21 Nov 2017:
○ 16:30 - 17:30 Hackathon sessions
■ Introduction to the biokinetics hackathon
■ Introduction to the data hackathon on estrogenic activity data
22 Nov 2017:
○ 08:30 - 11:00 Hackathon sessions
■ Hands-on session on the topics introduced the day before
Responsible(s): Egon Willighagen (UM)
■ Short reminder on how to browse ontologies
Prior knowledge: not required
Title: Biokinetics modelling
Responsible(s): Frederic Bois (INERIS) and Harry Sarimveis (NTUA)
■ Aim: understanding the use, form, inputs and outputs of physiologically based (PBPK) pharmacokinetic models.
■ General presentation of PBPK models (F. Bois, 45 minutes)
About the software PKSim, see http://www.open-systems-pharmacology.org/ and documentation herein:
See for example the recent https://github.com/Open-Systems-Pharmacology/OSP-based-publications-and-content/issues/104
Title: Workflow management systems
Responsible(s): Tim Dudgeon (IM), Cedric Notredame
We will describe and demonstrate workflow tools that will be incorporated into the OpenRiskNet platform, and form a key aspect of the ways end users interact with the OpenRiskNet services. This will primarily be a demo of the tools involved and a discussion of how we plan to use and integrate these in OpenRiskNet, along with a limited opportunity to use these tools in a hands-on manner.
1. Introduction to the OpenRiskNet platform
Squonk Computational Notebook (http://squonk.it)
Title: NanoQSAR modelling (Jaqpot online platform)
Responsible(s): Philip Doganis (NTUA)
Training aim: Provide a modeling experience on nanoQSAR in two directions: Users that wish an introduction to modeling tools will be able to create their first models using the user interface Jaqpot provides.
Expected outcomes: Provide a foundation course on online modeling to serve as basis for the hackathon and hands-on experience with tools.
Requirements: Understanding of QSAR concepts.
Title: QSAR and conformal predictions (CPSign, ModelingWeb)
Responsible(s): Ola Spjuth (UU)
■ A short introduction to conformal prediction
Documentation for CPSign -- http://cpsign-docs.genettasoft.com/
Title: Biokinetics modelling
Responsible(s): Frederic Bois (INERIS) and
The aim of this workshop is to create a biokinetics model using the PKSim software and then use ORN functionalities to expose the model as a service on the web.
During this workshop we will:
■ Show the basic functionalities of Jaqpot API and UI.
Title: Estrogenic activity data for endocrine disruption predictions
Responsible(s): Thomas Exner (DC)
Endocrine disruption is of major regulatory importance. ECHA and EFSA are developing at the moment scientific guidance to enable endocrine disruptors to be identified (unfortunately not public available yet). FDA have created over the years valuable resources in form of the Endocrine Disruptor Knowledge Base (EDKB) and the Estrogenic Activity Database (EADB) and the estrogen and androgen receptors are important targets in EPA’s ToxCast and Tox21.
The hackathon is meant to look at these data sources and different in silico and integrated in silico-in vitro approaches and identify areas in which especially the new FDA data in combination with other data sources could help to improve the existing methods.
US EPA Endocrine Disruptor Screening Program – The Pivot: https://cfpub.epa.gov/si/si_public_file_download.cfm?p_download_id=523453
US National Toxicology Program: https://ntp.niehs.nih.gov/pubhealth/evalatm/test-method-evaluations/endocrine-disruptors/index.html
FDA case study: https://dx.doi.org/10.1021/acs.chemrestox.5b00243
Nicole’s models: https://pubs.acs.org/doi/abs/10.1021/acs.chemrestox.6b00347, https://pubs.acs.org/doi/abs/10.1021/acs.est.5b02641 and https://www.endocrinescience.org/wp-content/uploads/2015/12/AmericanChemistry-EPA-Scientists-Working-PC-12-15.pdf