Ondex components and applications that are necessary for building genome-scale knowledge networks used in projects like KnetMiner. It includes the Ondex base, CLI, workflow engine and a set of plugins (parsers, mappers, transformers, filters and exporters) that are relevant for building genome-scale knowledge networks as described in Hassani-Pak et al. 2016.
- Java 8
- See the Downloads Page
Create a new folder e.g.
Download the latest KnetBuilder release and unzip in knetbuilder-folder
Download the tutorial files and unzip in knetbuilder-folder
Check the folder structure looks like this
-bash-4.1$ ls knetbuilder-folder/ ondex-mini-1.2 tutorial_files
- Go to the downloaded ondex-mini folder and run a workflow:
cd ondex-mini-1.2 ./runme.sh ../tutorial_files/Workflow/HumanDiseaseKNET.xml
The KnetBuilder workflow integrates several datasets and creates a OXL file
We keep most of our documentation on this repository's Wiki (note that there are many links on the right column in that page).