e-Infrastructure for developers

For service developers, infrastructure providers and data managers

OpenRiskNet offers the possibility to integrate additional tools, services and databases. This will create a greater visibility of your tools by being listed in the OpenRiskNet discovery service, additional features by combining with other tools, support for emerging techniques like API development and containerisation and deployment.

Participate

If you have developed a service, tool or database related to risk assessment that you would like to integrate in the OpenRiskNet e-infrastructure you can:

Also, you may take a this 10-minute survey aiming to investigate further your expertise and developments needs and requirements.

Getting started

  • Virtual Research Environments
    OpenRiskNet VRE requires a virtual infrastructure to be instantiated on either a public cloud (IaaS) provider or a local computer resource. Consult the procedures for creating the OpenShift cluster suitable for OpenRiskNet VRE on a virtual environment such as the SSC OpenStack environment.
  • Deployment
    Procedures for deploying the individual OpenRiskNet infrastructure components and applications.

OpenRiskNet Services for developers

In progress
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Bioinformatics
Topic:
Information extraction
Biological area:
Acute toxicity, Carcinogenicity, Mutagenicity, Genotoxicity, Skin sensitisation, Omics, Transcriptomics
For end-users
For developers
In progress
BridgeDb is a platform for database identifier mapping, both simple identifiers (e.g. CHEBI:1234) and universal resource identifiers (URIs, e.g. http://identifiers.org/chebi/CHEBI:1234). It is ...

Provided by:
Maastricht University
Type:
Database / data source, Service
Applicability domain:
Bioinformatics
Topic:
Identifier mapping
For developers
For end-users
Integrated
The model predicts Log D based on a support vector machine trained on data from ChEMBL version 23 comprising approximately 1.6 million compounds. The confidence interval is calculated for ...

Provided by:
Uppsala University
Type:
Trained model
Applicability domain:
Computational modelling
Topic:
Structure-activity relationship (SAR / QSAR), Predictive modelling, Chemical properties
For developers
For end-users
In progress
The eNanoMapper prototype database is part of the computational infrastructure for toxicological data management of engineered nanomaterials, developed within the EU FP7 eNanoMapper project. Provides support for upload, search and ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Information extraction, Nano safety, Chemical properties
For end-users
For developers
In progress
This service is a Virtuoso SPARQL endpoint that is loaded with RDF of the Adverse Outcome Pathway (AOP)-Wiki database (https://aopwiki.org/), based on the quarterly XML dumps that ...

Provided by:
Maastricht University
Type:
Database / data source
Applicability domain:
Toxicology, Bioinformatics
Topic:
Information extraction, Risk assessment
For end-users
For developers
Integrated
Generate, store and share predictive statistical and machine learning models
Jaqpot is a user-friendly web-based e-infrastructure containing many data analysis and modelling microservices integrated under harmonised APIs. The Jaqpot infrastructure allows the user to build applications that preprocess data, compute ...

Provided by:
National Technical University of Athens
Type:
Service, Data mining tool, Model, Model generation tool, Trained model, Processing tool, Analysis tool
Applicability domain:
Computational modelling, Predictive toxicology
Topic:
Predictive modelling, Biokinetics
For developers
For end-users
Integrated
Toxicity predictions
Lazar (Lazy Structure-Activity Relationships ) takes a chemical structure as input and provides predictions for a variety of toxic properties. Lazar uses an automated and reproducible read across procedure to calculate ...

Provided by:
in silico toxicology gmbh, Johannes Gutenberg Univertity
Type:
Trained model, Application, Service
Applicability domain:
Toxicology, Predictive toxicology
Topic:
Structure-activity relationship (SAR / QSAR)
Biological area:
Acute toxicity, Blood brain barrier, Carcinogenicity, NOAEL/LOAEL, Mutagenicity
For developers
For end-users
In progress
Machine learning models for site-of-metabolism prediction
FAME 2 is a cytochrome P450 site-of-metabolism predictor that uses extra trees machine learning models based on circular 2D atomic descriptors.

Provided by:
Universitaet Hamburg and UCT Prague and University of Bergen
Type:
Application, Service, Model, Trained model, Software
Applicability domain:
Predictive toxicology
Topic:
Predictive modelling, Structure-activity relationship (SAR / QSAR)
For end-users
For developers
Integrated
Chemical identifier conversion service
This REST Api allows you to submit chemical identifiers in one format and translate it into another format (e.g. SMILES -> InChi)

Provided by:
Douglas Connect
Type:
Helper tool
Topic:
Identifier mapping
For end-users
For developers
Integrated
The OpenRiskNet registry application
An overview of the OpenRiskNet compliant services running in this OpenRiskNet Virtual Research Environment.

Provided by:
Edelweiss Connect
Type:
Service
For system admins
For developers
In progress
Service to run Nextflow pipelines
The command line service provides the necessary environment to run any Nextflow pipeline. The basic command for using the service after logging in is: nextflow run <pipeline_name> For a collection of ...</pipeline_name>

Provided by:
Centre for Genomic Regulation (CRG)
Type:
Service, Workflow, Software
Applicability domain:
Bioinformatics
For developers
In progress
BridgeDb is a platform for database identifier mapping, both simple identifiers (e.g. CHEBI:1234) and universal resource identifiers (URIs, e.g. http://identifiers.org/chebi/CHEBI:1234). It is ...

Provided by:
Maastricht University
Type:
Database / data source, Service
Applicability domain:
Bioinformatics
Topic:
Identifier mapping
For developers
For end-users
In progress
Combining site-of-metabolism and reactivity for (P450) site-of-metabolism prediction. Includes structure-based predictor (from OpenRiskNet partner VU) and third-party (University of Copenhagen) reactivity predictor (SMARTCyp).

Provided by:
Vrije Universiteit Amsterdam
Type:
Service
Applicability domain:
Predictive toxicology
Topic:
Structure-activity relationship (SAR / QSAR)
For developers
For end-users
Integrated

Provided by:
Johannes Gutenberg University Mainz
Type:
Model generation tool, Trained model, Service
Applicability domain:
Computational modelling, Predictive toxicology
Topic:
Predictive modelling
For developers
For end-users
Integrated
Interactive computing and workflows sharing
A collection of Jupyter notebooks developed for and with the OpenRiskNet VRE. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved ...

Provided by:
Project Jupyter
Type:
Helper tool, Visualisation tool, Processing tool, Analysis tool, Software, Workflow
Applicability domain:
Computational modelling, Toxicology, Bioinformatics
For developers
For end-users
Integrated
MetPred predicts site-of-metabolism using a data mining approach based on Reaction SMARTS to define reaction types.

Provided by:
Uppsala University
Type:
Trained model, Service
Applicability domain:
Computational modelling
Topic:
Information extraction, Risk assessment
For developers
For end-users
Integrated
Computation research made simple and reproducible
We believe that the reason computational tools are not being utilised effectively in R&D is not because of a lack of functionality, but a lack of usability. And we ...

Provided by:
Informatics Matters
Type:
Database / data source, Service, Workflow
For developers
For end-users