BioStructures
A Julia package to read, write and manipulate macromolecular structures
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 1 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 16 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A Julia package to read, write and manipulate macromolecular structures
Basic Info
Statistics
- Stars: 105
- Watchers: 9
- Forks: 25
- Open Issues: 13
- Releases: 45
Topics
Metadata Files
README.md
BioStructures.jl
Latest Release:
Development status:
Description
BioStructures provides functionality to read, write and manipulate macromolecular structures, in particular proteins. Protein Data Bank (PDB), mmCIF and MMTF format files can be read in to a hierarchical data structure. Spatial calculations and functions to access the PDB are also provided. It compares favourably in terms of performance to other PDB parsers - see some benchmarks online - and should be lightweight enough to build other packages on top of.
Installation
Install BioStructures from the Julia package REPL, which can be accessed by
pressing ] from the Julia REPL:
add BioStructures
See the documentation for information on how to use BioStructures.
Citation
If you use BioStructures, please cite the paper:
- Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics 36(14):4206-4207 (2020) - link - PDF
Contributing and questions
We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.
If you have a question about contributing or using this package, you are encouraged to use the
biology channel of the Julia Slack or the
Owner
- Name: BioJulia
- Login: BioJulia
- Kind: organization
- Website: https://biojulia.dev
- Repositories: 79
- Profile: https://github.com/BioJulia
Bioinformatics and Computational Biology in Julia
Citation (CITATION.bib)
@article{BioStructures.jl-2020,
author="Greener, J G and Selvaraj, J and Ward, B J",
title="{BioStructures.jl: read, write and manipulate macromolecular structures in Julia}",
journal="Bioinformatics",
year="2020",
volume="36",
number="14",
pages="4206--4207",
doi="10.1093/bioinformatics/btaa502",
}
GitHub Events
Total
- Create event: 14
- Commit comment event: 13
- Issues event: 4
- Release event: 6
- Watch event: 10
- Delete event: 6
- Issue comment event: 51
- Push event: 114
- Pull request review comment event: 12
- Pull request review event: 11
- Pull request event: 27
- Fork event: 3
Last Year
- Create event: 14
- Commit comment event: 13
- Issues event: 4
- Release event: 6
- Watch event: 10
- Delete event: 6
- Issue comment event: 51
- Push event: 114
- Pull request review comment event: 12
- Pull request review event: 11
- Pull request event: 27
- Fork event: 3
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Joe Greener | j****r@h****k | 288 |
| Leandro Martinez | l****e@u****r | 13 |
| Tim Holy | t****y@g****m | 10 |
| github-actions[bot] | 4****] | 5 |
| Marco | m****s@g****m | 5 |
| Andreas Kröpelin | 4****n | 2 |
| dependabot[bot] | 4****] | 2 |
| Ben J. Ward | w****0@g****m | 2 |
| Dan Kool | k****d@g****m | 1 |
| Michael Krabbe Borregaard | m****d@s****k | 1 |
| Morten Piibeleht | m****t@g****m | 1 |
| Nate Guerin | g****n | 1 |
| Shu Li | s****i@p****u | 1 |
| The ultimate Renan | u****n@g****m | 1 |
| nhz2 | 3****2 | 1 |
| tanhevg | t****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 21
- Total pull requests: 65
- Average time to close issues: 4 months
- Average time to close pull requests: 12 days
- Total issue authors: 15
- Total pull request authors: 18
- Average comments per issue: 5.52
- Average comments per pull request: 2.38
- Merged pull requests: 50
- Bot issues: 0
- Bot pull requests: 15
Past Year
- Issues: 4
- Pull requests: 25
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 3
- Pull request authors: 6
- Average comments per issue: 2.75
- Average comments per pull request: 2.28
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 3
Top Authors
Issue Authors
- timholy (5)
- lmiq (2)
- marcom (2)
- abahm (1)
- hellmrf (1)
- kool7d (1)
- emrekuecuek (1)
- George3d6 (1)
- Wang-Lin-boop (1)
- babaid (1)
- amaurypm (1)
- tanhevg (1)
- ivanpmartell (1)
- dependabot[bot] (1)
- Nick-Mul (1)
Pull Request Authors
- timholy (21)
- github-actions[bot] (12)
- lmiq (10)
- marcom (5)
- jgreener64 (5)
- andreasKroepelin (4)
- dependabot[bot] (4)
- SabrinaJaye (2)
- BradyAJohnston (2)
- mortenpi (1)
- gusennan (1)
- kool7d (1)
- tanhevg (1)
- femtocleaner[bot] (1)
- h3nnn4n (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- julia 87 total
- Total dependent packages: 5
- Total dependent repositories: 8
- Total versions: 43
juliahub.com: BioStructures
A Julia package to read, write and manipulate macromolecular structures
- Documentation: https://docs.juliahub.com/General/BioStructures/stable/
- License: MIT
-
Latest release: 4.6.0
published 9 months ago
Rankings
Dependencies
- actions/cache v1 composite
- actions/checkout v2 composite
- codecov/codecov-action v1 composite
- julia-actions/julia-buildpkg v1 composite
- julia-actions/julia-processcoverage v1 composite
- julia-actions/julia-runtest v1 composite
- julia-actions/setup-julia v1 composite