OpenRiskNet e-infrastructure available to end-users

1 October 2018

Current implementations and tools integrated

The reference environment is available at https://home.prod.openrisknet.org/. There is a continuously updated list of integrated services and example workflows, which show how to combine services to fully exploit the benefits of the harmonisation and interoperability concepts.

Besides this reference instance, OpenRiskNet provides resources to enable users to instantiate their own virtual infrastructures populated with the applications and middleware making up the VRE on public or private cloud resources, as well as in-­house server/workstations.

The currently available services and tools include:

  • OpenRiskNet and Third-Party Workflow Managers and Scripting Tools: Squonk Computational Notebook, Jupyter Notebooks
  • Graphical User Interface Access to OpenRiskNet Applications: Lazar Toxicity Predictions, Jaqpot Modeling and Analysis Services
  • OpenRiskNet Data Sources: Nanomaterial database (eNanoMapper), Data Explorer serving ToxCast, ToxRefDB and TG-Gates data
  • Example Workflows based on OpenRiskNet Tools: Jupyter Notebook: Access TG-Gates data for selected compounds, select differentially expressed genes and identifier relevant pathways
  • API Definitions for OpenRiskNet Applications and Data: Model Generation (Lazar Toxicity Predictions, JGU WEKA REST Service, Jaqpot Modeling and Analysis Services), Trained Models (LogP Predictor, Metabolic Site Predictor) and Helper Tools (Chemical ID Converter Service), Data and Knowledge Sources (BridgeDb identifier mapping service, eNanoMapper database, ToxCast, ToxRefDB)

The OpenRiskNet e-­infrastructure aims to support many aspects of risk assessment by allowing the integration of toxicology-­related data sources, for the implementation and execution of processing and analysis pipelines and for the execution of modelling workflows.