https://github.com/biojulia/biomakie.jl
Plotting and interface tools for biology.
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Committers with academic emails
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords from Contributors
Repository
Plotting and interface tools for biology.
Basic Info
- Host: GitHub
- Owner: BioJulia
- License: mit
- Language: Julia
- Default Branch: master
- Homepage: https://biojulia.dev/BioMakie.jl/
- Size: 61.2 MB
Statistics
- Stars: 68
- Watchers: 4
- Forks: 5
- Open Issues: 12
- Releases: 11
Metadata Files
README.md
Status:
Documentation:
Installation
To install BioMakie, access the Julia package manager by
pressing ] from the Julia REPL, then run add BioMakie.
Contributing and questions
Anyone can contribute to this package, by doing things like reporting bugs, fixing issues, improving performance, adding new features, and adding examples. Feel free to open an Issue or Pull Request, or communicate on the #biology or #makie channels of the Julia Slack.
About
This package provides plotting functions for protein structures, multiple sequence alignments, and some other related plots like protein structure contact maps. It also provides more complicated examples that show off additional functionality and interfaces. The main plotting functions are plotstruc and plotmsa, along with their mutating versions, plotstruc! and plotmsa!.
```julia using BioMakie using GLMakie using BioStructures struc = retrievepdb("2vb1") |> Observable
or
struc = read("2vb1.pdb", BioStructures.PDBFormat) |> Observable
fig = Figure() plotstruc!(fig, struc; plottype = :ballandstick, gridposition = (1,1), atomcolors = aquacolors) plotstruc!(fig, struc; plottype = :covalent, gridposition = (1,2)) ```
To view a multiple sequence alignment, use the plotmsa function with a Pfam MSA or fasta file.
```julia using FASTX reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta") msa = [reader...] |> Observable close(reader)
or
using MIToS.MSA msa = read_file("pf00062.stockholm.gz", Stockholm)
fig = plotmsa(msa; colorscheme = :tableaubluegreen) ```
Other examples
Viewing the frequencies of amino acids in a multiple sequence alignment
Alpha shapes can be used to visualize the surface of a protein structure
Database information can be displayed for a protein (including a GPT response, OpenAI.jl)
Protein residue mutation and changing rotamers (with ProtoSyn.jl)
Owner
- Name: BioJulia
- Login: BioJulia
- Kind: organization
- Website: https://biojulia.dev
- Repositories: 79
- Profile: https://github.com/BioJulia
Bioinformatics and Computational Biology in Julia
GitHub Events
Total
- Create event: 17
- Commit comment event: 2
- Release event: 3
- Issues event: 3
- Watch event: 13
- Member event: 1
- Issue comment event: 16
- Push event: 17
- Pull request review comment event: 6
- Pull request review event: 6
- Pull request event: 42
- Fork event: 1
Last Year
- Create event: 17
- Commit comment event: 2
- Release event: 3
- Issues event: 3
- Watch event: 13
- Member event: 1
- Issue comment event: 16
- Push event: 17
- Pull request review comment event: 6
- Pull request review event: 6
- Pull request event: 42
- Fork event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Dan Kool | k****d@g****m | 273 |
| CompatHelper Julia | c****y@j****g | 40 |
| Tim Holy | t****y@g****m | 9 |
| github-actions[bot] | 4****] | 7 |
| dependabot[bot] | 4****] | 3 |
| Joe Greener | j****r@h****k | 1 |
| Diego Javier Zea | d****a@g****m | 1 |
| Anshul Singhvi | a****i@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 6
- Total pull requests: 118
- Average time to close issues: 2 months
- Average time to close pull requests: about 2 months
- Total issue authors: 6
- Total pull request authors: 5
- Average comments per issue: 2.17
- Average comments per pull request: 0.31
- Merged pull requests: 63
- Bot issues: 0
- Bot pull requests: 63
Past Year
- Issues: 2
- Pull requests: 37
- Average time to close issues: 5 months
- Average time to close pull requests: 3 months
- Issue authors: 2
- Pull request authors: 2
- Average comments per issue: 0.5
- Average comments per pull request: 0.86
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 30
Top Authors
Issue Authors
- stecrotti (1)
- DoktorMike (1)
- PGimenez (1)
- JuliaTagBot (1)
- dgleich (1)
Pull Request Authors
- github-actions[bot] (82)
- kool7d (42)
- timholy (7)
- diegozea (2)
- jgreener64 (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- julia 4 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 11
juliahub.com: BioMakie
Plotting and interface tools for biology.
- Homepage: https://biojulia.dev/BioMakie.jl/
- Documentation: https://docs.juliahub.com/General/BioMakie/stable/
- License: MIT
-
Latest release: 0.4.4
published about 1 year ago
Rankings
Dependencies
- actions/cache v1 composite
- actions/checkout v2 composite
- julia-actions/setup-julia v1 composite
- JuliaRegistries/TagBot v1.14 composite
- actions/cache v2 composite
- actions/checkout v2 composite
- codecov/codecov-action v2 composite
- julia-actions/julia-processcoverage v1 composite
- julia-actions/setup-julia v1 composite