cloud
VHP4Safety Cloud catalog
VHP4Safety needs a cloud with a high diversity of services to support their case studies. The services will run on (interal) but also outside (external) the VHP4Safety cloud, on a case by case basis.
This webpage gives an overview of the VHP4Safety Cloud Services on the Production and Development platforms. The second is where we develop and test cloud services, while the first runs a stable version of the service.
Below you find an overview of services available in the context of the VHP4Safety Platform. Additional services have been suggested and users can request additional services.
Cloud catalog
The VHP4Safety Cloud catalog of potential, internal, and external services is available here.
Service Contributions
You are welcome to contribute to this catalog by requesting or adding new services. Please see the manual to see the options for contribute to the catalog. Please contact us through the issues using the issue pages of this repository.
VHP4Safety Platform
The current development platform runs several services.
AOP Network Tool
Populate a network with AOPs and add weights to the edges based on custom tabular data, queries to other VHP tools and external databases, via BioDataFuse [more information]
AOP-Builder
A tool to explore scientific literature to extract relevant entities and their relations for AOP construction, using AI. [more information]
AOP-Wiki Snorql UI
A graphical interface to make queries to the AOP-Wiki SPARQL endpoint. [more information]
AOP-Wiki API
A REST API for AOP-Wiki content to make SPARQL queries. [more information]
BridgeDb
A framework to map identifiers between various biological databases and related sources. [more information]
CDK Depict
A webservice to convert SMILES into 2D depictions in either SVG, PNG, and PNG formats. [more information]
VHP4Safety Wikibase User Interface
A Synia-based graphical user interface to the content of the VHP4Safety Wikibase using SPARQL queries. [more information]
OP PBK Model
Physiologically based pharmacokinetic model for organophosphates [more information]
qAOP-App
An interactive tool offering an overview and dynamic time‐course predictions of KEs and AOs via ODE‐based qAOP models, based on VHP4Safety case studies. [more information]
QSPRpred
This tool allows users to predict the activity of their chemicals of interest for various endpoints. This prediction is done by target-specific, pretrained QSAR models. These models are specific for endpoints related to molecular initiation events from the VHP4Safety case studies. [more information]
SOM Prediction
A webservice to conduct protein-structure and reactivity based (P450) site-of-metabolism prediction. [more information]
ToxTempAssistant
A tool that uses Large Language Models to harmonize and complete method descriptions of in vitro toxicity tests based on the ToxTemp template. The tool alleviates the administrative burden on toxicologists by extracting methodological details from contextual documents, such as protocols, publications, or lab notebooks, and generating structured draft responses to the 77 questions of the ToxTemp template. [more information]
TXG-MAPr
An online application to implement weighted gene co-expression network analysis (WGCNA) derived from the Primary Human Hepatocytes (PHH) TG-GATEs data sets. [more information]
VHP4Safety Wikibase
A Wikibase instance to store and present information about toxic, safe and potentially toxic compounds related to the VHP4Safety project. [more information]
WikiPathways - AOP Portal
An Adverse Outcome Pathway (AOP) portal for WikiPathways to highlight the molecular basis of AOPs or events in AOPs. [more information]
xploreaop
A web application to visualize Adverse Outcome Pathway (AOP) networks and interactively explore the AOPs for two liver outcomes, Cholestasis and Steatosis. [more information]
External Services
BMDExpress-3
A tool to perform dose response modeling for high dimensional dose-response analysis. [more information]
CellDesigner
A structured diagram editor to draw gene-regulatory and biochemical networks. [more information]
CompTox
An online database to provide access to chemistry, toxicity, and exposure information for chemicals. [more information]
cpLogD
A model to predict water-octanol distribution coefficient (logD) for chemical compounds which is a proxy for the lipophilicity which is a major determinant of drug properties and overall suitability of drug candidates. [more information]
NIH Dietary Supplement Label Database
The Dietary Supplement Label Database was developed by the American Office of Dietary Supplements at the National Institutes of Health. This database includes printed on more than 200 thousand labels of dietary supplement products sold in the United States. [more information]
Flame
An open source framework to develop, host, and use machine-learning models, such as QSAR-like models, in production environments. [more information]
Google Search
Web search engine by Google. [more information]
Google Scholar
Search engine for (scientific) literature. [more information]
The OECD QSAR Toolbox
A software to support hazard assessment of chemicals as well as to increase mechanistic and other knowledge on chemical substances in a cost-efficient way. [more information]
O’QT: The OECD QSAR Toolbox AI Assistant
A tool to analyze chemicals, assess hazards, and get Read-Across recommendations using a powerful multi-agent AI system connected to the OECD QSAR Toolbox. [more information]
SysRev
An online service to conduct literature review, data extraction and systematic review. [more information]
Persona-Specific Catalogs
You can reach the list of services that are associated with specific persona’s below.
Funding
VHP4Safety – the Virtual Human Platform for safety assessment project NWA 1292.19.272 is part of the NWA research program ‘Research along Routes by Consortia (ORC)’, which is funded by the Netherlands Organization for Scientific Research (NWO). The project started on June 1, 2021 with a budget of over 10 million Euros and will last for the duration of 5 years.