org.biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Science Score: 77.0%
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
Links to: plos.org -
✓Committers with academic emails
18 of 115 committers (15.7%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Basic Info
- Host: GitHub
- Owner: biojava
- License: lgpl-2.1
- Language: Java
- Default Branch: master
- Homepage: https://biojava.org
- Size: 48.8 MB
Statistics
- Stars: 610
- Watchers: 76
- Forks: 391
- Open Issues: 68
- Releases: 40
Topics
Metadata Files
README.md
Welcome to 
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, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
Please visit our homepage.
Documentation
The BioJava tutorial is a great place to get started. It is most complete for the biojava-structure module.
The BioJava Cookbook contains an older and slightly outdated collection of simple examples that teach the basics for how to work with BioJava.
Full javadocs are available at the BioJava website.
Maven Repository
BioJava release are available from Maven Central.
Quick Installation
If you are using Maven you can add the BioJava repository by adding the following XML to your project pom.xml file:
xml
<dependencies>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.2</version>
</dependency>
<!-- other biojava modules as needed -->
</dependencies>
For developers
Release biojava to maven central:
- mvn -Prelease release:prepare
- mvn -Prelease release:perform
Publish new javadocs:
- mvn -Prelease site this will write target/site
- Push the contents of target/site/apidocs to the biojava.github.io repo under directory docs/apiM.m.p (e.g. docs/api7.1.4) and then link docs/api to docs/apiM.m.p, for it to be published in biojava.org
Mailing Lists
BioJava has one main mailing list. In order to avoid SPAM the list only accepts postings from list members. Anybody can become a list member, so please subscribe before you post. If you send without being subscribed your mail might get stuck in the moderation loop, which can cause several weeks of delay (no fun to read through all that spam).
biojava-l general discussion list
This list is intended for general discussion, advice, questions, offers of help, announcements, expressions of appreciation, bugs found in release code and requests for features.
biojava-dev developers list
A dev mailing list used to exist, but it has now been shut down. For dev discussions we now use github issues. Please search existing issues and if you don't find the answer to your question submit a new issue.
Please cite
BioJava 5: A community driven open-source bioinformatics library
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte
PLOS Computational Biology 15(2): e1006791
Owner
- Name: BioJava
- Login: biojava
- Kind: organization
- Website: http://www.biojava.org
- Repositories: 12
- Profile: https://github.com/biojava
Citation (CITATION.cff)
cff-version: 1.0.3
message: If you use BioJava, please cite the software and the most recent paper reference (Lafita 2019).
title: BioJava
version: 5.2.1
date-released: 2019-02-05
doi: 10.5281/zenodo.2557853
commit: 783065396f92f14c3fb6e2b9a684a17aa46bb974
url: http://www.biojava.org
repository-code: https://github.com/biojava/biojava/
license: LGPL-2.1-only
abstract: >-
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.
authors:
- family-names: Prlić
given-names: Andreas
- family-names: Lafita
given-names: Aleix
- family-names: ALHOSSARY
given-names: Amr
- family-names: Dräger
given-names: Andreas
- family-names: Yates
given-names: Andy
- family-names: Bradley
given-names: Anthony
- family-names: Foti
given-names: Carmelo
- family-names: Koh
given-names: Chuan Hock
- family-names: Myers-Turnbull
given-names: Douglas
- family-names: Rimsa
given-names: Gediminas
- family-names: Waldon
given-names: George
- family-names: Brandstätter-Müller
given-names: Hannes
- name: Elinow
- family-names: Gao
given-names: Jianjiong
- family-names: Warren
given-names: Jonathan
- family-names: Duarte
given-names: Jose Manuel
- family-names: Jacobsen
given-names: Jules
- family-names: Nicholas
given-names: Karl
- family-names: Chapman
given-names: Mark
- family-names: Heuer
given-names: Michael
- family-names: Rose
given-names: Peter
- family-names: Troshin
given-names: Peter
- family-names: Holland
given-names: Richard
- family-names: Thornton
given-names: Robert
- family-names: Willis
given-names: Scooter
- family-names: Bliven
given-names: Spencer
