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Hands-on training at EBI - Patterns, Similarities and Differences in Biological Data
Course Summary
 Title: Patterns, Similarities and Differences in Biological Data
Date: 9-11 June 2008
Venue: Hinxton, Cambridge, UK
Organisers: Kim Henrick & Vicky Schneider
Admin Support: Alison Barker & Janet Copeland
Registration Deadline: 27 May 2008
About this Course
Whatever the circumstance, when searching for information you need to be able to judge its quality and suitability. Today’s biological databases contain significant biological information and knowing what type of resources are available, and how to access this information is as crucial as evaluating the information and its source.
The course will start by addressing how to frame the most appropriate question and from there, what route to take to obtain biologically meaningful information. For example, imagine you are working on a specific protein, through the methods used in this course you will learn how to sit this protein within a wider context of related protein families, other proteins that share structural similarities, molecular pathways and networks. The course will show how, information from different resources is gathered by looking for patterns, and the methods this are based upon as well as their strength and weaknesses. The course will then address how patterns might lead to ratings of similarity. Finally the course will address ‘differences’ through lectures from scientists working on different types of data (e.g. nucleotide sequences evolution, protein signatures and structures.
The course consists of a series of lectures. Participants are asked to bring their own biological question which they will be using in a dedicated 90 minutes hands-on session, working in pairs and including interactive discussion with EBI experts and trainers.
Topics include
- Understanding how to frame question and building a search protocol
- Representative set (sequence and structures) patterns
- Families (Pfam and InterPro)
- Prosite
- Pattern methods for sequence motifs
- Structural patterns: Similarity and Differences
- Structures (e.g. MSDpro)
- Similarities in Chemistry
- Sequences (e.g. ClustalW2)
- Protein-protein interactions
Course requirements
A basic understanding of molecular biology. Familiarity with the use of biological databases would be an advantage.
The training is free, however we need to charge participants an administration fee of £25 per day.
Registration closed.
EBI lecturers and trainers
- Kim Henrick, EMBL-EBI.
- Rodrigo Lopez, EMBL-EBI.
- Jennifer McDowall, EMBL-EBI.
- Dietrich Rebholz, EMBL-EBI.
- Eugene Krissinel, EMBL-EBI.
- Tom Oldfield, EMBL-EBI.
Guest Speakers
- William Pearson, University of Virginia
- Aidan Budd, EMBL-Heidelberg
- Robert Finn, Wellcome Trust Sanger Centre
- Lorenzo Cerutti, Swiss Institute of Bioinformatics
- Terri Attwood, University of Manchester
Program Contents
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