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Collapse General Hands-on Information
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EBITrainingEBI User Training ProgrammeHands-onPlant BioinformaticsProgramme

Hands-on training at EBI - Plant Bioinformatics

Course Summary
Course Details Title: Plant Bioinformatics
Date: 29-31 March 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: Bert Overduin, James Watson
Admin Support: Alison Barker & Janet Copeland
Registration Deadline: 1 March 2010 - 12 noon (GMT)


Materials Download

Available course materials are now available for download. These materials are made freely available under the Creative Commons Attribution-Share Alike 2.5 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/2.5/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA. In summary you are free to:
  • Share — to copy, distribute and transmit the work
  • Remix — to adapt the work

Under the following conditions:
  1. Attribution - You must attribute the work but not in any way that suggests that the authors or EMBL-EBI endorse you or your use of the work.
  2. Share Alike - If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one.

To download a zip folder of each day's course materials click on the relevant link:

Materials from external speakers are only available to course attendees - please contact courses@ebi.ac.uk with any queries.

Programme

Time Topic
Day 1 - Mon 29 March 2010 - Sequence Searching and Bioinformatics Tools
11:45 Registration Lunch and Coffee
12:15 - 12:30 Welcome and introduction to the EBI (James Watson)
12:30 - 14:00 Sequence Searching With BLAST and FASTA (Andrew Cowley)
14:00 - 15:00 Bioinformatics using Emboss (Lisa Mullan)
15:00 - 15:30 Tea break
15:30 - 16:30 Bioinformatics using Emboss - continued
16:30 - 17:30 Sanger Centre Sequencing Facility Tour
Day 2 - Tue 30 March 2010 - Genome Browsing, BioMart and Transcriptomics
09:00 - 10:45 Browsing Plant Genomes With Ensembl Genomes (Jeff Almeida-King)
10:45 - 11:00 Tea break
11:00 - 12:00 Browsing Plant Genomes With Ensembl Genomes - continued
12:00 - 13:00 Lunch
13:00 - 14:00 Comparative Genomics using Ensembl (Bert Overduin)
14:00 - 15:00 Data Mining With BioMart (Bert Overduin)
15:00 - 15:15 Tea break
15:15 - 16:45 Analysing Plant Transcriptomics Data (Gabriella Rustici)
16:45 - 17:45 Case Study: Using Bioinformatics In Plant Based Research (Ericka Havecker)
19:30 - 21:30 Course Dinner at Conference Centre
Day 3 - Wed 31 March 2010 - Proteomics, Functional Annotation and Pathways
09:00 - 11:00 Analysing Plant Proteomics Data Using PRIDE (Richard Côté)
11:00 - 11:30 Tea Break
11:30 - 13:00 Identifying Plant Protein Features Using InterPro (Antony Quinn)
13:00 - 14:00 Lunch
14:00 - 15:00 Describing Plant Gene Products Using GO/GOA (Rachael Huntley)
15:00 - 15:30 Tea break
15:30 - 17:00 Pathways and Reactions - Arabidopsis Reactome (Steven Jupe)
17:00 - 17:30 Course Close and Survey


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