Is it right for me?
- This hands on course in plant bioinformatics is ideal for bioinformaticians and biological researchers working on plants who are looking to utilise bioinformatics tools and databases in their research.
- Participants should have a degree in a biological discipline and be working with plant data. No previous training in bioinformatics is required.
What will I learn?
- Understanding plant genome data and genome sequencing
- Principles of sequence searching tools
- How to detect Orthologues and Paralogues
- How to interpret plant microarray data
- Principles of proteomics data analysis and functional annotation
What will it cover?
- Browsing plant genome data using Ensembl
- Sequence searching tools and their effective use
- Analysis of microarray data using ArrayExpress and the Gene Expression Atlas
- Analysis of proteomics data and datasets in PRIDE
- Protein function prediction and annotation using the gene ontology and InterPro
- Accessing plant reaction and pathway data using Arabidopsis Reactome
- Real life use cases.
- Lisa Mullan
- Ericka Havecker (Department of Plant Sciences, University of Cambridge)
|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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