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Bio3DView

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

https://github.com/jgreener64/bio3dview.jl

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

bioinformatics ijulia julia jupyter-notebook pluto protein-structure structural-bioinformatics structural-biology

Keywords from Contributors

numeric interactive pdb programming-language julialang optim enzymes embedded autograding hacking
Last synced: 6 months ago · JSON representation ·

Repository

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

Basic Info
  • Host: GitHub
  • Owner: jgreener64
  • License: other
  • Language: Julia
  • Default Branch: master
  • Homepage:
  • Size: 10.8 MB
Statistics
  • Stars: 36
  • Watchers: 2
  • Forks: 7
  • Open Issues: 7
  • Releases: 7
Topics
bioinformatics ijulia julia jupyter-notebook pluto protein-structure structural-bioinformatics structural-biology
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

Bio3DView.jl

Build status codecov

Bio3DView.jl provides a viewer for molecular structures in Julia. It is a wrapper round the excellent 3Dmol.js package [1]. When used from the REPL or a file, the viewer shows in a popup using Blink.jl. When used from IJulia running in Jupyter or VS Code, or from Pluto.jl, the viewer shows in the output cell. You can also use Bio3DView.jl to generate standalone HTML, e.g. for use in a web page.

[1] Nicholas Rego and David Koes, 3Dmol.js: molecular visualization with WebGL, Bioinformatics (2015) 31(8): 1322-1324 - link

Contributions and bug reports are welcome.

Installation

Julia 1.0 or later is required, with Julia 1.9 or later required to get the latest version. Install Bio3DView from the package mode of the Julia REPL (press ]):

add Bio3DView

Bio3DView uses package extensions to minimise dependencies so you will also need to install either Blink, IJulia or Pluto to make this package useful, though you can generate HTML without them. If you are using Blink, you will need to run using Blink before the Bio3DView functions work. To view structural objects from BioStructures.jl you will need to run using BioStructures.

Usage

See the tutorial notebook.

Related software

See also BioMakie.jl and ProtPlot.jl.

Citation

If you use Bio3DView, please cite the BioStructures paper where it is mentioned:

  • 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

Owner

  • Name: Joe Greener
  • Login: jgreener64
  • Kind: user
  • Location: Cambridge, UK
  • Company: MRC Laboratory of Molecular Biology

Computational chemist/structural bioinformatician working on improving molecular simulation. See also https://github.com/greener-group.

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
  • Watch event: 2
  • Delete event: 1
  • Pull request event: 3
Last Year
  • Watch event: 2
  • Delete event: 1
  • Pull request event: 3

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 99
  • Total Committers: 6
  • Avg Commits per committer: 16.5
  • Development Distribution Score (DDS): 0.172
Past Year
  • Commits: 8
  • Committers: 2
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
Joe Greener j****r@h****k 82
Seth Axen s****n@g****m 6
Diego Javier Zea d****a@g****m 4
CorySimon C****n@b****u 4
dependabot[bot] 4****] 2
BenjaminDoran 2****n 1
Committer Domains (Top 20 + Academic)
berkeley.edu: 1 hotmail.co.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 9
  • Total pull requests: 8
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 18 hours
  • Total issue authors: 5
  • Total pull request authors: 5
  • Average comments per issue: 5.11
  • Average comments per pull request: 2.13
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • eahenle (3)
  • sethaxen (2)
  • SimonEnsemble (2)
  • abahm (1)
  • diegozea (1)
Pull Request Authors
  • dependabot[bot] (5)
  • SimonEnsemble (2)
  • diegozea (2)
  • sethaxen (1)
  • BenjaminDoran (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (5) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 9 total
  • Total dependent packages: 3
  • Total dependent repositories: 0
  • Total versions: 7
juliahub.com: Bio3DView

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

  • Versions: 7
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 9 Total
Rankings
Dependent repos count: 9.9%
Average: 15.4%
Dependent packages count: 16.6%
Forks count: 17.4%
Stargazers count: 17.6%
Last synced: 6 months ago