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knime-plants

KNIME nodes to configure, run and analyze PLANTS protein-ligand docking

https://github.com/3d-e-chem/knime-plants

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 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (14.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

KNIME nodes to configure, run and analyze PLANTS protein-ligand docking

Basic Info
  • Host: GitHub
  • Owner: 3D-e-Chem
  • License: apache-2.0
  • Language: Java
  • Default Branch: master
  • Size: 4.51 MB
Statistics
  • Stars: 4
  • Watchers: 6
  • Forks: 2
  • Open Issues: 3
  • Releases: 5
Created over 9 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Citation Zenodo

README.md

knime-plants

KNIME nodes to configure, run and analyze PLANTS protein-ligand docking

PLANTS homepage at http://www.tcd.uni-konstanz.de/research/plants.php

Java CI with Maven Quality Gate Status Coverage DOI

This project uses Eclipse Tycho to perform build steps.

License

Included in PLANTS nodes plugin is the PLANTS executable with academic license (http://www.tcd.uni-konstanz.de/research/plants.php). When installing the plugin you have to accept this license agreement, you agree to use the included PLANTS executable only for academic usage. To use these nodes in a commercial manner you need to acquire a valid license yourself and configure the PLANTS node to use the commercial executable.

The PLANTS KNIME nodes themselves have the Apache 2.0 license.

Installation

Requirements:

  • KNIME, https://www.knime.org, version 5.1 or higher

Steps to get the PLANTS KNIME node inside KNIME:

  1. Goto Help > Install new software ... menu
  2. Press add button
  3. Fill text fields with the https://3d-e-chem.github.io/updates/5.1 update site url.
  4. Select --all sites-- in work with pulldown
  5. Select the node
  6. Install software
  7. Restart KNIME

Usage

  1. Create a new KNIME workflow.
  2. Find node in Node navigator panel.
  3. Drag node to workflow canvas.

Examples

The examples/ folder contains example KNIME workflows.

Build

mvn verify

An Eclipse update site will be made in p2/target/repository directory. The update site can be used to perform a local installation.

Development

Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:

  1. Install Java 17
  2. Install Eclipse for RCP and RAP developers
  3. Configure Java 17 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 (5.1) - nl.esciencecenter.e3dchem.knime.plants.targetplatform/KNIME-AP-5.1.target target definition.

During import the Tycho Eclipse providers must be installed.

Meta nodes

This plugin uses metanodes as it's public nodes. They are created in the following way:

  1. The meta nodes are first created and tested inside the example workflows in the examples/ directory.
  2. The name and customDescription field inside examples/**/workflow.knime is filled.
  3. The examples are fully run and committed
  4. The meta nodes are internally completely reset, so we don't ship public nodes with example data in them.
  5. The meta nodes from the example workflows are then copied to the plugin/src/knime/ directory.
  6. The meta nodes are added to the plugin/plugin.xml as PersistedMetaNode in the org.knime.workbench.repository.metanode extension.
  7. The examples are checked-out to their fully run state.

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. Test results will be written to test/target/surefire-reports directory. Code coverage reports (html+xml) can be found in the tests/target/jacoco/report/ directory.

There are no tests for the meta nodes as they are copied from the plugin to a workflow each time, which would make the test test itself.

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

Speed up builds

Running mvn commands can take a long time as Tycho fetches indices of all p2 update sites. This can be skipped by running maven offline using mvn -o.

New release

  1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT command.
  2. Create package with mvn package, will create update site in p2/target/repository
  3. Run tests with mvn verify
  4. Optionally, test node by installing it in KNIME from a local update site
  5. Append new release to an update site
    1. Make clone of an update site repo
    2. Append release to the update site with mvn install -Dtarget.update.site=<path to update site>
  6. Commit and push changes in this repo and update site repo.
  7. Create a GitHub release
  8. Update Zenodo entry
    1. Correct authors
    2. Add https://doi.org/10.1007/11839088_22 as is referenced by this upload related identifier
  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
  10. Update CITIATION.cff with new DOI

Owner

  • Name: 3D-e-Chem NLeSC project
  • Login: 3D-e-Chem
  • Kind: organization
  • Location: Amsterdam, The Netherlands

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 PLANTS nodes
doi: 10.5281/zenodo.3258170
authors:
- given-names: Stefan
  family-names: Verhoeven
  affiliation: Nederlands eScience Center
- given-names: George
  family-names: Kanev
  affiliation: Vrije Universiteit Amsterdam
- given-names: Albert
  family-names: Kooistra
  name-particle: J.
  affiliation: Vrije Universiteit Amsterdam
- given-names: Marton
  family-names: Vass
  affiliation: Vrije Universiteit Amsterdam
- given-names: Ross
  family-names: McGuire
  affiliation: Radboud UMC
- given-names: Chris
  family-names: de Graaf
  affiliation: Vrije Universiteit Amsterdam
repository-code: https://github.com/3D-e-Chem/knime-plants
license: Apache-2.0
references:
- type: conference-paper
  doi: 10.1007/11839088_22
  title: 'PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design'
  authors:
  - given-names: Oliver
    family-names: Korb
  - given-names: Thomas
    family-names: Stützle
  - given-names: Thomas
    name-particle: E.
    family-names: Exner

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