Programmatic access to biological databases (Java)
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 Java 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 (watson@ebi.ac.uk)
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, Enfin, Encore)
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.
- Real life use cases.
| Time | Topic |
|---|---|
| Day 1 - Mon 9 May 2011 - Introduction to Web Services | |
| 12:00 - 12:30 | Coffee + Welcome and introduction to the EBI (James Watson - EMBL-EBI) |
| 12:30 - 13:00 | Introduction to Web Services (Hamish McWilliam - EMBL-EBI) |
| 13:00 - 14:00 | Technical introduction to Web Services (Hamish McWilliam - EMBL-EBI) |
| 14:00 - 14:30 | Tea break |
| 14:30 - 17:30 | Hands on: Introduction to Web Services (Hamish McWilliam - EMBL-EBI) |
| 19:00 - 21:00 | Course Dinner (Red Lion, Hinxton) |
| Day 2 - Tue 10 May 2011 - UniProt, IntAct | |
| 09:30 - 10:30 | Introduction to UniProt (Ricardo Antunes - EMBL-EBI) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | Hands on: Retrieving protein sequence data using UniProt (Ricardo Antunes - EMBL-EBI) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | IntAct (Bruno Aranda, Samuel Kerrien - EMBL-EBI) |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | IntAct (Bruno Aranda, Samuel Kerrien - EMBL-EBI) |
| Day 3 - Wed 11 May 2011 - Identifier cross-referencing, Small Molecules, Literature, Interactions and Microarrays | |
| 09:30 - 10:30 | Introduction to ChEBI (Gareth Owen - EMBL-EBI) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 12:00 | Hands on exercises using ChEBI (Adriano Dekker - EMBL-EBI) |
| 12:00 - 13:00 | OLS/PICR (Richard Côté - EMBL-EBI) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | CiteXplore (Xiaofei Wang - EMBL-EBI) |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | ArrayExpress/Atlas (Robert Petryszak - EMBL-EBI) |
| Day 4 - Thu 12 May 2011 - Multiple Data Resources, Integration And Case Studies | |
| 09:30 - 10:00 | Introduction to data integration (Rafael Jimenez - EMBL-EBI) |
| 10:00 - 11:00 | BioMart (Jack Hsu – Ontario Institute for Cancer Research) |
| 11:00 - 11:30 | Tea break |
| 11:30 - 13:00 | BioMart (Jack Hsu – Ontario Institute for Cancer Research) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | DAS (Andy Jenkinson - EMBL-EBI) |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Data integration using YABI (Matthew Bellgard and Andrew MacGregor - Centre for Comparative Genomics) |
| Day 5 - Fri 13 May 2011 - Workflows and Integration Pipelines | |
| 09:30 - 10:30 | Taverna (Katy Wolstencroft – University of Manchester) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 12:30 | Constructing workflows using Taverna (Katy Wolstencroft – University of Manchester) |
| 12:30 - 13:00 | Light lunch |
| 13:00 - 14:30 | Integration using Enfin/Encore (Rafael Jimenez - EMBL-EBI) |
| 14:30 - 15:00 | Course wrap up and survey |
Costs:
Registration Fee = £185.00
Please note that the registration fee does NOT include accommodation. We have provisionally reserved a limited number of rooms with the onsite accommodation centre, if you wish to book one of these rooms please contact the conference accommodation office (http://www.wtconference.org.uk/bedrooms.aspx) quoting "EBI Johanna Langrish", before 8th February 2011 as rooms cannot be guaranteed after this date.
All tea breaks, lunches, training and materials are covered by the course fee. There is an optional complimentary course dinner open to all participants and tutors to attend. The venue for this is yet to be determined.
Please complete the registration form through the link below. 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.
Registration Closed
The course materials are available from the following links:
/training/sites/ebi.ac.uk.training/files/materials/2011/110509_progjava/day1.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/110509_progjava/day2.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/110509_progjava/day3a.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/110509_progjava/day3b.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/110509_progjava/day4.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/110509_progjava/day5.zip