- family-names: Foisy
given-names: Sylvain
references:
- type: article
authors:
- family-names: Lafita
given-names: Aleix
orcid: http://orcid.org/0000-0003-1549-3162
- family-names: Bliven
given-names: Spencer E
orcid: http://orcid.org/0000-0002-1200-1698
- family-names: Prlić
given-names: Andreas
orcid: https://orcid.org/0000-0001-6346-6391
- family-names: Guzenko
given-names: Dmytro
orcid: https://orcid.org/0000-0002-8688-7460
- family-names: Rose
given-names: Peter W
orcid: http://orcid.org/0000-0001-9981-9750
- family-names: Bradley
given-names: Anthony
orcid: http://orcid.org/0000-0002-0881-3490
- family-names: Pavan
given-names: Paolo
- family-names: Myers-Turnbull
given-names: Douglas
orcid: http://orcid.org/0000-0003-3610-4808
- family-names: Valasatava
given-names: Yana
orcid: http://orcid.org/0000-0003-1018-5718
- family-names: Heuer
given-names: Michael
orcid: http://orcid.org/0000-0002-9052-6000
- family-names: Larson
given-names: Matt
orcid: http://orcid.org/0000-0003-2116-5747
- family-names: Burley
given-names: Stephen K
- family-names: Duarte
given-names: Jose M
orcid: http://orcid.org/0000-0002-9544-5621
title: "BioJava 5: A community driven open-source bioinformatics library"
year: 2019
journal: PLOS Computational Biology
volume: 15
number: "2"
section: e1006791
doi: 10.1371/journal.pcbi.1006791
url: http://dx.plos.org/10.1371/journal.pcbi.1006791
- type: article
authors:
- family-names: Prlić
given-names: Andreas
- family-names: Yates
given-names: Andrew
- family-names: Bliven
given-names: Spencer E
- family-names: Rose
given-names: Peter W
- family-names: Jacobsen
given-names: Julius
- family-names: Troshin
given-names: Peter V
- family-names: Chapman
given-names: Mark
- family-names: Gao
given-names: Jianjiong
- family-names: Koh
given-names: Chuan Hock
- family-names: Foisy
given-names: Sylvain
- family-names: Holland
given-names: Richard
- family-names: Rimša
given-names: Gediminas
- family-names: Heuer
given-names: Michael L
- family-names: Brandstätter-Müller
given-names: H
- family-names: Bourne
given-names: Philip E
- family-names: Willis
given-names: Scooter
title: "BioJava: an open-source framework for bioinformatics in 2012"
journal: Bioinformatics
year: 2012
volume: 28
number: "20"
section: 2693-2695
doi: 10.1093/bioinformatics/bts494
- type: article
authors:
- family-names: Holland
given-names: R C G
- family-names: Down
given-names: T A
- family-names: Pocock
given-names: M
- family-names: Prlić
given-names: A
- family-names: Huen
given-names: D
- family-names: James
given-names: K
- family-names: Foisy
given-names: S
- family-names: Dräger
given-names: A
- family-names: Yates
given-names: A
- family-names: Heuer
given-names: M
- family-names: Schreiber
given-names: M J
title: "BioJava: an open-source framework for bioinformatics"
journal: Bioinformatics
year: 2008
volume: 24
number: "18"
section: 2096-2097
doi: 10.1093/bioinformatics/btn397
GitHub Events
Total
- Create event: 8
- Release event: 3
- Issues event: 5
- Watch event: 23
- Delete event: 3
- Issue comment event: 7
- Push event: 52
- Pull request review comment event: 4
- Pull request review event: 10
- Pull request event: 18
- Fork event: 13
Last Year
- Create event: 8
- Release event: 3
- Issues event: 5
- Watch event: 23
- Delete event: 3
- Issue comment event: 7
- Push event: 52
- Pull request review comment event: 4
- Pull request review event: 10
- Pull request event: 18
- Fork event: 13
Committers
Last synced: almost 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andreas Prlic | a****c@g****m | 1,871 |
| Jose Manuel Duarte | j****e@g****m | 938 |
| lafita | a****a@g****m | 484 |
| Spencer Bliven | s****n@u****u | 426 |
| Anthony Bradley | a****y@g****m | 190 |
| dmyersturnbull | d****l@g****m | 150 |
| Jianjiong Gao | g****b@g****g | 104 |
| Paolo Pavan | p****n@g****m | 102 |
| richard | r****7@g****m | 92 |
| Mark Chapman | c****n@c****u | 89 |
| Andy Yates | a****s@e****k | 88 |
| Michael Heuer | h****h@a****g | 76 |
| Peter Rose | p****e@u****u | 75 |
| Chuan Hock Koh | k****k@g****m | 57 |
| Scooter Willis | w****f@g****m | 57 |
| Andreas Prlic | a****c@g****m | 57 |
| Spencer Bliven | s****n@g****m | 55 |
| Sylvain Foisy | s****y@d****t | 47 |
| Amr AL-HOSSARY | a****y@h****m | 46 |
| Amr ALHOSSARY | a****y@g****m | 44 |
| JonStargaryen | s****h@r****g | 41 |
| ulyssecarion | u****n@g****m | 40 |
| Jenkins | j****s@j****g | 35 |
| Dmytro Guzenko | d****o@r****g | 31 |
