Programmatic access in Java: webservices & work flows
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.
| Time | Topic |
|---|---|
| Day 1 - Mon 24 Nov 2008 | |
| 12:00 - 13:00 | Registration |
| 13:00 - 13:15 | Safety and Welcome (James Watson) |
| 13:15 - 13:35 | Overview of EBI (James Watson) |
| 13:35 - 14:00 | Introduction to webservices at EBI (Hamish McWilliam) |
| 14:00 - 15:00 | Technical intro to webservices (External Services) |
| 15:00 - 15:15 | Coffee/Tea |
| 15:15 - 17:15 | Hands On : Running Webservices (Hamish McWilliam) |
| 17:15 | End of day |
| Day 2 - Tue 25 Nov 2008 | |
| 09:30 - 11:00 | OLS/PICR + hands-on (Phil Jones) |
| 11:00 - 11:15 | Coffee/Tea |
| 11:15 - 13:00 | UniProt + hands-on (Michael Kleen) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:00 | IntAct + hands-on (Bruno Aranda/Samuel Kerrien) |
| 15:00 - 15:15 | Coffee/Tea |
| 15:15 - 16:00 | IntAct continued (Bruno Aranda/Samuel Kerrien) |
| 16:00 - 18:00 | ChEBI + hands-on (Janna Hastings) |
| 18:00 | End of day |
| Day 3 - Wed 26 Nov 2008 | |
| 09:30 - 10:00 | Introduction to BioMart/Ensembl (Bert Overduin) |
| 10:00 - 10:30 | Biomart as a service (Syed Haider) |
| 10:30 - 10:45 | Coffee/Tea |
| 10:45 - 11:45 | BioMart/Ensembl hands-on session (Phil Jones) |
| 11:45 - 12:45 | Integr8 + hands-on (Alan Horne/Andy Yates) |
| 12:45 - 13:45 | Lunch |
| 13:45 - 14:45 | Literature services + hands-on (Sharmila Pillai) |
| 14:45 - 15:45 | ArrayExpress + hands-on (Misha Kapushesky/Ibrahim Emam) |
| 15:45 - 16:00 | Coffee/Tea |
| 16:00 - 17:00 | ArrayExpress continued (Misha Kapushesky/Ibrahim Emam) |
| 17:00 - 17:15 | Questions |
| 17:15 | End of day |
| Day 4 - Thu 27 Nov 2008 | |
| 09:30 - 10:30 | Integration, workflows and open-ended problem session (All trainers) |
| 10:30 - 10:45 | Coffee/Tea |
| 10:45 - 13:00 | Integration, workflows and open-ended problem session (All trainers) |
| 13:00 | End of day |
The course materials are available at the following link:
/training/sites/ebi.ac.uk.training/files/materials/2008/course_081124_javawebservices.zip