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Open Source Science

https://github.com/biojava/biojava-legacy

Legacy BioJava 1 Code

https://github.com/biojava/biojava-legacy

Science Score: 13.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Legacy BioJava 1 Code

Basic Info
  • Host: GitHub
  • Owner: biojava
  • Language: Java
  • Default Branch: master
  • Size: 5.64 MB
Statistics
  • Stars: 4
  • Watchers: 24
  • Forks: 15
  • Open Issues: 5
  • Releases: 3
Created about 13 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

biojava-legacy

This repository contains code from BioJava 1.

The goal is to port all features present in BioJava 1 to the BioJava 3 codebase, available at https://github.com/biojava/biojava. However, until that goal is achieved this repository will remain active for minor changes and bug fixes.

Owner

  • Name: BioJava
  • Login: biojava
  • Kind: organization

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 1
  • Push event: 2
  • Pull request event: 4
  • Fork event: 1
Last Year
  • Issues event: 1
  • Issue comment event: 1
  • Push event: 2
  • Pull request event: 4
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 24
  • Total pull requests: 60
  • Average time to close issues: 6 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 3
  • Total pull request authors: 8
  • Average comments per issue: 1.08
  • Average comments per pull request: 0.5
  • Merged pull requests: 57
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • heuermh (22)
  • el1jaC (1)
  • dariober (1)
Pull Request Authors
  • heuermh (48)
  • dependabot[bot] (4)
  • el1jaC (2)
  • gwaldon (2)
  • andreasprlic (2)
  • brandstaetter (2)
  • brianrepko (1)
  • rylarson (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (4)

Packages

  • Total packages: 9
  • Total downloads: unknown
  • Total docker downloads: 8,655
  • Total dependent packages: 34
    (may contain duplicates)
  • Total dependent repositories: 61
    (may contain duplicates)
  • Total versions: 81
repo1.maven.org: org.biojava:core

BioJava core module

  • Versions: 9
  • Dependent Packages: 17
  • Dependent Repositories: 26
  • Docker Downloads: 2,885
Rankings
Dependent packages count: 3.7%
Docker downloads count: 3.8%
Dependent repos count: 4.6%
Average: 19.5%
Forks count: 34.8%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:alignment

BioJava alignment module

  • Versions: 9
  • Dependent Packages: 7
  • Dependent Repositories: 9
  • Docker Downloads: 2,856
Rankings
Docker downloads count: 3.8%
Dependent repos count: 8.2%
Dependent packages count: 8.4%
Average: 21.2%
Forks count: 34.8%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:sequencing

BioJava sequencing module

  • Versions: 9
  • Dependent Packages: 9
  • Dependent Repositories: 14
Rankings
Dependent repos count: 6.6%
Dependent packages count: 6.7%
Average: 24.7%
Forks count: 34.8%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:bytecode

BioJava bytecode module

  • Versions: 9
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Docker Downloads: 2,885
Rankings
Docker downloads count: 3.8%
Dependent repos count: 12.1%
Average: 26.9%
Dependent packages count: 33.0%
Forks count: 34.8%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:biosql

BioJava biosql module

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 24.1%
Dependent repos count: 32.0%
Average: 35.0%
Stargazers count: 35.0%
Dependent packages count: 48.9%
Last synced: 10 months ago
repo1.maven.org: org.biojava:biojava-legacy

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 3
Rankings
Dependent repos count: 13.8%
Forks count: 34.8%
Average: 37.4%
Dependent packages count: 50.1%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:blast

BioJava blast module

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 2
Rankings
Dependent repos count: 16.1%
Forks count: 34.8%
Average: 38.0%
Dependent packages count: 50.1%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:gui

BioJava gui module

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Docker Downloads: 29
Rankings
Dependent repos count: 16.1%
Forks count: 34.8%
Average: 38.0%
Dependent packages count: 50.1%
Stargazers count: 50.8%
Last synced: 10 months ago
repo1.maven.org: org.biojava:phylo

BioJava phylo module

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 20.8%
Forks count: 34.8%
Average: 39.1%
Dependent packages count: 50.1%
Stargazers count: 50.8%
Last synced: 11 months ago

Dependencies

alignment/pom.xml maven
  • org.biojava:core 1.9.6-SNAPSHOT compile
  • junit:junit test
biosql/pom.xml maven
  • org.biojava:core 1.9.6-SNAPSHOT compile
  • junit:junit test
blast/pom.xml maven
  • org.biojava:core 1.9.6-SNAPSHOT compile
  • junit:junit test
bytecode/pom.xml maven
  • junit:junit test
core/pom.xml maven
  • commons-dbcp:commons-dbcp compile
  • org.biojava:bytecode 1.9.6-SNAPSHOT compile
  • junit:junit test
gui/pom.xml maven
  • org.biojava:core 1.9.6-SNAPSHOT compile
  • org.biojava:sequencing 1.9.6-SNAPSHOT compile
  • junit:junit test
phylo/pom.xml maven
  • org.biojava:alignment 1.9.6-SNAPSHOT compile
  • org.biojava:core 1.9.6-SNAPSHOT compile
  • org.jgrapht:jgrapht-jdk1.5 compile
  • junit:junit test
pom.xml maven
  • commons-dbcp:commons-dbcp 1.4
  • javax.persistence:persistence-api 1.0.2
  • javax.xml.bind:jaxb-api 2.3.1
  • org.jgrapht:jgrapht-jdk1.5 0.7.3
  • xerces:xercesImpl 2.12.2
  • junit:junit 4.13.2 test
sequencing/pom.xml maven
  • com.google.guava:guava compile
  • org.biojava:core 1.9.6-SNAPSHOT compile
  • com.google.guava:guava 31.1-jre
  • junit:junit test
.github/workflows/ci.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
.github/workflows/deploy.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-java v2 composite