| jamesmorris | k****6@U****t | 30 |
| Peter Troshin | t****r@g****m | 29 |
| emckee2006 | e****6@g****m | 28 |
| valasatava | y****a@g****m | 26 |
| Matt Larson | l****m@d****m | 24 |
| Benjamin Boyle | b****e@g****m | 24 |
| and 85 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 62
- Total pull requests: 71
- Average time to close issues: 6 months
- Average time to close pull requests: about 2 months
- Total issue authors: 34
- Total pull request authors: 23
- Average comments per issue: 3.73
- Average comments per pull request: 1.89
- Merged pull requests: 55
- Bot issues: 0
- Bot pull requests: 5
Past Year
- Issues: 3
- Pull requests: 9
- Average time to close issues: 10 days
- Average time to close pull requests: 2 days
- Issue authors: 3
- Pull request authors: 2
- Average comments per issue: 1.33
- Average comments per pull request: 0.11
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jlerbsc (10)
- josemduarte (8)
- sbliven (6)
- richarda23 (4)
- aalhossary (4)
- pgrt (3)
- lafita (2)
- dabianzhixing (1)
- LobsterMan123 (1)
- FC123321 (1)
- erikedlund (1)
- kshitijgarg2609 (1)
- RoshanShrestha123 (1)
- sjaenick (1)
- yamule (1)
Pull Request Authors
- josemduarte (22)
- aalhossary (9)
- jlerbsc (7)
- heuermh (6)
- richarda23 (5)
- dependabot[bot] (5)
- hilbertglm (5)
- JonStargaryen (4)
- jamesmorris (3)
- xcalibur91 (3)
- JLLeitschuh (3)
- sbliven (3)
- cassandrabeaton (1)
- cometbroom (1)
- B246371-2023 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 16
- Total downloads: unknown
- Total docker downloads: 69,971
-
Total dependent packages: 64
(may contain duplicates) -
Total dependent repositories: 357
(may contain duplicates) - Total versions: 899
repo1.maven.org: org.biojava:biojava-core
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-core/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-structure
The protein structure modules of BioJava.
- Homepage: https://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-structure/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-alignment
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-alignment/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-ontology
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-ontology/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-genome
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.
- Homepage: https://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-genome/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-phylo
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-phylo/
- License: GNU LGPL v2
-
Latest release: 4.2.12
published over 7 years ago
Rankings
repo1.maven.org: org.biojava:biojava
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.
- Homepage: https://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-modfinder
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-modfinder/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-structure-gui
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-structure-gui/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-ws
This module deals with bioinformatics web services that could be used to process Biojava objects in a useful manner.
- Homepage: https://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-ws/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-aa-prop
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-aa-prop/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-sequencing
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-sequencing/
- License: GNU LGPL v2
-
Latest release: 4.2.12
published over 7 years ago
Rankings
repo1.maven.org: org.biojava:biojava-protein-disorder
This module is for predicting disordered regions in protein sequences
- Homepage: https://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-protein-disorder/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-integrationtest
A module which only has the purpose to run slow running integration tests. They can be executed by calling mvn verify
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-integrationtest/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-survival
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.
- Homepage: http://www.biojava.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-survival/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
repo1.maven.org: org.biojava:biojava-protein-comparison-tool
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.
