OpenTox Euro 2013

OpenTox InterAction Meeting

Innovation in Predictive Toxicology

Open Infrastructure and Application Development, Integrated Data Analysis, Visualisation,

Cheminformatics, Bioinformatics, Systems Biology

Organised in Collaboration with ToxBank

30 September - 2 October 2013

Johannes Gutenberg University of Mainz, Mainz, Germany

This meeting will discussed latest developments in predictive toxicology, including in silico modelling and application development, integrated data analysis, systems biology, visualisation, cheminformatics and bioinformatics. Discussions will include consideration of current research and development directions in addition to risk assessment and regulatory and industry needs. A hands-on workshop on developments and applications will enable participants to try out methods and software applied to predictive toxicology problems.

Conference Chairs

The meeting will be co-chaired by Dr. Barry Hardy (Douglas Connect) and Prof. Stefan Kramer (Johannes Gutenberg University of Mainz).

Organising Committee

Barry Hardy (Douglas Connect), Andreas Karwath, Stefan Kramer (Johannes Gutenberg University of Mainz), Nina Jeliazkova (Ideaconsult), Egon Willighagen (Maastricht University), and Juergen Borlak (Hannover Medical School). Andreas Karwath (Johannes Gutenberg University of Mainz) leads the local conference organisation function.

Abstract Submission

Abstracts should be submitted through the conference Easy Chair system and will be reviewed by the conference chairs and organising committee. Please submit your abstracts using the form located at: https://www.easychair.org/conferences/?conf=opentoxeuro2013

Poster Session

Posters loaded upon poster boards will be available throughout the conference. All posters will be reviewed at the meeting to provide presenters feedback. Awards for best posters and best software will be announced in the final meeting session. You can view the Poster program at www.opentox.org/meet/opentoxeu2013/opentoxeu2013posters/

Location

The meeting will be held at the Johannes Gutenberg University of Mainz located in Mainz, Germany. Mainz is is the capital of the state of Rhineland-Palatinate in Germany. It was most likely founded by the Romans "perhaps as early as 13/12 BC" (en.wikipedia.org/wiki/Mainz). It is located very close to the Frankfurt airport and easily accessible via public transport. For the meeting, you should organize your travel and hotel reservations individually. However, we have made arrangements with three local hotels and reserved a contingency of 60 single room for special conditions (prices between 73.5 and 88.5 Euros incl. breakfast). The meeting itself will take place on campus. which is easily accessible via public transport from the main train station (bus # 69, leave at "Staudingerweg"). Accommodation information can be found here.

A map with all locations can be found at the bottom of the page

Arrival

In general, the best way to come to the meeting is by bus from the main train station. From bus stop G, there are buses (lines 54, 55, 58) to “Friedrich-von-Pfeiffer Weg” and from bus stop F (line 69) to “Staudinger Weg”. “Staudinger Weg” is closer, but during non term time the buses are less frequent. See the campus map with details about the bus stops and the venue location. If you arrive by car, then drive up the “Saarstrasse”, turn left at “Albert-Schweizer-Strasse” and after a few hundred meters turn right into “Dahlheimer Weg”. At the end, there is a free car park.

Registration

There is a modest local registration fee for the meeting (details can be found here). Furthermore, places are limited so please complete the registration form to reserve a place at the meeting:

https://www.surveymonkey.com/s/OpenToxEU2013

Conference Program

For Detailed Speaker Program with Abstracts: View OpenTox Euro 2013 Speaker Program (www.opentox.org/meet/opentoxeu2013/opentoxeu2013program)

A. Data Management and Analysis, chaired by Nina Jeliazkova (Ideaconsult Ltd)

XMetDB - Xenobiotics Metabolism Database, Patrik Rydberg (University of Copenhagen) (see presentation PDF)
PathVisio 3: new features for pathway analysis and visualization, Martina Kutmon (Maastricht University) (see presentation PDF)
ToxML: Community Based Development of a Common Data Exchange Standard for Toxicology, Mohammed Ali (Lhasa Ltd) (see presentation PDF)
The ISA infrastructure: from experimental planning to data publication, Alejandra Gonzalez-Beltran (University of Oxford) (see presentation PDF)
The Open Pharmacological Triple Store Concepts, Egon Willighagen (Maastricht University) (see presentation PDF)

