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

Installation

Requirements:

Steps to get KripoDB Python templates inside KNIME:

  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:

  1. Download KNIME SDK from https://www.knime.org/downloads/overview

  2. Install/Extract/start KNIME SDK

  3. Start SDK

  4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit + 3D-e-Chem node category

    1. Goto Help > Install new software ...
    2. Make sure Update site http://update.knime.org/analytics-platform/3.1 and https://3d-e-chem.github.io/updates are in the pull down list otherwise add them
    3. Select --all sites-- in work with pulldown
    4. Select m2e (Maven integration for Eclipse)
    5. Select Test Knime workflows from a Junit test
    6. Select Splash & node category for 3D-e-Chem KNIME nodes
    7. Install software & restart
  5. Import this repo as an Existing Maven project

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> command.
  2. Manually update version of "source" feature in p2/category.xml file.
  3. Commit and push changes
  4. Create package with mvn package, will create update site in p2/target/repository
  5. Append new release to 3D-e-Chem update site
  6. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
  7. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
  8. Commit and push changes in this repo and 3D-e-Chem.github.io repo
  9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release

Offline Knime update site

If Knime update site can not be contacted then use a local version.

  1. Download zip of update site from https://www.knime.org/downloads/update
  2. Unzip it
  3. To maven commands add -Dknime.update.site=file://-Dknime.update.site=file://<path to update site directory>