knime-sstea
Knime node to calculate ss-TEA score of sequence alignment and subfamily members.
Science Score: 67.0%
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 -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.5%) to scientific vocabulary
Repository
Knime node to calculate ss-TEA score of sequence alignment and subfamily members.
Basic Info
Statistics
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 3
- Releases: 6
Metadata Files
README.md
KNIME node to calculate subfamily specific two entropy analysis (ss-TEA) score.
The ss-TEA can identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information.
See reference at https://doi.org/10.1186/1471-2105-12-332 for a description of the score.
Installation
Requirements:
- KNIME, https://www.knime.org
Steps install ss-TEA KNIME node:
- Goto Help > Install new software ... menu
- Press add button
- Fill text fields with
https://3d-e-chem.github.io/updates/5.1/ - Select --all sites-- in work with pulldown
- Open KNIME 3D-e-Chem Contributions folder
- Select ss-TEA
- Install software & restart
Usage
See example workflow at examples/ss-TEA-example.zip.
It can be run by importing it into KNIME as an archive.
Build
mvn verify
Jar has been made in /target folder.
An Eclipse update site will be made in p2/target/repository repository.
Development
Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
- Install Java 17
- Install Eclipse for RCP and RAP developers
- Configure Java 17 inside Eclipse Window > Preferences > Java > Installed JREs
- Import this repo as an Existing Maven project
- Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the
KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.sstea.targetplatform/KNIME-AP-5.1.targettarget definition.
During import the Tycho Eclipse providers must be installed.
Tests
Tests for the node are in tests/src directory.
Tests can be executed with mvn verify, they will be run in a separate Knime environment.
Unit tests
Unit tests written in Junit4 format can be put in tests/src/java.
Workflow tests
See https://github.com/3D-e-Chem/knime-testflow#3-add-test-workflow
New release
- Update versions in pom files with
mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOTcommand. - Commit and push changes
- Create package with
mvn package, will create update site inp2/target/repository - Append new release to 3D-e-Chem update site
- Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
- Append release to 3D-e-Chem update site with
mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
- Commit and push changes in this repo and 3D-e-Chem.github.io repo
- Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
Owner
- Name: 3D-e-Chem NLeSC project
- Login: 3D-e-Chem
- Kind: organization
- Location: Amsterdam, The Netherlands
- Website: https://www.esciencecenter.nl/project/3d-e-chem
- Repositories: 33
- Profile: https://github.com/3D-e-Chem
Software repositories for 3D-e-Chem project of Netherlands eScience Center
Citation (CITATION.cff)
# YAML 1.2
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.0.3
message: If you use this software, please cite it as below.
title: KNIME ss-TEA node
doi: 10.5281/zenodo.3257702
authors:
- given-names: Stefan
family-names: Verhoeven
affiliation: Netherlands eScience Center
orcid: https://orcid.org/0000-0002-5821-2060
version: 1.0.6
date-released: 2019-06-26
repository-code: https://github.com/3D-e-Chem/knime-sstea
license: Apache-2.0
references:
- type: article
doi: 10.1186/1471-2105-12-332
title: 'ss-TEA: Entropy based identification of receptor specific ligand binding
residues from a multiple sequence alignment of class A GPCRs'
authors:
- given-names: Marijn PA
family-names: Sanders
- given-names: Wilco WM
family-names: Fleuren
- given-names: Stefan
family-names: Verhoeven
- given-names: Sven
family-names: van den Beld
- given-names: Wynand
family-names: Alkema
- given-names: Jacob
family-names: de Vlieg
- given-names: Jan PG
family-names: Klomp