B. Open Data, Open Source, and Open Standards for Toxicology, chaired by Egon Willighagen (Maastricht University)

AMBIT Web services: chemical data and models via OpenTox API, Nina Jeliazkova (IdeaConsult Ltd) (see presentation PDF)
Chemical decision support in toxicology and pharmacology, Ola Spjuth (Uppsala University) (see presentation PDF)
Phenotype Database, Jildau Bouwman (TNO) (see presentation PDF)
Assessing compound carcinogenicity in vitro using connectivity mapping, Florian Caiment (Maastricht University) (see presentation PDF)
The ChEMBL Database: Open data for use in Toxicity Prediction, Anne Hersey (EMBL-EBI) (see presentation PDF)

C. Visualization & Visual Analytics, chaired by Andreas Karwath (Johannes Gutenberg University of Mainz)

The Chemical Space Project, Jean-Louis Reymond (University of Berne)
Visual Analytics for the Comparison of Chemical and Biologic Data, Tatiana von Landesberger (Technische Universität Darmstadt)
Visual Analysis of Chemical Space with Scaffold Hunter, Nils Kriege (TU Dortmund) (see presentation PDF)
CheS-Mapper, Martin Gütlein (University of Freiburg) (see presentation PDF)

D. Systems Biology & Predictive Toxicology, chaired by Jürgen Borlak (Hannover Medical School)

Integrated Analysis of Toxicology Data supported by ToxBank, Barry Hardy (Douglas Connect) (see presentation PDF)
Application of toxicogenomics and TG-GATEs database for drug safety screening, Takeki Uehara (Shionogi Pharmaceutical Research Center)
The Systems Biology Simulation Core Library: A numerical method for the quantitative simulation of biochemical reaction networks , Alexander Dörr (University of Tuebingen) (see presentation PDF)
The Adverse Outcome Pathways Knowledge Base, Clemens Wittwehr (EU Joint Research Centre)
Human Embryonic Stem Cell-Derived Hepatocytes as a Predictive Model for Drug Screening, Seokjoo Yoon (Korea Institute of Toxicology)

E. Innovative Developments in Predictive Toxicology, chaired by Barry Hardy (Douglas Connect) and Stefan Kramer (Johannes Gutenberg University of Mainz)

Approaches to analyze the eTOX database from a data mining perspective, Jörg Wichard (Bayer Healthcare)
HeMiBio - Generation of hepatic microfluidic bioreactors with a regenerative cell source of parenchymal and non-parenchymal liver cells for high throughput long-term hepatotoxicity testing, Stefan Heinz (Medicyte)
InCroMAP – a tool for the integrated analysis and pathway-centered visualization of cross-omics datasets, Johannes Eichner (University of Tuebingen) (see presentation PDF)
Integration of molecular detail from OMICS-technologies for prediction of toxicity, André Schrattenholz (ProteoSys AG)
DNA Repair and Damage Response Following Exposure of Cells to Alkylating Carcinogens, Bernd Kaina (University Medical Center, Mainz)

Hands-on Workshops

A number of hands-on workshop sessions will be organised where participants can work on predictive toxicology problems using software applications supported by workshop leaders. Sessions will include:

A. Predicting Chemical Liabilities with Bioclipse and OpenTox, Ola Spjuth (Uppsala University) and Egon Willighagen (Maastricht University) (More Information)

B. Adverse Outcome Pathway (AOP) building with the AOP Knowledge Base, Clemens Wittwehr (EU Joint Research Centre) (More Information)

C. Using ToxML for Data Exchange, Philip Judson and Mohammed Ali (Lhasa Ltd) (More Information)

D. Use lazar-GUI for predictions with QSAR models based on the lazar-OpenTox framework, Micha Rautenberg and David Vorgrimmler (in silico toxicology) (More information)

