Knime nodes to interact with KLIFS
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README.md

KLIFS knime nodes

Build Status Codacy Badge DOI

Knime plugin for retrieving data from KLIFS (http://klifs.vu-compmedchem.nl). KLIFS is a structural kinase-ligand interaction database. For more information regarding KLIFS see the website and the references at the bottom.

Installation

Requirements:

Steps to get KLIFS nodes inside KNIME:

  1. Goto Help > Install new software ... menu
  2. Press add button
  3. Fill text fields with https://3d-e-chem.github.io/knime-node-collection
  4. Select --all sites-- in work with pulldown
  5. Select KLIFS knime nodes
  6. Install software & restart (for now an "Unsigned Content" warning can popup during the installation, you can safely ignore this)

Usage

See the example workflow in examples folder.

Build

mvn verify

Jar has been made in plugin/target folder. An Eclipse update site will be made in p2/target/repository repository.

Development

Steps to get development enviroment 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)

    1. Goto Help > Install new software ...
    2. Make sure Update site is http://update.knime.org/analytics-platform/3.1 in the pull down list otherwise add it
    3. Select --all sites-- in work with pulldown
    4. Select m2e (Maven integration for Eclipse)
    5. Install software & restart
  5. Import this repo as an Existing Maven project

  6. Import client/ directory in repo as an Existing Maven project.

During import the Tycho Eclipse providers must be installed.

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://<path to update site directory>

Create KLIFS client

  1. Compile client
cd nl.vu_compmedchem.klifs.client
mvn package
  1. Make client jar and it's dependencies available in plugin
cp -r target/lib/* target/*jar ../nl.vu_compmedchem.klifs/lib/
  1. Update plugin/META-INF/MANIFEST.MF, plugin/build.properties files to reflect contents of lib/

References

  • Kooistra, A. J.; Kanev, G. K.; van Linden, O. P.; Leurs, R.; de Esch, I. J.; de Graaf, C. Klifs: A Structural Kinase-Ligand Interaction Database. Nucleic Acids Res. 2016, 44, D365-371. 10.1093/nar/gkv1082
  • van Linden, O. P.; Kooistra, A. J.; Leurs, R.; de Esch, I. J.; de Graaf, C. Klifs: A Knowledge-Based Structural Database to Navigate Kinase–Ligand Interaction Space. J. Med. Chem. 2013, 57, 249-277. 10.1021/jm400378w