Bacting

Bacting: a next generation, command line version of Bioclipse - Published in JOSS (2021)

https://github.com/egonw/bacting

Science Score: 98.0%

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
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codemeta.json file
Found codemeta.json file
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Found .zenodo.json file
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DOI references
Found 7 DOI reference(s) in README and JOSS metadata
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Links to: joss.theoj.org, zenodo.org
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

bioclipse bioinformatics blueobelisk cheminformatics excel hacktoberfest rdf

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: egonw
License: other
Language: Java
Default Branch: main
Homepage:
Size: 1.38 MB

Statistics

Stars: 17
Watchers: 5
Forks: 5
Open Issues: 21
Releases: 65

Topics

bioclipse bioinformatics blueobelisk cheminformatics excel hacktoberfest rdf

Created almost 7 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Authors

Bacting

Bacting := acting as the Bioclipse TNG (The Next Generation)

Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences. Like Bioclipse, Bacting is written in the Java language, making use in Java-derived languages like Groovy easy, but also accessible to Python. Deposition of the Bacting package on Maven Central allows it to be easily used in Groovy scripts with @Grab instructions.

How to cite

If you use this software, please cite the article in JOSS:

Install

For the below use cases, Bacting is actually installed on demand. In Groovy this is done with @Grab and in Python with from pybacting import cdk (see pybacting) or scyjava.config. This section explains how Bacting can be installed from the source code.

From the source code

First, you need a working Maven installation and the code is tested with Java 11, 17, and 19, and can be installed with:

shell mvn clean install -Dgpg.skip -Dmaven.javadoc.skip=true

Making releases

Before making a release, update the version number in this README.md and in CITATION.cff.

Releases are created by the release manager and requires permission to submit the release to Maven Central (using an approved Sonatype (oss.sonatype.org) account). If these requirements are fulfilled then the following commands to the job:

shell export MAVEN_OPTS="--add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.text=ALL-UNNAMED --add-opens=java.desktop/java.awt.font=ALL-UNNAMED" mvn versions:set -DnewVersion=1.0.7 git commit -m "New release" -a mvn deploy -P release

Making snapshots

shell mvn versions:set -DnewVersion=1.0.8-SNAPSHOT mvn deploy

Updating the JavaDoc

After the release is avaiable on Maven Central, the JavaDoc needs to be updated. The JavaDoc is generated with the below command, and the results are stored in the target/site/apidocs/ folder:

shell mvn clean javadoc:javadoc javadoc:aggregate

That created content needs to be copied into the docs/ folder of this git repository.

Usage

Groovy

It can be used in Groovy by including the Bacting managers you need. The following example tells Groovy to download the CDKManager and instantiate it for the given workspace location (as it if was running in Bioclipse itself), and then converts a SMILES string to a Bioclipse IMolecule data object:

```groovy @Grab(group='io.github.egonw.bacting', module='managers-cdk', version='1.0.7')

workspaceRoot = "." def cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);

println cdk.fromSMILES("COC") ```

Python

Bacting can also be used in Python 3.7 (and higher) with pybacting and scyjava.

Pybacting

Pybacting can be installed with pip install pybacting (or pip3, depending on your platform). The above code example looks like:

```python from pybacting import cdk

print(cdk.fromSMILES("COC")) ```

Pybacting uses a specific Bacting version, so check the website to see which Bacting version you are using.

