PhytoPath Training Course
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Date:
Wednesday 19 September 2012Application opens:
Tuesday 01 May 2012Application deadline:
Friday 03 August 2012Contact:
Frank O’DonnellRegistration closed
Overview
This course is aimed at PhD students and post-doctoral researchers who are working on all aspects of fungal and oomycete-induced disease in plants. The primary aim of this course is to familiarize the participants with the toolset and data available for analysis of host and pathogen genomes, and infectious phenotypes.
Lectures will provide an overview with the data available for plant pathogens, the technologies used to generate these data and the resources that make them available. Practicals will consist of computer exercises that will familliarise users with tools and resources at first hand, using relevent examples from the study of pathogenesis.
The course will cover primarily the PhytoPath resource, the associated Ensembl databases for plants, fungi and protists, and PHI-base.
Additional tools and resources used in the analysis of genome-scale data will also be covered, including the Ondex software for network analysis. An introductory practical on genome assembly and alignment (using next-generation sequencing data) will also be provided.
Additional information
This course will take place in the EMBL-EBI IT Training room which has 40 computers set up with the relevant disk images required for this course.
Food and Accommodation
Food at the Red Lion Pub, Hinxton
There will be a course dinner held on the 19 September at the Red Lion Pub, Hinxton. This is within walking distance of the campus and is included in your registration fee.
Accommodation
The accommodation should be arranged by the participants. If you would like to reserve a room then please contact the Wellcome Trust and mention the course title and that you would like to book one of the reserved rooms for this event. You can contact the Wellcome Trust Conference Centre on +44 (0)1223 495 000 or info@wtconference.org.uk.
The reserved rooms will only be availble until the 30 June 2012 so please hurry. Please call +44 (0)1223 494626 for further details.
Programme
| Time | Topic | Speaker |
|---|---|---|
| Day 1 - Wednesday 19 September 2012 | ||
| 12:00-13:00 | Lunch | |
| 13:00-13:15 | Introductions | Paul Kersey |
| 13:15-14:15 | Lecture: PhytoPathogens: The Genomic Landscape | Uma Maheswari |
| 14:15-15:15 | Ensembl Browser workshop | Bert Overduin / Helder Pedro |
| 15:15-15:35 | Coffee/Tea Break | |
| 15:35-16:35 | Ensembl Browser Workshop (continued) | Bert Overduin / Helder Pedro |
| 16:35-17:35 | BioMart Workshop | Bert Overduin / Helder Pedro |
| 17:35-18:00 | Assembly/alignment introduction | Paul Kersey |
| 18:00- | End of Day 1 | |
| 19:00- | Dinner | |
| Day 2 - Thursday 20 September 2012 | ||
| 09:00-10:00 | Guest lecture (to be confirmed) | |
| 10:00-10:15 | PHI-base: Introduction | Kim Hammond-Kosack |
| 10:15-10:55 | Submitting data to PHI-base | Kim Hammond-Kosack / Mansoor Saqi |
| 10:55-11:15 | Coffee/Tea Break | |
| 11:15-13:00 | Introduction to Ensembl API | Bert Overduin |
| 13:00-14:00 | Lunch | |
| 14:00-15:00 | Exploring integrated datasets with ONDEX: an application to plant pathogens | Artem Lysenko, Jan Taubert, Mansoor Saqi |
| 15:00 | End of Course | |
Course Materials: materials_phytopath.zip
How to apply
Registration - £75
Please note that the registration fee includes:
* Lunch and refreshments during the course
* Course materials & USB stick
* Use of EBI IT Training Room computer during the 2 day course
* Dinner at the Red Lion
There will be a maximum of 40 participants on this course and registration is on a first come first serve basis. Registration will close on 03 August 2012 @ 23:59 GMT.
A number of bursaries will be available for applicants to this course. The bursary will cover registration fees and cover your travel and accommodation costs only up to a maximum of €500. Priority will be given to applicants who might otherwise find it difficult to attend the course, and who provide the strongest scientific justification for their attendance. Please select the option for a bursary which can be found on our registration page and complete this form if you would like to be considered. All successful bursary applicants will be notified after the registration deadline.
These bursaries are sponsored by AllBio Bioinformatics.
To register for this workshop please use the following link (Items marked * are mandatory. Incomplete registrations will not be processed). You will need to pay by credit card as you submit your registration, therefore please have your card to hand.
Registration is now closed
Application deadline
03 August 2012
Organisers
Paul Kersey
Trainers
Uma Maheswari - EMBL-EBI, UK
Helder Pedro - EMBL-EBI, UK
Mansoor Saqi - Rothamsted Research, UK
Kim Hammond-Kosack - Rothamsted Research, UK