AllBio Course on Data Resources and Tools for Plant-Omics 2013
AllBIo travel bursaries are available for this course; please apply when you complete the application form.
This practical course will provide an overview of data resources and tools for plant scientists, with an emphasis on managing and analysing large-scale datasets from genomics, transcriptomics, proteomics and metagenomics projects. It will bring together lead researchers in the field of plant bioinformatics, experts in biological data resources, and a highly motivated group of experimental researchers through a common theme centred on plant-based research. The course will combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks. There will be computer-based practical sessions using plant-based use cases and public-domain data resources.
Target audience
Owing to the practical nature of the course, and to optimise interactions, group activities and tutorials, we will accept a maximum of 30 students.
The course is aimed at early-stage researchers, and participants will be selected by a scientific committee in consultation with AllBio.
Prerequisites
Although many of the resources and tools that we will be using in this course are web-browser based, some of the practical sessions will involve using unix commands. We will provide support to those who have not used the command-line before but we recommend that you familiarise yourself with the basics of unix beforehand if possible. Free tutorials are available from http://www.ee.surrey.ac.uk/Teaching/Unix/
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 18 February 2013 (Materials) |
||
| 13:00 | Registration and lunch | |
| 14:00 | Welcome and introduction | Laura Emery |
| 14:30 | Lecture - Plant Genome Data and NGS technologies | Paul Kersey |
| 15:30 | Tea/Coffee break | |
| 15:50 | Practical session -DNA archiving | Rajesh Radhakrishnan and Marc Rosello |
| 17:00 | Poster Session | |
| 18:00 | Close | |
| 19:00 | Dinner at WTCC | |
| Day 2 - Tuesday 19 February 2013 (Materials) |
||
| 09:00 | Practical - Ensembl Genomes | Bert Overduin |
| 10:30 | Tea/Coffee break | |
| 11:00 | Ensembl Genomes cont... | Bert Overduin |
| 12:30 | Lunch | |
| 13:30 | Practical - PlantsDB | Manuel Spannagl, MIPS |
| 15:30 | Tea/Coffee break | |
| 16:00 | Practical - Comparative genomics using the PLAZA tool | Sebastian Proost, Postdam |
| 18:00 | Close | |
| 19:00 | Dinner at WTCC | |
| Day 3 - Wednesday 20 February 2013 (Materials) | ||
| 09:00 | Practical - DNA assembly | Bernardo Clavijo |
| 10:30 | Tea/Coffee break | |
| 11:00 | Practical -Metagenomics | John Walshaw |
| 12:30 | Lunch | |
| 13:30 | Metagenomics cont. | John Walshaw |
| 15:00 | Tea/Coffee break | |
| 15:30 | RNA assembly | Steve Kelly |
| 18:00 | Close | |
| 19:00 | Dinner at WTCC | |
| Day 4 - Thursday 21 February 2013 (Materials) | ||
| 09:00 | Lecture - Introduction to Expression Analysis | Manuel Corpas, TGAC |
| 09:45 | Lecture - Non-coding and small RNA's in plants | Krys Kelly, U. Cambridge |
| 10:30 | Tea/Coffee break | |
| 11:00 | Practical - Small RNA expression analysis | Krys Kelly, U. Cambridge |
| 12:30 | Lunch | |
| 13:30 | Practical - SNP discovery | Dan Bolser |
| 15:00 | Tea/Coffee break | |
| 15:30 | Practical - ArrayExpress and Atlas | Emma Hastings |
| 18:00 | Close | |
| 19:00 | Coach will depart from the Conference Centre to Cambridge | |
| 19:30 | Dinner in Wordsworth Room at St John's College in Cambridge | |
| 22:00 | Coach will depart from Cambridge to the Conference Centre | |
| Day 5 - Friday 22 February 2013 (Materials) |
||
| Delegates to check out of rooms | ||
| 09:00 | Practical - PRIDE | Joe Foster |
| 10:30 | Tea/Coffee break | Joe Foster |
| 11:00 | Practical - PRIDE continued | |
| 12:00 | Wrap-up and feedback session Click here to take survey |
|
| 12:30 | Lunch | |
| 13:30 | Departures (delegates to make their own travel arrangements) | |
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for a 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 17th December 2012 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 7th January 2013 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Registration Fees:
There will be a £100 administration fee for this course, the remaining costs are being funded by AllBio.
Please note that the course includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 4 nights (check in 18th February 2013, check out 22nd February 2013), in the Wellcome Trust Conference Centre, Hinxton, Cambridge
- Course College Dinner in Cambridge
- Course materials
- Use of EBI IT Training Room computer during the 5 day course.
NOTE: All delegates will need to arrange their own travel to and from the course. There will be some travel bursary funding available for the successful delegates, more information will be provided if your application is successful.
Registration/application:
Registration for this course has now closed.