Scyjava

Scyjava can be installed with pip install scyjava (or pip3, depending on your platform). The code example looks like:

```python from scyjava import config, jimport config.add_endpoints('io.github.egonw.bacting:managers-cdk:1.0.7')

workspaceRoot = "." cdkClass = jimport("net.bioclipse.managers.CDKManager") cdk = cdkClass(workspaceRoot)

print(cdk.fromSMILES("COC")) ```

Code examples

Full code examples can be found in the following sources:

Open Notebooks for Wikidata, including:
- script that compares a SMILES string with Wikidata, and creates QuickStatements for missing information
- script that reads melting points from an Excel spreadsheet to enter into Wikidata
Open Notebooks for WikiPathways:
- script to recognize IUPAC names in WikiPathways
Some examples from A lot of Bioclipse Scripting Language examples:

API Coverage

For the time being, the coverage of the original API is incomplete. Particularly, manager functionality around graphical UX in the original Bioclipse may never be implemented. Each Bacting release will implement more APIs and the release notes will mention which managers and which methods have been added. An overview of the supports APIs can be found in this overview.

For a description of the API, I refer to the book A lot of Bioclipse Scripting Language examples that Jonathan and I compiled. However, a JavaDoc API is also available.

All Bacting scripts will be backwards compatible with Bioclipse. If you want to install Bioclipse and see its wonderful UX in actions, download Bioclipse 2.6.2 here.

Using SNAPSHOT versions

You may need to occassionally delete the modules cached by Groovy, by doing something like, to remove earlier SNAPSHOT versions:

shell \rm -Rf ~/.groovy/grapes/io.github.egonw.bacting/

Copyright and authors

Code in this repository contains mostly code that originated from Bioclipse and the headers of the individual source code files describe who contributed to that code of that class, but unfortunately this code ownership is not always clear. I refer to the various Bioclipse code repositories for the git history for detailed information.

Owner

Name: Egon Willighagen
Login: egonw
Kind: user
Location: Maastricht, The Netherlands
Company: @BiGCAT-UM

Website: https://chem-bla-ics.blogspot.com/
Repositories: 530
Profile: https://github.com/egonw

Open scientist teaching and doing research at Maastricht University.

JOSS Publication

Bacting: a next generation, command line version of Bioclipse

Published

June 23, 2021

DOI

10.21105/joss.02558

Volume 6, Issue 62, Page 2558

Authors

Egon Willighagen

Dept of Bioinformatics - BiGCaT, NUTRIM, Maastricht University

Editor

Mark A. Jensen

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Willighagen
    given-names: Egon
    orcid: https://orcid.org/0000-0001-7542-0286
title: Bacting
version: 1.0.7
date-released: 2025-08-16
doi: 10.5281/zenodo.2638709
url: "https://github.com/egonw/bacting"
preferred-citation:
  type: article
  authors:
    - family-names: Willighagen
      given-names: Egon L.
  title: "Bacting: a next generation, command line version of Bioclipse"
  year: 2021
  month: 6
  day: 23
  journal: Journal of Open Source Software
  volume: 6
  issue: 62
  doi: 10.21105/joss.02558
  url: https://doi.org/10.21105/joss.02558

GitHub Events

Total

Create event: 5
Issues event: 1
Release event: 4
Watch event: 1
Issue comment event: 4
Push event: 23
Pull request event: 11
Fork event: 2

Last Year

Create event: 5
Issues event: 1
Release event: 4
Watch event: 1
Issue comment event: 4
Push event: 23
Pull request event: 11
Fork event: 2

Committers

Last synced: 7 months ago

All Time

Total Commits: 813
Total Committers: 2
Avg Commits per committer: 406.5
Development Distribution Score (DDS): 0.001

Past Year

Commits: 75
Committers: 1
Avg Commits per committer: 75.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Egon Willighagen	e**n@g**m	812
Daniel Mietchen	d**n@g**m	1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 55
Total pull requests: 77
Average time to close issues: 5 months
Average time to close pull requests: 22 days
Total issue authors: 5
Total pull request authors: 5
Average comments per issue: 0.95
Average comments per pull request: 1.08
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 6

Past Year

Issues: 1
Pull requests: 13
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Issue authors: 1
Pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 0.85
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

egonw (48)
Zethson (3)
kozo2 (2)
arcuri82 (1)
DeniseSl22 (1)

Pull Request Authors

egonw (72)
dependabot[bot] (6)
Haoyu-Gao (2)
Daniel-Mietchen (1)
larsgw (1)

Top Labels

Issue Labels

article (12) enhancement (8) hacktoberfest (4) bug (3) help wanted (2)

Pull Request Labels

dependencies (6) enhancement (1)

Packages

Total packages: 27
Total downloads: unknown

Total dependent packages: 51
(may contain duplicates)
Total dependent repositories: 16
(may contain duplicates)
Total versions: 1,373

repo1.maven.org: io.github.egonw.bacting:bacting-core

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/bacting-core/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 58
Dependent Packages: 15
Dependent Repositories: 1

Rankings

Dependent packages count: 4.2%

Dependent repos count: 20.8%

Average: 28.1%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-ui

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-ui/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 11
Dependent Repositories: 1

Rankings

Dependent packages count: 5.6%

Dependent repos count: 20.8%

Average: 28.4%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-cdk

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-cdk/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 9
Dependent Repositories: 1

Rankings

Dependent packages count: 6.7%

Dependent repos count: 20.8%

Average: 28.7%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-rdf

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-rdf/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 3
Dependent Repositories: 1

Rankings

Dependent packages count: 17.6%

Dependent repos count: 20.8%

Average: 31.4%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-inchi

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-inchi/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 2
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 23.2%

Average: 32.8%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-excel