E. Predicting interactions with drug metabolizing enzymes, Patrik Rydberg (University of Copenhagen) (More Information)

F. Visualise and Explore Chemical Feature Space of a Dataset, Martin Gütlein (Univ. Freiburg) and Andreas Karwath (Johannes Gutenberg University of Mainz) (More Information)

G. Integrated Enrichment and Analysis of Omics datasets mapped to Pathways, Johannes Eichner (University of Tuebingen) (More Information)

H. Using Scaffold Hunter for the Visual Analysis of Chemical Datasets, Nils Kriege and Till Schäfer (TU Dortmund) (More Information)

I. Identifying and Selecting ChEMBL datasets for toxicology modelling, Anne Hersey (EMBL-EBI) (More Information)

Knowledge Café

Participants will discuss their interests in predictive toxicology topics in small groups. You can view the discussion program at www.opentox.org/meet/opentoxeu2013/opentoxeuro2013knowledgecafe/

Schedule and Locations

Sunday, September 29, 2013

Pre-Conference Technical Meeting on OpenTox Open Standards

Location: Staudinger Weg 9, 3rd floor, Room 03-424

14:00 - Welcome
14:15 - OpenTox API Needs (short 5 minutes summaries)
14:45 - OpenTox API Discussions
16:00 - Coffee break
16:30 - OpenTox API Discussions & Decisions
18:00 - End

Monday, September 30, 2013

08:00 - Registration opens (Foyer, Neubau Hörsaalgebäude der Chemie, Duesbergweg 10-14)

NOTE: All conference presentations will be given in: Room C02 in the Neubau Hörsaalgebäude der Chemie

08.45 - Chair's Welcome
09:00 - Section A. Data Management and Analysis, chaired by Nina Jeliazkova (Ideaconsult Ltd)
11:00 - Coffee break
11:30 - Section E1. Innovative Developments in Predictive Toxicology, chaired by Barry Hardy (Douglas Connect) and Stefan Kramer (Johannes Gutenberg University of Mainz)
13:00 - Lunch (Mensa)
14:00 - Hands-on Workshop Sessions (Location: Staudinger Weg 9, 1st floor, foyer)
17:00 - Poster session with drinks/snacks (Location: Foyer, Neubau Hörsaalgebäude der Chemie, Duesbergweg 10-14)

Tuesday, October 1, 2013

09:00 - Section B. Open Data, Open Source, and Open Standards for Toxicology, chaired by Egon Willighagen (Maastricht University)
11:00 - Coffee break
11:30 - Secton D. Systems Biology & Predictive Toxicology, chaired by Jürgen Borlak (Hannover Medical School)
13:00 - Lunch (Mensa)
14:00 - Secton D. Systems Biology & Predictive Toxicology, chaired by Jürgen Borlak (Hannover Medical School)

15:00 - Knowledge Café Discussions with Refreshments (Location: Staudinger Weg 9, 1st floor, foyer)

16:30 - Excursion and Dinner - Participants can take a boat down the Rhine together and socialise before dinner

16:40 - Meeting on campus for bus transfer

17:00 - Leaving from Fischtor for boat trip

19:45 - Return from boat trip

20:00 - Dinner in the Proviant Magazin

Wednesday, October 2, 2013

09:00 -Section C. Visualization & Visual Analytics, chaired by Andreas Karwath (Johannes Gutenberg University of Mainz)
10:45 - Coffee break
11:15 - Section E2. Innovative Developments in Predictive Toxicology, chaired by Barry Hardy (Douglas Connect) and Stefan Kramer (Johannes Gutenberg University of Mainz)
12:15 - Best Poster and Best Software Awards
12:30 - Session Summaries and Closing Remarks, Session and Conference Chairs
13:00 - Close of Meeting

Here is a map with all important locations:

OpenTox Euro 2013, Mainz view in a larger map

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