FSK-Lab repository

This project contains the PMM-Lab and FSK-Lab extension plugins to the data analytics software KNIME (www.knime.org). They are developed at the Federal Institute for Risk Assessment in Germany (BfR).

FSK-Lab

FSK-Lab is an open source extension plugin to the Konstanz Information Miner (KNIME). FSK-Lab enables KNIME users to work with FSK models within KNIME.

Installation

FSK-Lab may be installed throught the update site https://gitlab.bfr.berlin/silebat/repositories/raw/master/fsklab/. More information about the installation can be found at the Food Risk Labs website

Nodes

• FSK Creator
• FSK Runner
• FSK to R
• FSKX Reader
• FSKX Writer
• FSK Editor
• FSK to metadata

Project hierarchy

The project hierarchy is described in the wiki.

Changelog

Changelog is available at changelog.md.

PMM-Lab

Predictive Microbial Modeling Lab (PMM-Lab) is an open source extension to the Konstanz Information Miner (KNIME). PMM-Lab aims to ease and standardize the statistical analysis of experimental microbial data and the development of predictive microbial models (PMM).

It consists of three components:

• a library of KNIME nodes (called PMM-Lab)
• a library of "standard" workflows
• a HSQL databaase to store experimental data and microbial models

Installation

PMM-Lab may be installed using the FSK-Lab update site https://gitlab.bfr.berlin/silebat/repositories/raw/master/fsklab/. More information about the installation can be found at the Food Risk Labs website

Extension nodes

• Converters
  • XML To Table
• Editors
  • DB Data Deleter
  • Data Creator
  • Data Editor
  • Formula Creator
  • Model Creator
  • Model Editor
• Model Fitting
  • Model Fitting
  • PMM Joiner
• Readers
  • ComBase Reader
  • Data Reader
  • Formula Reader
  • Model Reader
  • NuML Reader
  • OpenFSMR Converter
  • PMFX Reader
  • SBML Reader
  • Variable Data Reader
  • XLS Data Reader
  • XLS Model Reader
• Selectors & Viewers
  • Data Selection
  • Fitted Parameter View
  • Predictor View
  • Predictor View JS (deprecated)
  • Primary Model Selection
  • Secondary Model View
  • Secondary Predictor View
  • Tertiary Model Selection
• Writers
  • ComBase Writer
  • Data Writer
  • Formula Writer
  • Model Writer
  • PMFX Writer

Eclipse plugin projects:

• com.jgoodies
• com.thoughtworks.xstream
• de.bund.bfr.formats
• de.bund.bfr.knime.pmm.bfrdbiface.lib
• de.bund.bfr.knime.pmm.common
• de.bund.bfr.knime.pmm.nodes
• de.bund.bfr.knime.pmm.sbml.test
• de.bund.bfr.knime.pmm.target
• de.bund.bfr.knime.pmm.tests
• de.bund.bfr.knime.pmmlab.update.p2
• de.bund.bfr.knime.pmmlab.update.p2.deploy
• JSBML_PMF
• net.sf.jabref
• org.freixas.jcalendar
• org.javers
• org.jdom2
• PMM_FEAT
• quick.dbtable