Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
20 of 27 committers (74.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary
Keywords
bioinformatics
metabolic-models
metabolic-network
python
Last synced: 6 months ago
·
JSON representation
Repository
Curation and analysis of metabolic models
Basic Info
- Host: GitHub
- Owner: zhanglab
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://zhanglab.github.io/psamm/
- Size: 104 MB
Statistics
- Stars: 35
- Watchers: 13
- Forks: 15
- Open Issues: 12
- Releases: 28
Topics
bioinformatics
metabolic-models
metabolic-network
python
Created over 12 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
License
README.rst
PSAMM metabolic modeling tools
==============================
.. image:: https://travis-ci.org/zhanglab/psamm.svg?branch=develop
:alt: Build Status
:target: https://travis-ci.org/zhanglab/psamm
.. image:: https://readthedocs.org/projects/psamm/badge/?version=latest
:alt: Documentation Status
:target: https://readthedocs.org/projects/psamm/?badge=latest
.. image:: https://badge.fury.io/py/psamm.svg
:alt: Package Status
:target: https://pypi.python.org/pypi/psamm
.. image:: https://coveralls.io/repos/zhanglab/psamm/badge.svg?branch=develop&service=github
:alt: Test Coverage Status
:target: https://coveralls.io/github/zhanglab/psamm?branch=develop
.. image:: https://zhanglab.github.io/psamm/doi-flat.svg
:alt: Digital Object Identifier
:target: https://doi.org/10.1371/journal.pcbi.1004732
PSAMM is an open source software that is designed for the curation and analysis
of metabolic models. It supports model version tracking, model annotation, data
integration, data parsing and formatting, consistency checking, automatic gap
filling, and model simulations.
See NEWS_ for information on recent changes. The ``master`` branch
tracks the latest release while the ``develop`` branch is the latest version in
development. Please apply any pull requests to the ``develop`` branch when
creating the pull request.
.. _NEWS: NEWS.md
Install
-------
Use ``pip`` to install (it is recommended to use a Virtualenv_):
.. code:: shell
$ pip install psamm
.. _Virtualenv: https://virtualenv.pypa.io/
Documentation
-------------
The documentation for PSAMM is available at `Read the Docs`_.
.. _Read the Docs: https://psamm.readthedocs.org/
Citing PSAMM
------------
If you use PSAMM in a publication, please cite:
Steffensen JL, Dufault-Thompson K, Zhang Y. PSAMM: A Portable
System for the Analysis of Metabolic Models. PLOS Comput Biol. Public
Library of Science; 2016;12: e1004732. `10.1371/journal.pcbi.1004732`_.
.. _10.1371/journal.pcbi.1004732: https://doi.org/10.1371/journal.pcbi.1004732
Software license
----------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see
Owner
- Name: Zhang Laboratory URI
- Login: zhanglab
- Kind: organization
- Location: Kingston, RI
- Website: http://zhanglab.uri.edu/
- Repositories: 14
- Profile: https://github.com/zhanglab
Dr. Ying Zhang’s laboratory of Computational Molecular Ecology at the University of Rhode Island
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jon Lund Steffensen | j****t@g****m | 1,126 |
| Ke Zhang | k****g@m****u | 277 |
| Keith Dufault-Thompson | k****7@m****u | 211 |
| Chris Powers | c****0@m****u | 80 |
| esameth | e****1@g****m | 63 |
| JingWang | w****u@g****m | 59 |
| freestraws | s****1@g****m | 37 |
| kelxy14 | k****t@m****u | 36 |
| spikeliu | l****x@g****m | 28 |
| Jason Vailionis | j****s@u****u | 23 |
| kylesexton | k****n@m****u | 18 |
| Ying Zhang | y****g@u****u | 13 |
| Keith Thompson | k****n@b****u | 12 |
| Christopher Powers | c****s@b****u | 9 |
| Austin Menge | a****e@m****u | 6 |
| yingzhanguri | z****e@g****m | 6 |
| Christopher Powers | c****s@n****m | 4 |
| chrispowers | c****0@u****u | 4 |
| bishopbrian25 | b****p@m****u | 3 |
| Elysha Sameth | e****1@b****u | 2 |
| kzhang | k****g@1****u | 2 |
| ying | y****g@b****u | 2 |
| yingzhanguri | y****g@m****u | 2 |
| Chris Powers | c****s@8****u | 1 |
| Ke Zhang | a****n@7****u | 1 |
| Ke Zhang | k****g@u****u | 1 |
| Ke Zhang | k****g@b****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 2
- Total pull requests: 101
- Average time to close issues: over 1 year
- Average time to close pull requests: about 2 months
- Total issue authors: 2
- Total pull request authors: 8
- Average comments per issue: 1.5
- Average comments per pull request: 0.19
- Merged pull requests: 77
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mmundy42 (1)
- arturomarin (1)
Pull Request Authors
- jonls (75)
- keithdt (12)
- bishopbrian25 (5)
- yingzhanguri (3)
- zhenjiaofenjie (2)
- spikeliu (2)
- jgyllinsky (1)
- dozingpip (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 141 last-month
- Total dependent packages: 0
- Total dependent repositories: 3
- Total versions: 32
- Total maintainers: 2
pypi.org: psamm
PSAMM metabolic modeling tools
- Homepage: https://github.com/zhanglab/psamm
- Documentation: https://psamm.readthedocs.io/
- License: GNU GPLv3+
-
Latest release: 1.2.1
published almost 4 years ago
Rankings
Dependent repos count: 9.0%
Forks count: 9.6%
Dependent packages count: 10.0%
Stargazers count: 10.9%
Average: 11.9%
Downloads: 20.2%
Last synced:
7 months ago
Dependencies
setup.py
pypi
- future *
- numpy *
- pandas *
- pyyaml >=4.2b1
- scipy *
- six *
- xlsxwriter *