Programmatic Access To Biological Databases (Perl)
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Date:
Monday 1 October 2012Application opens:
Friday 01 June 2012Application deadline:
Monday 06 August 2012Contact:
Frank O’DonnellRegistration closed
Overview
Is it right for me?
This hands on course in programmatic access to biological databases is ideal for bioinformaticians and biological researchers looking to develop data analysis pipelines or access data in an automated manner for integration into their own applications.
Participants should have competence in Perl as there is not enough time in the programme to teach the basics of programming. If you are concerned about what level of expertise you will need, please get in touch with the course organisers.
What will I learn?
- Introduction to Web Services and resources available at the EBI
- REST & SOAP - their application to EBI services and databases
- BioMart and BioMart Web Services
- Principles of the Distributed Annotation System (DAS)
- Linking services together to construct workflows (Taverna)
What will it cover?
- Overview of public domain biological databases at the EBI.
- Principles of Web Services, how they work and how to find them.
- Integrating data from multiple sources.
- Programmatic access to a variety of bioinformatic analysis tools.
Programme
| Time | Topic | Speaker |
|---|---|---|
| Day 1 (Mon 1 October 2012) – Introduction and background - Materials | ||
| 09.30 – 11.00 | Welcome, Introduction and Participant Expectations | OTT |
| 11.00 – 11.30 | Coffee | |
| 11.30 – 12.00 | Introduction to webservices (Webservices game) | Rafael Jimenez |
| 12.00 – 12.30 | Data standards | Rafael Jimenez |
| 12.30 – 13.30 | Lunch | |
| 13.30 – 14.30 | Technical introduction to webservices | Hamish McWilliam |
| 14.30 – 15.30 | Practical session on webservices | Hamish McWilliam |
| 15.30 – 16.00 | Coffee | |
| 16.00 – 17.30 | Practical session on webservices (continued) | Hamish McWilliam |
| 19.00 - | Dinner | |
| Day 2 (Tue 2 October 2012) - Ensembl, UniProt, OLS/PICR - Materials | ||
| 09.00 – 10.30 | Introduction to Ensembl API | Andy Yates & Magali Ruffier |
| 10.30 – 11.00 | Coffee | |
| 11.00 – 12.30 | Practical session on Ensembl API | Andy Yates & Magali Ruffier |
| 12.30 – 13.30 | Lunch | |
| 13.30 – 14.30 | Introduction to UniProt (REST service) | Hamish McWilliam |
| 14.30 – 16.00 | Practical session on UniProt | Hamish McWilliam |
| 16.00 – 16.30 | Coffee | |
| 16.30 – 17.30 | OLS/PICR | Daniel Rios |
| 19.00 - | Dinner | |
| Day 3 (Wed 3 October 2012) – ChEBI, AE/Atlas, CiteXplore, and other resources - Materials | ||
| 09.00 – 10.30 | ChEBI | Adriano Dekker & Luis Filipe de Figuiredo |
| 10.30 – 11.00 | Coffee | |
| 11.00 – 12.00 | ChEBI (continued) | Adriano Dekker & Luis Filipe de Figuiredo |
| 12.00 – 13.00 | Lunch | |
| 13.00 – 14.30 | ArrayExpress/Atlas | Robert Petryszak |
| 14.30 – 16.00 | QuickGO | Rachel Huntley & Tony Sawford |
| 16.00 – 16.30 | Coffee | |
| 16.30 – 17.30 | CiteXplore/Literature services | Senay Kafkas & Nikos Marinos |
| 19.00 - | Dinner | |
| Day 4 (Thu 4 October 2012) – Integrative methods and workflows - Materials | ||
| 09.00 – 10.30 | BioMart (Pride, Reactome and other services) | Daniel Rios & David Croft |
| 10.30 – 11.00 | Coffee | |
| 11.00 – 12.30 | PSICQUIC (IntAct, ChEMBL, Mint, String, and other services) | Marine Dumousseau & Noemi Del Toro Ayllon |
| 12.30 – 13.30 | Lunch | |
| 13.30 – 15.30 | DAS | Rafael Jiminez & Leyla J Garcia |
| 15.30 – 16.00 | Coffee | |
| 16.00 – 17.00 | Taverna (as a service) | Rafael Jimenez |
| 17.00 – 17.15 | BioCatalogue | Rafael Jimenez |
| 17.15 – 17.30 | Course survey | |
| 17.30 - | Departures | |
How to apply
This is a first come first serve course with a maximum of 25 delegates so please do register as soon as possible to be sure of a place.
Registration for this course will open on the 28 May 2012.
Please complete the registration form indicating the type of registration you require. Items marked * are mandatory. Incomplete registrations will not be processed. Note: Payment is required online during the registration process. Please do not begin the registration process unless you can pay.
Costs:
Registration Fee = £475.00
All tea breaks, lunches, training and materials are covered by the course fee.
Registration Closed
Please note that the course includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 3 nights (check in Monday 01 October 2012, check out Thursday 4 October 2012), in the Wellcome Trust Conference Centre, Hinxton, Cambridge CB10 1SD
- Course materials
- Use of EBI IT Training Room computer during the 4 day course.
NOTE: All delegates will need to arrange their own travel to and from the course.
Any additional nights accommodation must be arranged directly with the Wellcome Trust Conference Centre.
Application deadline
06 August 2012
Organisers
Rafael Jiminez - EMBL-EBI, United Kingdom
Michael Schubert
Trainers
David Croft - EMBL-EBI, UK
Rachael Huntley - EMBL-EBI, UK
Michael Schubert - EMBL-EBI, UK
Andy Yates - EMBL-EBI, UK
Daniel Rios - EMBL-EBI, Cambridge
Adriano Dekker - EMBL-EBI, UK
Robert Petryszak - EMBL-EBI, UK
Magali Ruffier - EMBL-EBI, UK
Luis de Figueiredo - EMBL-EBI, UK
Tony Sawford - EMBL-EBI, UK
Senay Kafkas - EMBL-EBI, UK
Nikos Marinos - EMBL-EBI, UK
Marine Dumousseau - EMBL-EBI, UK
Noemi Del Toro Ayllon - EMBL-EBI, UK
Leyla Jael Garcia Castro - EMBL-EBI, UK