Hands-on training at EBI - Programmatic Access To Biological Databases (Perl)

Course Summary

Title: Programmatic Access To Biological Databases (Perl)
Date: 22–26 February 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: James Watson & Hamish McWilliam
Admin Support: Alison Barker & Janet Copeland
Registration Opens: 21 August 2009 - 12 noon (GMT)
Extended Deadline: 29 January 2010 - 12 noon (GMT)

Programme

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

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