Final OpenRiskNet Workshop: Creating powerful workflows combining data and software services demonstrated on risk assessment case studies

Workshop (organized by OpenRiskNet)
23 – 24 Oct 2019 / Amsterdam, NL

Activity details

Venue: Vrije Universiteit, Auditorium, O|2 Human Life Sciences building, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands (Map)

  • Booklet (agenda, abstract, additional information)

The OpenRiskNet project, developing and implementing an open e-infrastructure addressed to research and industrial communities performing risk assessment of consumer products like chemicals, cosmetics or drugs, is in its third and final year.

To disseminate the achievements and implemented concepts of the project, make the stakeholders aware of the solutions developed, find the best options for the adoption by other projects or organisations, a final workshop is organized. The event will create the perfect environment for current and future users of OpenRiskNet services, developer and administrators as well as  the members of related (e-)infrastructure communities to interact with OpenRiskNet developers, modellers and project managers, learn more about the success of the community building efforts fostered by the associated partner programme and the implementation challenges, establish and strengthen links to other projects and organize the transfer of the technology into these.

The workshop is addressing all OpenRiskNet stakeholders (scientific, industrial and regulatory communities) that are invited to participate in this interactive event. This will ensure that all relevant and target groups that need to be aware of the project achievements have access to this information and are enabled to give feedback, and also be trained on the provided solutions.

Therefore we invite members of research organisations, academia, regulators and governmental agencies, SMEs and CROs, members of EU infrastructure initiatives to join us for the final workshop. Besides researchers, risk assessors and regulators, the workshop is specifically designed to provide the needed information for developers on how to integrate additional services and for system administrators on deployment options of the virtual research environments in parallel session.

A significant part of the event (day 1) will focus on the case studies, demonstrations and hands-on training sessions, where the teams involved in the development and implementation will present and demonstrate the use of the services included in the OpenRiskNet e-infrastructure.

Day 2 will then focus on the outreach and sustainability aspects:

  1. The implementation challenges were implemented as an innovative part of the associated partners programme during the project and linked ten new organisations intensively to project as service providers and early adopters. Complementary services from these partners can now be used and were integrated in the case studies workflow

  2. The sustainability measures, the support and maintenance of the infrastructure after the end of the project, collaborations and links created with other communities will be highlighted and discussed with representatives of other major pan-European infrastructures and policy makers.

Agenda

Day 1 - 23 October 2019

8:30-9:00

Registration

9:00-9:10

Welcome and introduction to the workshop

Thomas Exner (Edelweiss Connect, GmbH, Switzerland)

9:10-9:30

OpenRiskNet Case studies introduction and concept

Paul Jennings (Vrije Universiteit Amsterdam, The Netherlands)

9:30-10:30


8 min /

case study

OpenRiskNet Case studies (flash presentations):

10:30-11:00

Coffee break (incl. posters viewing)

OpenRiskNet demo & training sessions

11:00-12:30

  • Workflows: practical example of Jupyter notebooks use, Data curation example, workflow across multiple case studies

Marvin Martens (UM) and Thomas Exner (EwC)

12:30-13:30

Lunch break

13:30-15:30

Parallel sessions:



Tim Dudgeon and Alan Christie (IM)

Philip Doganis and Pantelis Karatzas (NTUA), Denis Gebele (JGU), Tomaž Mohorič (EwC), and Jonathan Alvarsson (UU)

15:30-16:00

Coffee break (incl. posters viewing)

16:00-17:30

Parallel sessions:

Tim Dudgeon and Alan Christie (IM)

Egon Willighagen (UM)

18:00-

Dinner - Buffet organised at workshop venue


Day 2 - 24 October 2019

Associated partners session

Chair: Rex FitzGerald (Swiss Centre for Applied Human Toxicology, University of Basel, Switzerland)

9:00-10:45


20 min /

presentation

Strategy used to build confidence in PROSILICO's in silico methods for prediction of human clinical ADME/PK

Urban Fagerholm (Prosilico, Sweden)

FAME 3: Predicting the Sites of Metabolism in Small Molecules for Phase 1 and Phase 2 Metabolic Enzymes

FAME 3 API in OpenRiskNet

Johannes Kirchmair and Martin Šícho (University of Hamburg, Germany)

Using SPARQL to explore human protein data in neXtProt and beyond

Lydie Lane (CALIPHO group, SIB Swiss Institute of Bioinformatics, Switzerland)

ToxicoGx: An R platform for integrated toxicogenomics data analysis

Sisira Kadambat Nair (Princess Margaret Cancer Centre, University Health Network, Toronto, Canada)

US EPA AOP-DB: A database resource for the exploration of Adverse Outcome Pathways

