Programmatic Access to biological databases (Java)
This course has been organised with support from ENFIN:
This course will give you the skills to leverage webservice technology to access and manipulate bioinformatics data resources and tools. You will start with simple scripts accessing individual services and then build upon this to create work flows to solve more complex problems in a reusable manner.
Participants will be exposed to open standards such as Simple Object Access Protocol (SOAP); the Distributed Annotation System (DAS); REST services and the BioMart web service. Several examples of specific web services will be included, covering programmatic access to both databases and tools at the EBI.
Topics include
- Introduction to the EBI and Webservices
- Rest and SOAP; application to EBI services (e.g. OLS, PICR, see http://www.ebi.ac.uk/Tools/webservices/)
- DAS
- BioMart and Biomart Webservices
- Workflows: TAVERNA, Enfin, Encore.
| Time | Topic |
|---|---|
| Day 1 - Mon 27 Apr 2009 | |
| 12:00 - 12:30 | Welcome and Introduction (James Watson) |
| 12:30 - 13:00 | Introduction to webservices (Hamish McWilliam) |
| 13:00 - 14:00 | Technical introduction to webservices (Hamish McWilliam) |
| 14:00 - 14:15 | Tea |
| 14:15 - 17:15 | Hands on: Introduction to webservices (Hamish McWilliam) |
| Day 2 - Tue 28 Apr 2009 | |
| 09:00 - 09:30 | Introduction to Ensembl and BioMart (Bert Overduin and Syed Haider) |
| 09:30 - 10:30 | Lecture/Hands on: BioMart/Ensembl (Phil Jones) |
| 10:30 - 10:45 | Tea/Coffee |
| 10:45 - 11:30 | Lecture/Hands on: BioMart/Ensembl (Phil Jones) |
| 11:30 - 12:00 | DAS (Phil Jones) |
| 12:00 - 13:00 | Lunch |
| 13:00 - 15:00 | Lecture/Hands on: UniProt (Samuel Patient/Michael Kleen) |
| 15:00 - 15:15 | Tea/Coffee |
| 15:15 - 16:15 | Lecture/Hands on: UniProt continued (Samuel Patient/Michael Kleen) |
| 16:15 - 17:15 | Lecture/Hands on: IntAct (Richard Cote) |
| Day 3 - Wed 29 Apr 2009 | |
| 09:00 - 10:30 | OLS/PICR (Richard Cote) |
| 10:30 - 10:45 | Tea/Coffee |
| 10:45 - 12:30 | ChEBI (Janna Hastings) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Literature Services (Sharmilla Pillai) |
| 14:30 - 14:45 | Tea/Coffee |
| 14:45 - 15:45 | ArrayExpress (Misha Kapushesky/Ibrahim Emam) |
| 15:45 - 17:15 | Integration of services: Enfin and Encore, Taverna (Florian Reisinger) |
Course fee includes refreshments and lunches for the duration of the course. This is a non-residential course therefore if you need accommodation you should book this yourself (see link above).
Places will be strictly allocated on a first come first serve basis, max 30 places. A place on the course will not be allocated until payment has been received in full. Payment must be received by 30th March 12:00 Noon. Late applications will only be accepted if the course is not full and provided the applicant is able to pay immediately, in full, via on-line credit/debit card payment.
Registration Closed.
The course materials are able to be downloaded using the following links:
Monday: /training/sites/ebi.ac.uk.training/files/materials/2009/Java/monday.zip
Tuesday: /training/sites/ebi.ac.uk.training/files/materials/2009/Java/tuesday.zip
Wednesday: /training/sites/ebi.ac.uk.training/files/materials/2009/Java/wednesday.zip
Additional info: /training/sites/ebi.ac.uk.training/files/materials/2009/Java/misc.zip