Welcome to the VHP4Safety documentation!

Hi There! You have reached the public documentation pages for the Virtual Human Platform for Safety Evaluation of Chemicals. This is a large Dutch research project, funded by NWO. These pages contain information, documentation, installation instructions and demos on how to use the software, models and data generated in the project.

Project Information

• Our Mission and Vision
  • Towards Safety Assessment Based on Human Data
  • Moving away from animal experimentation
• VHP4Safety Research Lines
  • RL1: Building the Virtual Human Platform
  • RL2: Feeding the Virtual Human Platform
  • RL3: Implementing the Virtual Human Platform
• Case Studies and Regulatory Questions
• Partners and Consortium
• Contact Us

Service Tutorials

• AOP Suite Tutorial
  • 1. Introduction
  • 2. Accessing the Tool
  • 3. Tool Functionalities
  • 4. Interpreting the Output
  • 5. Summary / Conclusion
• AOP-Wiki Service Tutorial
  • AOP-Wiki SNORQL for Direct User Access
  • AOP-Wiki SPARQL Endpoint for Automated Access
  • AOP-Wiki RDF Schema
  • Conclusion
• AOP-Wiki API Tutorial
  • The Swagger Interface
  • External access to API
  • Conclusion
• BridgeDb: Mapping Gene Identifiers
  • Using BridgeDb with Python
  • Using BridgeDb with R
• cpLogD: Predicting Water–Octanol Distribution Coefficient (logD) for Chemical Compounds
  • Introduction
  • Using cpLogD through a Web Browser
• Molecular Adverse Outcome Pathway analyser tutorial
  • Step 1: Selecting or Uploading a Dataset
  • Step 2: Column Selection and Data Preview
  • Step 3: Volcano Plot Visualisation
  • Step 4: AOP Selection and Enrichment Analysis
  • Step 5: Enrichment Table
  • Step 6: AOP Network Visualisation
  • Output Files
  • Acknowledgements
• O-QT Assistant: Multi-Agent Chemical Analysis
  • Configuration and Connection
  • Chemical Identification and Analysis Context
  • Automated Assessment
• qAOP App: Predicting Key Events and Adverse Outcomes Over Time
  • Model Selection and Inputs
  • Run Simulation
• QSPRpred App: Predicting Molecular Initiating Event Activation based on chemical structure
  • Introduction
  • Accessing the Tool
  • Tool Functionalities
  • Interpreting the Output
  • Summary
  • References
• Transcriptomic data analysis with R-ODAF
  • 1. Introduction
  • 2. Accessing the Tool
  • 3. Tool Functionalities
  • 4. Interpreting the Output
  • 5. Summary / Conclusion
• SOM Prediction: Site-of-Metabolism Prediction
  • Using SOM Prediction with Python

Workflows

• AOPLink: Extracting and Analyzing Data Related to an AOP of Interest
  • Loading the Required Packages
  • Defining the AOP of Interest
  • AOP-Wiki RDF
  • ChemIdConvert and CDK Depict
  • AOP-DB RDF
  • WikiPathways RDF
• Information about chemicals
  • Name to Structure
  • Visualize a Structure
  • External databases
  • Identifier Mapping
  • Metabolite prediction

Service Catalog

• AOP-Wiki Snorql UI
• AOP-Wiki API
• BridgeDb
• CDK Depict
• cpLogD
• DECIMER
• PopGen
• SysRev
• TXG-MAPr
• VHP4Safety Wikibase

Glossary

• VHP4Safety Glossary
  • DEVELOPMENT VERSION
  • Toxicology in General
  • Risk assessment-related terms
  • Adverse Outcome Pathway-related terms
  • Server-related terms
  • Tool/service-related terms
  • Project-related terms
  • Organizations

Sustainability

• Service Monitoring with Icinga 2
  • Installing Icinga 2
  • Creating Services
  • Applying Changes in Configuration Files

Miscellaneous

• Data collection templates
• Documentation Format

Indices and tables

• Index

• Module Index

• Search Page