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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.

Build Status DOI Quality Gate Status Coverage

Installation

Requirements:

Steps install ss-TEA KNIME node:

  1. Goto Help > Install new software ... menu
  2. Press add button
  3. Fill text fields with https://3d-e-chem.github.io/updates
  4. Select --all sites-- in work with pulldown
  5. Open KNIME 3D-e-Chem Contributions folder
  6. Select ss-TEA
  7. 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:

  1. Install Java 8
  2. Install Eclipse for RCP and RAP developers
  3. Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs
  4. Import this repo as an Existing Maven project
  5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the KNIME Analytics Platform (4.0) - nl.esciencecenter.e3dchem.knime.sstea.targetplatform/KNIME-AP-4.0.target target 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

  1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT command.
  2. Commit and push changes
  3. Create package with mvn package, will create update site in p2/target/repository
  4. Append new release to 3D-e-Chem update site
  5. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
  6. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
  7. Commit and push changes in this repo and 3D-e-Chem.github.io repo
  8. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release

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Knime node to calculate ss-TEA score of sequence alignment and subfamily members.

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