Multiple Sequence Alignment and Analysis with Jalview -- Tutorial and Hackathon
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Date:
Monday 21 January 2013Application deadline:
Thursday 10 January 2013Contact:
Alison BarkerRegistration closed
Overview
A two day workshop to introduce all aspects of the widely used Jalview sequence analysis workbench, including hands-on tutorials, seminars, a Jalview user clinic, and a hackathon for developers interested in extending Jalview for their own needs.
Jalview is a powerful tool for the creation, visualisation and analysis of protein and nucleic acid sequences that is widely used in teaching and research. This course covers all aspects of Jalview’s use. In the first day, hands on tutorials and lectures are provided to introduce Jalview’s capabilities, and explore the sequence alignment, annotation, analysis and structure visualization functions Jalview provides. The second day covers advanced topics, and provides an opportunity for users and bioinformatics software developers to work alongside the Jalview team to analyse their own data, configure and deploy their own Java Bioinformatics Analysis Server (JABAWS), or extend and adapt Jalview for their own needs.
Is it right for me?
The course is suitable for anyone who needs to create, manipulate, annotate and publish nucleotide or protein sequence alignments, and use them to explore biological function. There will be introductory material for people with little or no experience in biological sequence analysis, but the course is also an opportunity for people with more extensive bioinformatics knowledge to gain a deeper understanding of Jalview.
The hackathon provides an opportunity for developers wishing to work on Jalview or JABAWS for their own projects to meet and work together to extend Jalview and JABAWS’ capabilities.
Materials for this course can now be found here:
Additional information
This course will take place in the EMBL-EBI IT Training room which has 35 computers set up with the relevant disk images required for this course.
Accommodation
PLEASE NOTE: Registrants must book their own travel and accommodation.
We would recommend that you book your accommodation at any of the following locations:
Wellcome Trust Conference Centre
Information regarding travelling to the EBI can be found here: A free shuttle bus will be arranged for registrants staying off-campus in the Whittlesford or Duxford area.
Programme
| Time | Topic |
|---|---|
| Day 1 - Monday 21 January 2013 | |
| 08:30-09:00 | Arrival and Registration |
| 09:00-09:10 | Welcome |
| 09:10-10:30 | Hands on: Introduction to Jalview |
| 10:30-11:00 | Coffee/Tea Break |
| 11:00-12:30 | Hands on: Introduction to Jalview continued |
| 12:30-13:30 | Lunch |
| 13:30-14:30 | Multiple sequence alignment and analysis |
| 14:30-15:00 | Hands on: Alignment and analysis with Jalview |
| 15:00-15:30 | Coffee/Tea Break |
| 15:30-16:50 | Hands on: Alignment and analysis with Jalview continued |
| 16:50-17:00 | Day 1 Wrap-up |
| 17:00 | Departure to accommodation |
| 18:30 | Meet for evening dinner Red Lion Hinxton. (5 minute walk from Campus) Please arrive in time to eat at 19:00 |
| Day 2 - Tuesday 22nd January 2013 | |
| 09:00-10:30 | Advanced Jalview and Jalview Hackathon |
| 10:30-11:00 | Coffee/Tea Break |
| 11:00-12:30 | Advanced Jalview and Jalview Hackathon continued |
| 12:30-13:30 | Lunch |
| 13:30-15:00 | Jalview Clinic and Jalview Hackathon |
| 15:00-15:30 | Coffee/Tea Break |
| 15:30-15:50 | Jalview Clinic and Jalview Hackathon continued |
| 15:50-16:15 | Wrap-up |
| 16:15 | Departure |
How to apply
Registration - £30
Please note that the registration fee includes:
* Lunch and refreshments during the course
* Course materials
* Use of EBI IT Training Room computer during the 2 day course
* Dinner on Monday 21st January
There will be a maximum of 35 participants on this course and registration is on a first come first serve basis. Registration will close on 10th January 2013 at 12:00 (noon) (GMT)
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 for this event.
Application deadline
10 January 2013
Organisers
Jim Procter - Dundee University
Geoff Barton - Dundee University
Trainers
Geoff Barton - Dundee University
Jim Procter - Dundee University