Agricultural-Omics
This course will provide an overview of data resources, tools and analysis pipelines for 'omics datasets within the agricultural sciences. It will be delivered using a mixture of lectures, practical computer sessions and discussions based on agricultural case studies and public domain data. Additionally there will be opportunity to review the key opportunities and challenges within this field.
Audience
This course is aimed at researchers working within the agricultural sciences who have some previous experience of bioinformatics. Some of the tools to be introduced on the course will require the use of Unix commands and the R statistics package. We strongly recommend that you familiarise yourself with these. Free tutorials are available from:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction
Syllabus, Tools and Resources
During this course you will learn about…
- Genomics : Velvet, Soap, BWA, SAMtools, BCFtools, VCFtools, Ensembl Genomes, PhyBase, PlantsDB, Plaza
- Transcriptomics: Fastx, Allpaths-LG, Velvet, Bowtie, R, Bioconductor
- Metagenomics: The Metagenomics Portal, RDP classifier, MEGAN, CARMA
- Proteomics: PRIDE, OMSSA, PX submission tool
- Metabolomics: MetaboLights
Learning Objectives
After this course you should be able to…
- Discuss a variety of workflow approaches to omics technologies
- Browse and access a range of agricultural omics data available in public repositories
- Use tools to aid with the analysis of agricultural omics data
- Appreciate some advantages and limitations of some omics methods and analyses
- Assess the significance of specific analyses in the context of wider omics workflow
| Time | Topic | Trainer |
|---|---|---|
| 16 February 2014 - Check in to onsite accommodation (after 15:00) |
||
| Day 1 -17 February 2014 | ||
| 12:00 | Registration and lunch | |
| 13:00 | An introduction to the EBI | Laura Emery |
| 13:30 | Applications and Workflow of Omics Technologies (activity session) | Laura Emery and Participants |
| 14:15 | Tea/coffee break | |
| 14:45 | NGS technologies and genome data (lecture) | Paul Kersey |
| 15:45 | Participants’ Presentation | Participants |
| 17:15 | Poster session | |
| 19:00 | Onsite Dinner | |
| Day 2 - 18 Febraury 2014 | ||
| 09:00 | Genomics workflow (mini lecture) | Laura Emery |
| 09:45 | DNA assembly (hands-on) | Bernardo Clavijo |
| 11:30 | Tea/coffee break | |
| 12:00 | SNP Discovery | Dan Bolser |
| 13:30 | Lunch | |
| 14:00 | Exploring your data with Ensembl Genomes (hands-on) | Ensembl Outreach |
| 15:30 | Tea/coffee break | |
| 16:00 | Other data resources for Agricultural Bioinformatics (demo) | Paul Kersey |
| 17:00 | Submitting sequence data to ENA (demo) | Rajesh Radhakrishnan |
| 19:00 | Onsite Dinner | |
| Day 3 - 19 February 2014 | ||
| 09:00 | Transcriptomics workflow (mini lecture) | John Marioni |
| 09:45 | Processing raw transcriptomics data (lecture and hands-on) | Mar Gonzalez-Porta |
| 11:30 | Tea/coffee break | |
| 12:00 | RNA assembly (lecture and hands-on) | Steve Kelly |
| 13:30 | Lunch | |
| 14:30 | Mapping, expression estimation, normalisation, and differential expression (lecture) | Mar Gonzalez-Porta |
| 15:30 | Tea/coffee break | |
| 16:00 | Mapping, expression estimation, normalisation, and differential expression (hands-on) | Mar Gonzalez-Porta |
| 17:30 | Exploring transcriptomics data with ArrayExpress and Atlas | Speaker tbc |
| 19:00 | Onsite Dinner | |
| Day 4 - 20 February 2014 | ||
| 09:00 | An introduction to Metagenomics and the Metagenomics Portal (mini lecture and demo) | Sarah Hunter |
| 10:00 | Analysing metagenomics (mini lecture) | John Walshaw |
| 10:45 | Tea/coffee break | |
| 11:15 | Analysing metagenomes (hands-on) | John Walshaw |
| 13:00 | Lunch | |
| 14:00 | An introduction to Proteomics using PRIDE (hands-on) | Juan Antonio Vizcaino |
| 15:00 | Tea/coffee break | |
| 15:30 | An introduction to Proteomics using PRIDE (hands-on) continued… | Juan Antonio Vizcaino |
| 16:30 | Discussion session | Trainers & Participants |
| 17:15 | Free time | |
| 18:45 | Coach transport from WTCC to Cambridge College | |
| 19:30 | Cambridge College Dinner | |
| 22:00 | Coach transport back to WTCC | |
| Day 5 - 21 February 2014 | ||
| 08:30 | Check out of on-site accommodation | |
| 09:00 | Metabolomics in plants (Hands on) | Matthew Davey |
| 10:30 | Tea/coffee break | |
| 11:00 | An introduction to the MetaboLights database (hands on) | Reza Salek |
| 12:30 | Course feedback and wrap up | Laura Emery |
| 13:00 | Lunch | |
Please note that this is a draft agenda and subject to change.
Application will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 20 December 2013 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 8 January 2014 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Please note that the registration fee of £525.00 includes:
- All meals listed in the agenda (breakfast, lunch, dinner and refreshment breaks)
- Course materials on a USB
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- Onsite accommodation at the Wellcome Trust Conference Centre (16-21 February 2014)
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.