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-excel/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 60
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-bridgedb

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-bridgedb/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 60
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-pubchem

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-pubchem/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-chemspider

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-chemspider/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 59
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-cdkdebug

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-cdkdebug/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.wikidata

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/net.bioclipse.managers.wikidata/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 42
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-opsin

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-opsin/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.jsoup

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/net.bioclipse.managers.jsoup/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 36
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-biojava

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-biojava/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 52
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-xml

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-xml/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 54
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-oscar

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-oscar/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 49
Dependent Packages: 1
Dependent Repositories: 1

Rankings

Dependent repos count: 20.8%

Dependent packages count: 33.0%

Average: 35.3%

Stargazers count: 43.6%

Forks count: 43.8%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-bioinfo

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-bioinfo/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 60
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-search

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-search/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 36
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.pubmed

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/net.bioclipse.managers.pubmed/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 29
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.doi

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/net.bioclipse.managers.doi/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 29
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-semweb

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-semweb/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 58
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-nm

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-nm/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 25
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:bacting-bundle

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/bacting-bundle/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 45
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.duckduckgo

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/net.bioclipse.managers.duckduckgo/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 36
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-core

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-core/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 36
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Stargazers count: 30.3%

Dependent repos count: 32.0%

Average: 35.3%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:managers-cheminfo

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/managers-cheminfo/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Dependent repos count: 32.0%

Stargazers count: 32.1%

Average: 35.8%

Dependent packages count: 48.9%

Last synced: 6 months ago

repo1.maven.org: io.github.egonw.bacting:bacting

Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy.

Homepage: http://www.github.com/egonw/bacting
Documentation: https://appdoc.app/artifact/io.github.egonw.bacting/bacting/
License: Eclipse Public License v1.0 + GPL Exception
Latest release: 1.0.7
published 6 months ago

Versions: 61
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 30.2%

Dependent repos count: 32.0%

Stargazers count: 32.1%

Average: 35.8%

Dependent packages count: 48.9%

Last synced: 6 months ago

Dependencies

bacting-core/pom.xml maven

io.github.egonw.bacting:bioclipse-core ${bioclipse.version}

bundle/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:managers-biojava 0.0.39
io.github.egonw.bacting:managers-bridgedb 0.0.39
io.github.egonw.bacting:managers-cdk 0.0.39
io.github.egonw.bacting:managers-cdkdebug 0.0.39
io.github.egonw.bacting:managers-chemspider 0.0.39
io.github.egonw.bacting:managers-excel 0.0.39
io.github.egonw.bacting:managers-inchi 0.0.39
io.github.egonw.bacting:managers-opsin 0.0.39
io.github.egonw.bacting:managers-oscar 0.0.39
io.github.egonw.bacting:managers-pubchem 0.0.39
io.github.egonw.bacting:managers-rdf 0.0.39
io.github.egonw.bacting:managers-ui 0.0.39
io.github.egonw.bacting:managers-xml 0.0.39
io.github.egonw.bacting:net.bioclipse.managers.wikidata 0.0.39

managers-bioinfo/net.bioclipse.managers.biojava/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
org.biojava:core ${biojava.version}
org.biojava:sequencing ${biojava.version}
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:bioclipse-bridgedb ${bioclipse.version}
org.bridgedb.webservice:org.bridgedb.webservice.bridgerest ${bridgedb.version}
org.bridgedb:org.bridgedb.bio ${bridgedb.version}
org.bridgedb:org.bridgedb.rdb ${bridgedb.version}
io.github.egonw.bacting:managers-ui 0.0.39 test
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.cdk/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:bioclipse-cdkbusiness ${bioclipse.version}
org.openscience.cdk:cdk-depict ${cdk.version}
org.openscience.cdk:cdk-extra ${cdk.version}
org.openscience.cdk:cdk-interfaces ${cdk.version}
xom:xom ${xom.version}
io.github.egonw.bacting:managers-ui 0.0.39 test
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml maven

io.github.egonw.bacting:managers-cdk 0.0.39
org.openscience.cdk:cdk-diff ${cdk.version}
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml maven

io.github.egonw.bacting:managers-cdk 0.0.39
