Chemical and Biological resources for Toxicology and Toxicogenomics

Date: 3rd - 5th September 2013
Venue: European Bioinformatics Institute
Registration deadline: Sunday, August 25, 2013
Participation: First come, first served

The Data Infrastructure for Chemical Safety (diXa) project works with past and current EU FP7 projects, developing Alternatives to Animal testing, to safeguard data for the future. diXa aims to develop a sustainable data infrastructure to capture all data produced by toxicogenomics projects in a standardized, harmonized and sustainable manner. The lack of such an infrastructure currently prevents innovative breakthroughs from meta-analyses of joint databases and systems modeling. The diXa Data Warehouse will link to other globally available chemical/toxicological databases and data bases on molecular data of human disease to facilitate interdisciplinary research.

This 3-day diXa course will give participants an overview of the chemical and biological resources that are available for researchers in the field of Toxicology and Toxicogenomics. The course is aimed at researchers and scientists from academia as well as Industry with an interest in toxicology, toxicogenomics and life sciences.

The first part introduces EBI resources ChEMBL, Ensembl, PDBe, ArrayExpress, and UniProt with use cases specifically chosen to be relevant to the toxicology and toxicogenomics community e.g. cross-species homology, comparisons, structure similarity, function prediction.

The diXa Data Warehouse will be openly accessible from September; this course will show you the capabilities of the warehouse and discuss plans for future development. You will also receive an overview of the research conducted by the diXa project.  

Genedate will provide a workflow based demonstration of Quality control and data cross checking; starting from downloading data to performing a quality assessment of the raw data, methods to condense data, annotating the experiments, how to normalize and/or transform the data, through to performing adequate statistical tests and interpreting results using GO annotations and/or pathway annotations using ConsensuPathDb. 



Day 1

12:30 - 13:00    Registration

13:00 - 13:45    Welcome and Introduction to the EBI - Vera Matser [pdf]

13:45 - 14:30    Industry drivers for advancement of in silico toxicology methods  - Richard Stark (Unilever) [pdf]

14:30 - 15:00    Coffee & tea break

15:00 - 17:00    ChEMBL - small molecule resources [Slides]

18:00                  Conference dinner at the Red Lion in Hinxton

Day 2    Bite-sized EBI resources

9:15 - 9:45    Exploring genes and phenotypes with the Ensembl Genome Browser - Giulietta Spudich

                        [Slides] [Coursebook] [Answers]

9:45 - 10:30   The Protein Data Bank in Europe: bringing structure to biology - Garry Battle [Slides]

10:30 - 11:00    Coffee and tea break

11:00 - 11.45    Exploring functional genomic data (ArrayExpress - Expression Altas) - Amy Tang

                            [Slides] [ Excercises]

11:45 - 12:30    Toxicology and Toxicogenomics data in UniProt sequence database - Sandra Orchard                             [Slides] [ Excercises]

12:30 - 13:30    Lunch

13:30 - 15:00    Bite-sized EBI resources - hands-on

15:00 - 15:30    Coffee & tea break

15:30 - 17:00    Bite-sized EBI resources - hands-on

Day 3

09:15 - 09:30    Introduction to the diXa project - Vera Matser [Slides]

09:30 - 10:15    Public release of the diXa data warehouse - Ekaterina Pilicheva [Slides]

10:15 - 10:45    Coffee & tea break

10:45 - 11:15    OpenPHACTS - Anna Gaulton [Slides]

11:15 - 12:30    Cross check of data quality control and initial data analysis; Genedata workflow                             demonstration - Hans Gmuender [Slides]

12:30 - 13:30    Lunch

13:30 - 14:00    The robustness of pathway based predictive models - Marcelo Segura [Slides]

14:00 - 14:30    Construction of a predictive molecular network for DILI - Ralf Herwig [Slides]


Registration is now closed,  the registration fee for this course is £150.00.  

Please note that the course fee includes:

All course refreshments and lunches
Course materials
Course dinner on the 3 September 2013
Use of the EBI Training Room throughout the duration of the course.

Members of the EBI Industry programme will have their course fees covered by the Industry Programme

Additional Information:

PLEASE NOTE: Registrants must book their own travel and accommodation.
We would recommend that you book your accommodation at any of the following locations:

Wellcome Trust Conference Centre

Red Lion Hinxton

Red Lion Whittlesford

Information regarding travelling to the EBI and further accommodation options can be found here:

If you have any questions about this course, please email