National Labs.
You can read more about PyFBA on our github.io pages.
Installing PyFBA
PyFBA is available in bioconda and we recommend installing it that way. It's what we use!
commandline
conda create -n pyfba -c bioconda pyfba
conda activate pyfba
pyfba -v
pyfba help
There are other options described in the installation documents, but just use conda!
Getting Started with PyFBA
Once you have installed PyFBA, you will most likely want to build a model from a genome, gap fill that model, and test it for growth on different media. We have detailed instructions that walk you through the step-by-step procedures that you need to use to run flux balance analysis on your own genome.
Citing PyFBA
Please use the command:
commandline
pyfba citations
to get the citations for PyFBA. They are available in plain text and bibtex format, please let us know if you would like other formats!
Copyright and License
PyFBA is copyright Daniel Cuevas, Taylor O'Connell, and Rob Edwards, and is released under the MIT license.
Owner
- Name: Rob Edwards
- Login: linsalrob
- Kind: user
- Location: Adelaide, Australia
- Company: Flinders University
- Website: http://edwards.flinders.edu.au/
- Twitter: linsalrob
- Repositories: 31
- Profile: https://github.com/linsalrob
Professor of CS and Biology Writing bioinformatics code to study viruses, phages, and metagenomes.
Citation (CITATION.md)
# If you use PyFBA please cite: [Cuevas DA, Garza D, Sanchez SE, Rostron J, Henry CS, Vonstein V, Overbeek RA, Segall A, Rohwer F, Dinsdale EA, Edwards RA. 2014. Elucidating genomic gaps using phenotypic profiles. F1000Research. 3:210 doi: 10.12688/f1000research.5140.2](https://f1000research.com/articles/3-210) [Cuevas, Daniel A., Janaka Edirisinghe, Chris S. Henry, Ross Overbeek, Taylor G. O’Connell, and Robert A. Edwards. 2016. From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. Frontiers in Microbiology 7 (June): 907.](http://journal.frontiersin.org/article/10.3389/fmicb.2016.00907/full) The model SEED is used extensively by PyFBA and its citation is [Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. 2010. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28:977–982](https://www.nature.com/articles/nbt.1672)
GitHub Events
Total
- Watch event: 4
Last Year
- Watch event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Rob Edwards | r****s@g****m | 715 |
| dacuevas | d****8@g****m | 64 |
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 10
- Total pull requests: 4
- Average time to close issues: about 4 hours
- Average time to close pull requests: 7 months
- Total issue authors: 9
- Total pull request authors: 2
- Average comments per issue: 0.6
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- linsalrob (2)
- thh32 (1)
- liaochen1988 (1)
- ozelnu (1)
- rmueller35 (1)
- annazhukova (1)
- SimonPPf (1)
- dacuevas (1)
- Angela-Source-Lab (1)
Pull Request Authors
- slevi105 (3)
- linsalrob (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 44 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 20
- Total maintainers: 2
pypi.org: pyfba
A Python implementation of flux balance analysis
- Homepage: http://linsalrob.github.io/PyFBA/
- Documentation: https://pyfba.readthedocs.io/
- License: The MIT License (MIT)
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Latest release: 2.62
published over 4 years ago
Rankings
Dependencies
- sphinx-better-theme ==0.1.4
- beautifulsoup4 *
- glpk *
- jupyter *
- lxml *
- nose *
- python-libsbml *
- beautifulsoup4 *
- glpk *
- importlib_resources *
- jupyter *
- lxml *
- nose *
- python-libsbml *