biomass
A Python Framework for Modeling and Analysis of Signaling Systems
Science Score: 67.0%
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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 8 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 11 committers (18.2%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A Python Framework for Modeling and Analysis of Signaling Systems
Basic Info
- Host: GitHub
- Owner: biomass-dev
- License: apache-2.0
- Language: Python
- Default Branch: master
- Homepage: http://biomass-core.rtfd.io
- Size: 26 MB
Statistics
- Stars: 30
- Watchers: 1
- Forks: 13
- Open Issues: 1
- Releases: 36
Topics
Metadata Files
README.md
BioMASS is a computational framework for modeling and analysis of biological signaling systems in Python.
- Documentation: https://biomass-core.rtfd.io
- Source code: https://github.com/biomass-dev/biomass
- Bug reports: https://github.com/biomass-dev/biomass/issues
- Citing in your work: https://biomass-core.rtfd.io/en/latest/citing.html
It provides useful tools for numerical simulation, parameter estimation, network analysis, and result visualization.
Installation
The BioMASS library is available at the Python Package Index (PyPI).
shell
$ pip install biomass
BioMASS supports Python 3.10 or newer.
References
Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. Cancers 12, 2878 (2020). https://doi.org/10.3390/cancers12102878
Imoto, H., Yamashiro, S. & Okada, M. A text-based computational framework for patient -specific modeling for classification of cancers. iScience 25, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944
Arakane, K., Imoto, H., Ormersbach, F. & Okada, M. Extending BioMASS to construct mathematical models from external knowledge. Bioinformatics Advances 4, vbae042 (2024). https://doi.org/10.1093/bioadv/vbae042
Author
License
Owner
- Name: BioMASS
- Login: biomass-dev
- Kind: organization
- Repositories: 2
- Profile: https://github.com/biomass-dev
Open-source software project providing tools for modeling and analysis of biological signaling systems.
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software in your work, we suggest citing the following paper:"
preferred-citation:
type: article
authors:
- family-names: "Arakane"
given-names: "Kiwamu"
- family-names: "Imoto"
given-names: "Hiroaki"
orcid: "https://orcid.org/0000-0002-6817-642X"
- family-names: "Ormersbach"
given-names: "Fabian"
orcid: "https://orcid.org/0000-0003-1838-5976"
- family-names: "Okada"
given-names: "Mariko"
orcid: "https://orcid.org/0000-0002-6210-8223"
doi: "10.3390/cancers12102878"
journal: "Cancers"
title: "Extending BioMASS to construct mathematical models from external knowledge"
issue: 1
volume: 4
start: vbae042
end: vbae042
year: 2024
url: "https://doi.org/10.1093/bioadv/vbae042"
GitHub Events
Total
- Create event: 3
- Issues event: 1
- Release event: 1
- Watch event: 3
- Delete event: 3
- Push event: 16
- Pull request review event: 1
- Pull request event: 9
Last Year
- Create event: 3
- Issues event: 1
- Release event: 1
- Watch event: 3
- Delete event: 3
- Push event: 16
- Pull request review event: 1
- Pull request event: 9
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 950
- Total Committers: 11
- Avg Commits per committer: 86.364
- Development Distribution Score (DDS): 0.381
Top Committers
| Name | Commits | |
|---|---|---|
| himoto | 3****o@u****m | 588 |
| himoto | h****o@p****p | 292 |
| johannesnicolaus | j****s@g****m | 19 |
| ulrmu | u****r@g****m | 15 |
| formersbach | 4****h@u****m | 10 |
| pre-commit-ci[bot] | 6****]@u****m | 9 |
| Hiroaki Imoto | h****o@u****e | 6 |
| Hiroaki Imoto | u****a@e****p | 5 |
| SHMAKI | 4****I@u****m | 4 |
| johannesnicolaus | 3****s@u****m | 1 |
| lgtm-com[bot] | 4****]@u****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 2
- Total pull requests: 15
- Average time to close issues: N/A
- Average time to close pull requests: 2 months
- Total issue authors: 1
- Total pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 4
Past Year
- Issues: 1
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: about 2 months
- Issue authors: 1
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- himoto (2)
Pull Request Authors
- himoto (8)
- pre-commit-ci[bot] (4)
- k-arakane (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 700 last-month
- Total dependent packages: 1
- Total dependent repositories: 3
- Total versions: 31
- Total maintainers: 1
pypi.org: biomass
A Python Framework for Modeling and Analysis of Signaling Systems
- Documentation: https://biomass.readthedocs.io/
- License: Apache-2.0
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Latest release: 0.14.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- actions/checkout v3 composite
- github/codeql-action/analyze v2 composite
- github/codeql-action/autobuild v2 composite
- github/codeql-action/init v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- matplotlib >=3.0
- numba >=0.56
- numpy >=1.17
- pandas >=0.24
- scipy >=1.6
- seaborn >=0.11.2
- tqdm >=4.50.2