Plant Bioinformatics
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.
Guest Speakers
- Lisa Mullan
- Ericka Havecker (Department of Plant Sciences, University of Cambridge)
| 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 |
This course is now full, if you would like to be put on a waiting list in the event of places becoming available, please contact courses@ebi.ac.uk
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:
- 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.
- 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:
Day 1: /training/sites/ebi.ac.uk.training/files/materials/2010/plants/day1.zip
Day 2: /training/sites/ebi.ac.uk.training/files/materials/2010/plants/day2.zip
Day 3: /training/sites/ebi.ac.uk.training/files/materials/2010/plants/day3.zip
Materials from external speakers are only available to course attendees - please contact courses@ebi.ac.uk with any queries.