Programmatic Access To Biological Databases (Perl)
This course has been organised with support from ENFIN:
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, 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 from academia & industry.
Guest Speakers
- Philip Verdemato (Pfizer)
- Katy Wolstencroft (University of Manchester)
- Thomas Kappler (Swiss Institute of Bioinformatics)
| Time | Topic |
|---|---|
| Day 1 - Mon 22 February 2010 - Introduction to Web Services | |
| 12:00 - 12:30 | Coffee + Welcome and introduction to the EBI (James Watson) |
| 12:30 - 13:00 | Introduction to Web Services (Hamish McWilliam) |
| 13:00 - 14:00 | Technical introduction to Web Services (Hamish McWilliam) |
| 14:00 - 14:30 | Tea break |
| 14:30 - 17:30 | Hands on: Introduction to Web Services (Hamish McWilliam) |
| 19:00 - 21:00 | Course Dinner (Venue to be confirmed) |
| Day 2 - Tue 23 February 2010 - Ensembl, BioMart, DAS, UniProt | |
| 09:00 - 10:30 | Introduction to Ensembl (Ian Longden) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | Hands on: Mining genomic data using the Ensembl API (Ian Longden) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Introduction to UniProt (Thomas Kappler) |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Hands on: Retrieving protein sequence data using UniProt (Thomas Kappler) |
| Day 3 - Wed 24 February 2010 - Identifier cross-referencing, Small Molecules, Literature, Interactions and Microarrays | |
| 09:00 - 09:30 | Energiser Activity (James Watson) |
| 09:30 - 10:30 | Ontologies and identifier cross-referencing using OLS/PICR (Phil Jones) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 13:00 | Accessing small molecule data using ChEBI (Janna Hastings) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:00 | Programmatic access to literature services using CiteXplore (Sharmila Pillai) |
| 15:00 - 15:30 | Tea break |
| 15:30 - 16:30 | Mining protein interaction data using IntAct (Bruno Aranda/Samuel Kerrien) |
| 16:30 - 17:30 | Microarray Services (Misha Kapushesky) |
| Day 4 - Thu 25 February 2010 - Multiple Data Resources, Integration And Case Studies | |
| 09:00 - 11:00 | Querying multiple data sources using BioMart (Damian Smedley) |
| 11:00 - 11:30 | Tea break |
| 11:30 - 13:00 | Annotating sequences using DAS (Andy Jenkinson, Bernat Gel Moreno) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Data Integration through Enfin and EnCore (Rafael Jimenez) |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:00 | Industry perspective: Bioservices - dynamic discovery and execution of services (Philip Verdemato, Pfizer) |
| Day 5 - Fri 26 February 2010 - Workflows, Integration And Case Studies continued | |
| 09:00 - 10:30 | Introduction to workflows and Taverna (Katy Wolstencroft) |
| 10:30 - 11:00 | Tea break |
| 11:00 - 12:30 | Creating workflows to solve biological problems using Taverna (Katy Wolstencroft) |
| 12:30 - 13:00 | Course Survey, Closing Comments and Course DVD Distribution |
| 13:00 - 14:00 | Optional supplemental exercises |
Registration Deadline Extended To 29th January!
Registration for this course will open on the 21st August 2009.
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 = £145.00
Please note that the registration fee does NOT include accommodation.
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.
Registration links:
Registration Closed.
The course materials are now available for download from the following links:
File 1: /training/sites/ebi.ac.uk.training/files/materials/2010/Perl/perl_course_materials_1.zip
File 2: /training/sites/ebi.ac.uk.training/files/materials/2010/Perl/perl_course_materials_2.zip
File 3: /training/sites/ebi.ac.uk.training/files/materials/2010/Perl/perl_course_materials_3.zip