Holly M. Mortensen (US Environmental Protection Agency, Office of Research and Development, USA)

10:45-11:15

Coffee break (incl. posters viewing)

11:15-12:00

ToxPlanet: demo, information on API, discussion on use case scenarios

Matt Timberlake (ToxPlanet, USA)

12:00-12:15
Diamond Light Source: OpenRiskNet’s first external Virtual EnvironmentTim Dudgeon (Informatics Matters Ltd, UK)

12:15-12:30

Lessons learned from the associated partner programme

Thomas Exner (Edelweiss Connect, GmbH, Switzerland)

12:30-13:30

Lunch break


EU infrastructures & sustainability session

Chair: Stefan Kramer (Johannes Gutenberg University Mainz, Germany)

13:30-14:00

Adoption of OpenRisknet solutions by NanoSafety community and NanoCommons infrastructure

Iseult Lynch (University of Birmingham, UK)

14:00-15:00

Introduction to the European Open Science Cloud (EOSC) and OpenAIRE: an EOSC implementation project (20 min)

Alessia Bardi (Institute of Science and Technology of Information, CNR, Italy)

eInfraCentral: an EOSC implementation project (10 min)

Bjorn Backeberg (EGI Foundation, The Netherlands) on behalf of Jelena Angelis (EFIS Centre, Belgium)

EOSC-hub: an EOSC implementation project (10 min)

Bjorn Backeberg (EGI Foundation, The Netherlands)

Technical demo of cloud and storage services in EOSC (20 min)

Yin Chen (EGI Foundation, The Netherlands)

15:00-15:30

Coffee break

15:30-16:00

Panel discussion: lesson learned and looking ahead to the next steps

16:00-16:15

Closing session

Organisations involved

Edelweiss Connect GmbH (EwC)
Johannes Gutenberg-Universität Mainz (JGU)
Fundacio Centre de Regulacio Genomica (CRG)
Universiteit Maastricht (UM)
The University Of Birmingham (UoB)
National Technical University of Athens (NTUA)
Fraunhofer Gesellschaft zur Förderung der Angewandten Forschung e.V. (Fraunhofer)
Uppsala Universitet (UU)
Vrije Universiteit Amsterdam (VU)
Informatics Matters Limited (IM)
Institut National de l’Environnement et des Risques (INERIS)

Links and additional materials

Documents:
0-OpenRiskNet_Final_workshop_eInfraCentral.pdf - eInfraCentral: an EOSC implementation project
EOSC-OpenAIRE.pdf - OpenAIRE: an EOSC implementation project
0-EOSC-hub_overview.pdf - Introduction to the European Open Science Cloud (EOSC)
The_NanoCommons_knowledge_infrastructure-OpenRiskNet.pdf - Adoption of OpenRisknet solutions by NanoSafety community and NanoCommons infrastructure
Lessons_Learned.pdf - Lessons learned from the associated partner programme
ORN_-_Diamond_Virtual_Environment.pdf - Diamond Light Source: OpenRiskNet’s first external Virtual Environment
ORN_ToxPlanet.pdf - ToxPlanet: demo, information on API, discussion on use case scenarios
Mortensen_OpenRiskNetFinalWrkshp_Oct24_2019_AOP_DB_Final.pdf - US EPA AOP-DB: A database resource for the exploration of Adverse Outcome Pathways
ToxicoGx_Sisira-WS-241019.pdf - ToxicoGx: An R platform for integrated toxicogenomics data analysis
Using_SPARQL_to_explore_human_protein_data_in_neXtProt_and_beyond.pdf - Using SPARQL to explore human protein data in neXtProt and beyond
ORN_Meeting_Martin_Šícho.pdf - FAME 3 API in OpenRiskNet
2019-10-24_amsterdam_openrisknet_workshop_kirchmair.pdf - FAME 3: Predicting the Sites of Metabolism in Small Molecules for Phase 1 and Phase 2 Metabolic Enzymes
PROSILICO_-_Presentation_ORN_Amsterdam_2019.pdf - Strategy used to build confidence in PROSILICO's in silico methods for prediction of human clinical ADME/PK
RevK.pdf - RevK flash presentation
AOPLink.pdf - AOPLink flash presentation
MetaP.pdf - MetaP flash presentation
TGX__SysGroup.pdf - TGX and SysGroup flash presentation
ModelRX.pdf - ModelRX flash presentation
DataCure.pdf - DataCure flash presentation
Case_studies_introduction_and_concept.pdf - Case studies introduction and concept
Welcome_and_introduction_to_the_workshop.pdf - Welcome and introduction to the workshop

Audience reached

Mixed audience (scientists, regulatory, industry, developers, etc.): 53