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.inchi/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:bioclipse-cdkbusiness ${bioclipse.version}
io.github.egonw.bacting:bioclipse-inchi ${bioclipse.version}
org.openscience.cdk:cdk-interfaces ${cdk.version}
xom:xom ${xom.version}
io.github.egonw.bacting:managers-cdk 0.0.39 test
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.opsin/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:managers-cdk 0.0.39
uk.ac.cam.ch.opsin:opsin-core 2.6.0
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.oscar/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:managers-cdk 0.0.39
net.htmlparser.jericho:jericho-html 3.4
org.apache.logging.log4j:log4j-core 2.17.2
uk.ac.cam.ch.wwmm.oscar:oscar4-all 5.1.2
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-cheminfo/net.bioclipse.managers.pubchem/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:bioclipse-cdkbusiness ${bioclipse.version}
io.github.egonw.bacting:bioclipse-inchi ${bioclipse.version}
io.github.egonw.bacting:managers-cdk 0.0.39
io.github.egonw.bacting:managers-rdf 0.0.39
io.github.egonw.bacting:managers-ui 0.0.39
org.apache.httpcomponents:httpclient 4.5.13
org.openscience.cdk:cdk-interfaces ${cdk.version}
xom:xom ${xom.version}
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-core/managers-jsoup/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
org.jsoup:jsoup 1.15.1
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-core/managers-ui/pom.xml maven

com.github.egonw:jqudt 1.4.0
io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:bioclipse-report ${bioclipse.version}
org.apache.httpcomponents:httpclient 4.5.13
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-excel/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
org.apache.poi:poi-ooxml 5.2.2
io.github.egonw.bacting:managers-ui 0.0.39 test
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-search/managers-doi/pom.xml maven

io.github.egonw.bacting:managers-ui 0.0.39
org.json:json 20220320
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-search/managers-pubmed/pom.xml maven

io.github.egonw.bacting:managers-ui 0.0.39
org.json:json 20220320
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-search/net.bioclipse.managers.duckduckgo/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
io.github.egonw.bacting:managers-ui 0.0.39
io.github.egonw.bacting:net.bioclipse.managers.jsoup 0.0.39
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-semweb/managers-rdf/pom.xml maven

io.github.egonw.bacting:bioclipse-core ${bioclipse.version}
io.github.egonw.bacting:bioclipse-rdf ${bioclipse.version}
org.apache.jena:jena-shex ${jena.version}
org.slf4j:slf4j-simple 1.7.36
io.github.egonw.bacting:managers-ui 0.0.39 test
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-semweb/managers-xml/pom.xml maven

io.github.egonw.bacting:bacting-core 0.0.39
xom:xom 1.3.7
io.github.egonw.bacting:managers-ui 0.0.39 test
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-semweb/net.bioclipse.managers.wikidata/pom.xml maven

io.github.egonw.bacting:bioclipse-core ${bioclipse.version}
io.github.egonw.bacting:managers-cdk 0.0.39
io.github.egonw.bacting:managers-inchi 0.0.39
io.github.egonw.bacting:managers-rdf 0.0.39
io.github.egonw.bacting:managers-ui 0.0.39
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

.github/workflows/maven.yml actions

actions/checkout v2 composite
actions/setup-java v1 composite

managers-cheminfo/net.bioclipse.managers.nm/pom.xml maven

io.github.egonw.bacting:bacting-core 0.3.0
io.github.egonw.bacting:managers-cdk 0.3.0
io.github.egonw:nanojava 2.0.1
org.slf4j:slf4j-api ${slf4j.version}
org.slf4j:slf4j-simple ${slf4j.version}
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-bioinfo/pom.xml maven

managers-cheminfo/pom.xml maven

managers-core/pom.xml maven

managers-search/managers-find/pom.xml maven

io.github.egonw.bacting:managers-ui 0.4.1
io.github.egonw.bacting:managers-xml 0.4.1
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-search/managers-zenodo/pom.xml maven

io.github.egonw.bacting:managers-ui 0.4.1
org.json:json ${json.version}
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

managers-search/pom.xml maven

managers-semweb/pom.xml maven

pom.xml maven

managers-search/net.bioclipse.managers.mwmbl/pom.xml maven

io.github.egonw.bacting:bacting-core 1.0.0
io.github.egonw.bacting:managers-ui 1.0.0
org.json:json ${json.version}
org.junit.jupiter:junit-jupiter ${junit.version} test
org.junit.jupiter:junit-jupiter-engine ${junit.version} test

Bacting

Science Score: 98.0%

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Bacting

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Bacting: a next generation, command line version of Bioclipse

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repo1.maven.org: io.github.egonw.bacting:bacting-core

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repo1.maven.org: io.github.egonw.bacting:managers-ui

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repo1.maven.org: io.github.egonw.bacting:managers-cdk

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repo1.maven.org: io.github.egonw.bacting:managers-rdf

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repo1.maven.org: io.github.egonw.bacting:managers-inchi

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repo1.maven.org: io.github.egonw.bacting:managers-excel

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repo1.maven.org: io.github.egonw.bacting:managers-bridgedb

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repo1.maven.org: io.github.egonw.bacting:managers-pubchem

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repo1.maven.org: io.github.egonw.bacting:managers-chemspider

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repo1.maven.org: io.github.egonw.bacting:managers-cdkdebug

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repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.wikidata

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repo1.maven.org: io.github.egonw.bacting:managers-opsin

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repo1.maven.org: io.github.egonw.bacting:net.bioclipse.managers.jsoup

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repo1.maven.org: io.github.egonw.bacting:managers-biojava

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repo1.maven.org: io.github.egonw.bacting:managers-xml

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repo1.maven.org: io.github.egonw.bacting:managers-oscar