DAS Workshop 2010
This workshop has been organised with support from ENFIN:
DAS is an important system for exchanging and viewing of biological data, with more than 600 DAS sources available world wide. Several different projects are working on applications and resources to provide DAS support. The purpose of this meeting is to improve communication between these projects and let interested people learn what they can do with DAS and how to do it.
Is it right for me?
This workshop aims to cater to a number of differing backgrounds so all days on the workshop are optional. To make the most of having many DAS experts in one place there is an extra day this year for break off groups to push forward with their DAS projects. People new to DAS will likely want to attend the first day, conversely experts may decide only to attend the 2nd and 3rd day.
What will I learn?
- what you can do with DAS
- how to talk to a DAS server
- how to set up your own servers
What will it cover?
- The first day is a practical day where you can learn how to work with DAS.
- What DAS commands look like
- How to request via Perl / Java
- How to set up a DAS server
- How to get a list from available servers from the DAS registry
- The second day is the first of the DAS client developers days where developers present their DAS related applications, websites and discuss new ideas. Each participating group is invited to give a 15 min presentation. There is time for a short discussion after each talk. Please contact Jonathan Warren if you want to give a presentation on this day.
- Present the progress over the last year
- Find synergies
- See if/how interoperability can be improved
- Discuss possible future extensions to DAS
- The final day will work on pushing forward with specific projects/aspects of DAS. Please suggest subjects when you register by sending an email to Jonathan Warren
| Time | Topic |
|---|---|
| Day 1 - Wed 7th April 2010 - Hands on DAS | |
| Opening | Safety and Introduction |
| Session 1 | What DAS commands look like |
| Session 2 | How to request via Perl / Java |
| Session 3 | How to set up a DAS server |
| Session 4 | How to get a list from available servers from the DAS registry |
| Day 2 - Thu 8th April 2010 - DAS client developers day 1 | |
| 09:30 - 10:00 | Tea/Coffee |
| 10:00 - 10:20 | Opening talk. (Tim Hubbard) |
| 10:20 - 10:40 | Collaborative genomics with DAS- a new interactive DAS client (Thomas Down) |
| 10:40 - 11:00 | Progress to report on linking EMBOSS and DAS (Peter Rice) |
| 11:00 - 11:20 | Visualization of sequence features with STRAP (Christoph Gille) |
| 11:20 - 11:40 | easyDAS: a hosted solution for DAS server creation (Bernat Gel) |
| 11:40 - 12:00 | Update on the collaborative, web-based version of Apollo (Suzanna Lewis/Gregg Helt) |
| 12:00 - 12:15 | GenoViz DAS/2 framework (David Nix) |
| 12:15 - 13:30 | Lunch |
| 13:30 - 13:50 | Ensembl (t.b.c.) |
| 13:50 - 14:10 | DAS service to provide information on 3D motifs- PDBe (Adel Golovin) |
| 14:10 - 14:30 | DAS Writeback and its integration in Dasty2 as a proof of concept (Gustavo Salazar) |
| 14:30 - 14:50 | Interaction DAS (Hagen Blankenburg) t.b.c. |
| 14:50 - 15:10 | DAS for ENCODE data coordination (Felix Kokocinski) t.b.c. |
| 15:10 - 15:30 | Tea break |
| 15:30 - 15:50 | A web resource for selecting epitopes for antibodies (Niall Haslam) |
| 15:50 - 16:10 | DAS searches (Andreas Prlic) t.b.c. |
| 16:10 - 16:30 | KaryoDAS: An Interactive Genome Visualization Tool Using DECIPHER Data (Eugene Bragin/Manuel Corpas) |
| 16:30 - 17:00 | jsDAS: A javascript DAS client library (Jose Villaveces/ Bernat Gel) |
| 17:00 - 17:30 | Data integration in ENFIN using standards; the EnCore DAS service (Rafael Jimenez) |
| 17:30 - 18:00 | Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups |
| 19:00 - 21:30 | Course Dinner - venue to be confirmed |
| Day 3 - Fri 9th April 2010 - DAS client developers day 2 | |
| Session | To be decided |
For the final day sessions the topics suggested for this year:
- DAS 1.6 spec implications and updating of clients/servers
Suggestions from last year were:
- DAS1/DAS2 merger
- DAS writeback
- Adapting Java DAS client libraries for alignment and PDB file retrieval for clients that dont use BioJava
- Ajax das client/server library (allow DAS server discovery and retrieval on the browser page)
- Graphical Representation of data
- DAS interfaces to sequence analysis tools
- BioSapiens ontology lookup
- DAS vs. ontologies, how and why.
- DAS 1.6 spec and where to go with the Registry
The registration for this workshop is free and includes lunches and coffee for the first two days. You will need to pay for your own travel and accomodation.
We are recommending staying at the travel lodge in Cambridgeand buses will be provided to and from the campus and the restaurant. People not able to catch a bus at the travel lodge will need to make their own arrangements for travel.
Registration is now closed.