- Homepage: http://source.rcsb.org
- Documentation: https://appdoc.app/artifact/org.biojava/biojava-protein-comparison-tool/
- License: GNU LGPL v2
-
Latest release: 7.2.2
published 9 months ago
Rankings
Dependencies
- javax.xml.bind:jaxb-api
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.biojava:biojava-core 6.0.6-SNAPSHOT
- org.biojava:biojava-structure 6.0.6-SNAPSHOT
- org.glassfish.jaxb:jaxb-runtime
- org.slf4j:slf4j-api
- junit:junit test
- org.biojava:biojava-core 6.0.6-SNAPSHOT compile
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.biojava.thirdparty:forester
- org.slf4j:slf4j-api
- junit:junit test
- javax.xml.bind:jaxb-api
- junit:junit
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.glassfish.jaxb:jaxb-runtime
- org.junit.jupiter:junit-jupiter-engine
- org.junit.jupiter:junit-jupiter-params
- org.junit.vintage:junit-vintage-engine
- org.slf4j:slf4j-api
- com.google.guava:guava 31.1-jre compile
- org.biojava:biojava-alignment 6.0.6-SNAPSHOT compile
- org.biojava:biojava-core 6.0.6-SNAPSHOT compile
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.slf4j:slf4j-api
- junit-addons:junit-addons 1.4 test
- junit:junit test
- junit:junit
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.biojava:biojava-structure 6.0.6-SNAPSHOT
- org.junit.jupiter:junit-jupiter-engine
- org.junit.jupiter:junit-jupiter-params
- org.junit.vintage:junit-vintage-engine
- org.slf4j:slf4j-api
- org.biojava:biojava-structure 6.0.6-SNAPSHOT compile
- javax.xml.bind:jaxb-api
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.glassfish.jaxb:jaxb-runtime
- org.slf4j:slf4j-api
- junit:junit test
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.slf4j:slf4j-api
- junit:junit test
- net.sourceforge.jmol:jmol 13.0.14
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.biojava:biojava-alignment 6.0.6-SNAPSHOT
- org.biojava:biojava-core 6.0.6-SNAPSHOT
- org.biojava:biojava-structure 6.0.6-SNAPSHOT
- org.biojava:biojava-structure-gui 6.0.6-SNAPSHOT
- org.slf4j:slf4j-api
- junit:junit test
- javax.xml.bind:jaxb-api
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.biojava:biojava-core 6.0.6-SNAPSHOT
- org.glassfish.jaxb:jaxb-runtime
- org.slf4j:slf4j-api
- junit:junit test
- org.biojava:biojava-alignment 6.0.6-SNAPSHOT compile
- org.biojava:biojava-core 6.0.6-SNAPSHOT compile
- org.rcsb:mmtf-api ${mmtf.version} compile
- org.rcsb:mmtf-codec ${mmtf.version} compile
- org.rcsb:mmtf-serialization ${mmtf.version} compile
- java3d:vecmath 1.3.1
- javax.xml.bind:jaxb-api
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.glassfish.jaxb:jaxb-runtime
- org.jgrapht:jgrapht-core 1.4.0
- org.junit.jupiter:junit-jupiter-engine
- org.junit.jupiter:junit-jupiter-params
- org.junit.vintage:junit-vintage-engine
- org.rcsb:${ciftools.artifact} ${ciftools.version}
- org.slf4j:slf4j-api
- junit:junit test
- xmlunit:xmlunit 1.6 test
- org.biojava:biojava-core 6.0.6-SNAPSHOT compile
- org.biojava:biojava-structure 6.0.6-SNAPSHOT compile
- net.sourceforge.jmol:jmol 14.31.10
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.biojava:jcolorbrewer 5.2
- org.slf4j:slf4j-api
- junit:junit test
- org.apache.commons:commons-math 2.2
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.slf4j:slf4j-api
- junit:junit test
- org.biojava:biojava-core 6.0.6-SNAPSHOT compile
- net.sf.json-lib:json-lib 2.4
- org.apache.logging.log4j:log4j-api
- org.apache.logging.log4j:log4j-core
- org.apache.logging.log4j:log4j-slf4j-impl
- org.slf4j:slf4j-api
- junit:junit test
- javax.xml.bind:jaxb-api 2.3.1
- org.apache.logging.log4j:log4j-api 2.17.1
- org.apache.logging.log4j:log4j-core 2.17.1
- org.apache.logging.log4j:log4j-slf4j-impl 2.17.1
- org.biojava.thirdparty:forester 1.039
- org.glassfish.jaxb:jaxb-runtime 2.3.5
- org.slf4j:slf4j-api 1.7.30
- junit:junit 4.13.2 test
- org.junit.jupiter:junit-jupiter-engine 5.7.2 test
- org.junit.jupiter:junit-jupiter-params 5.7.2 test
- org.junit.vintage:junit-vintage-engine 5.7.2 test
- actions/checkout v1 composite
- actions/setup-java v1 composite
- actions/checkout v1 composite
- actions/setup-java v1 composite