Small molecules, gene products and their interaction


EBI Roadshow, Pathway-Network course and diXa Training Course 

Date: Monday, July 1, 2013 - Friday, July 5, 2013
Venue: Maastricht (Maastricht School of Management)
Registration Opens Date:  16/05/2013
Registration Closing Date: 27/06/2013         
Minimum number of participants: This course is now confirmed
Participation:  first come, first served
*

Registration
Registration has now closed. Please note that you will be redirected to the NBIC website. It is advised to register as early as possible since the course has a limited number of spaces. 
After registration you will receive further information about hotel accommodation possibilities.

Additional remarks:

  • DiXa funding can be used to participate in this course
  • Both parts of the course (day 1-3 and day 4-5) can be followed together, or independently of each other.


Course topics:

This course has been organised by EMBL-EBI,  BiGCaT (University of Maastricht (UM)), Netherlands Bioinformatics Centre (NBIC) and the diXa project.

EMBL-EBI: Core resources for advanced analysis around: genes and genomes, proteins, small molecules, interactions, pathways.
UM: Pathways and network analysis using WikiPathways, PathVisio and Cytoscape.
diXa: Introduction to data gathering and reanalysis.

Course description:

This five day course introduces various databases and data analysis tools to get to grips with the big data in the life sciences.

The course consists of two parts: Part 1 (day 1-3) introduces the advanced uses of the gene and genomes databases, small molecule resources, the protein sequence databases, and interaction and pathway databases at the EBI (a.o. UniPROT, ENSEMBL, CHEMBL, IntAct and Reactome). This first part is provided by EMBL-EBI as an EBI roadshow.

The second part (day 4-5) focuses on real data analysis using pathway and network approaches with links to the databases covered in first part. Tools that will be used include WikiPathways, PathVisio and Cytoscape. Covered aspects include pathway creation, data preparation for analysis, pathway analysis. network analysis and network extension using target information. This second part is provided by the department of Bioinformatics-BiGCaT at Maastricht University in collaboration with the diXa FP7 project on systems biology approaches in toxicogenomics. The diXa project will provide examples about (re)use and (re)analysis of large genomics datasets.

Programme
*
Day 1
12:30-13:30         Welcome and registration
13:30-14:00         Introduction to the EBI  (Denise Carvalho-Silva) [pdf EBI intro]
14:00-15:00         Browsing genes and genomes with Ensembl (Denise Carvalho-Silva) [pdf Ensembl]
15:00-15:30         Break
15:30-17:00         Browsing genes and genomes with Ensembl [pdf Ensembl tutorial]
17:00                     End of day 1
Day 2
09:00-10:30         Browsing genes and genomes with Ensembl (Denise Carvalho-Silva)
10:30-11:00         Break
11:00-12:30         Browsing genes and genomes with Ensembl      
12:30-13:30         Lunch
13:30-15:00         Small Molecule Resources (Louisa Bellis) [pdf ChEMBL]
15:00-15:30         Break
15:30-17:00         Small Molecule Resources [pdf ChEMBL tutorial]          
17:00                     End of day 2
Day 3
09:00-10:30         Protein Sequence Databases (Sandra Orchard) [pdf UniProt] [pdf UniProt tutorial
10:30-11:00         Break
11:00-12:30         Protein Sequence Databases [pdf MIs]
12:30-13:30         Lunch
13:30-15:00         Interactions and Pathways [pdf IntAct] [pdf IntAct tutorial
15:00-15:30         Break
15:30-17:00         Interactions and Pathways [pdf Reactome]         
17:00                     End of day 3
Day 4
09:00-10:30         Pathway analysis with WikiPathways and PathVisio (Martina Kutmon & Egon Willighagen)                                [pdf pathway analysis]
10.30-11:00         Break
11:00-12:30         Pathway analysis with WikiPathways and PathVisio [course website]
12:30-13:30         Lunch
13:30-15:00         Introduction to the diXa project (Stathis Kanterakis) [pdf diXa intro]
15:00-15:30         Break
15:30-17:00         Introduction ArrayAnalysis.org (Lars Eijssen) [pdf ArrayAnalysis]              
17:00                     End of day 4
Day 5
09:00-10:30         Cytoscape tutorial – basic (Martina Kutmon & Anwesha Dutta) [pdf network analysis]
10.30-11:00         Break
11:00-12:30         Cytoscape tutorial – advanced (Martina Kutmon & Anwesha Dutta)
12:30-13:30         Lunch
13:30-15:00         ConsensusPathDB (Christopher Hardt) [pdf CPDB]
15:00                     End of course
*
Registration
Registration for this course is now closed. Please note that you will be redirected to the NBIC website. It is advised to register as early as possible since the course has a limited number of spaces. 
After registration you will receive further information about hotel accommodation possibilities.
*
If you have any questions about this course, please email training@dixa-fp7.eu
*
Trainers:
EBI Roadshow
Denise Carvalho-Silva
Louisa Bellis
Sandra Orchard - orchard@ebi.ac.uk
diXa Training Course
Martina Kutmon
Anwesha Dutta
Egon Willighagen
Stathis Kanterakis
Christopher Hardt
Lars Eijssen