Difference between revisions of "DASWorkshop2012"

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Some knowledge/experience of PERL or Java and or Javascript would be beneficial for the hands on training day.
 
Some knowledge/experience of PERL or Java and or Javascript would be beneficial for the hands on training day.
 
===Example DAS commands can be found here as a DAS quick reference guide: [http://www.dasregistry.org/DASCommandExamples.jsp DAS examples]===
 
===Example DAS commands can be found here as a DAS quick reference guide: [http://www.dasregistry.org/DASCommandExamples.jsp DAS examples]===
 +
 +
The draft schedule for Day 1 is below. Please note that session times are a rough indication only and will vary according to progress on the day.
  
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
Line 16: Line 18:
 
! Resources
 
! Resources
 
|-  
 
|-  
−
| 9:00
+
| 9:15
 +
| Welcome and Information
 +
| JW
 +
|
 +
|-
 +
| 9:20
 
| DAS - Introduction/Overview
 
| DAS - Introduction/Overview
−
|  
+
| AJ
−
| [http://www.biotnet.org/training-materials/introduction-das Introduction] [http://www.biotnet.org/training-materials/technical-introduction-das Technical Introduction]
+
| [http://www.ebi.ac.uk/~aj/das_workshop_2012/DAS-Introduction.pptx DAS Introduction]
 
|-
 
|-
−
|  
+
| 9:40
 
| The DAS Game
 
| The DAS Game
−
|
+
| LG
 
| [http://www.biotnet.org/training-materials/das-game The DAS Game]
 
| [http://www.biotnet.org/training-materials/das-game The DAS Game]
 
|-
 
|-
−
|  
+
| 10:00
−
| Hands-on tutorial: using DAS software, 10 minute introduction of some DAS implementations (Bernat)
+
| DAS - Technical Introduction
−
|  
+
| AJ
−
| Implementations. [http://www.lsi.upc.edu/~bgel/research/easydas/tutorial/Implementations.ppt PPT] [http://code.google.com/p/easydas/wiki/tutorialDASWorkshop2011 Creating DAS sources from GFF files supplied using easyDAS] (Bernat), Viewing DAS sources using Dalliance (Thomas) [http://www.biodalliance.org/people/thomas/dalliance-for-das-workshop.pdf PDF]-or- Dasty3 (Jose) [http://www.ebi.ac.uk/~ljgarcia/Presentations/Tutorials/DASTY3_DASWorkshop_2011.pdf PDF]
+
| [http://www.ebi.ac.uk/~aj/das_workshop_2012/DAS-Introduction-Technical.pptx DAS Technical Introduction]
 +
|- style="background:#ffdead;"
 +
| 10:20
 +
| colspan="3" | Coffee break
 +
|-
 +
| 10:40
 +
| Using DAS software, an introduction to some DAS implementations
 +
| RJ
 +
| [http://www.biotnet.org/training-materials/using-das-software-introduction-some-das-implementations Implementations Introduction]
 
|-
 
|-
−
|  
+
| 11:00
 +
| Demo: creating a DAS source from a file with EasyDAS
 +
| RJ
 +
| [http://code.google.com/p/easydas/wiki/easyDAS_tutorial easyDAS tutorial]
 +
|-
 +
| 11:10
 +
| Hands-on: viewing DAS sources with Ensembl
 +
| AJ
 +
| [http://www.ebi.ac.uk/~aj/das_workshop_2012/ensembl/das-ensembl.html DAS in Ensembl]
 +
|-
 +
| 11:20
 +
| Introduction to DAS server frameworks
 +
| JW
 +
| [http://www.biotnet.org/training-materials/das-servers 10 minute introduction to DAS servers]
 +
|-
 +
| 11:30
 
| Hands-on programming tutorial: Creating a custom DAS source
 
| Hands-on programming tutorial: Creating a custom DAS source
−
|  
+
| AJ/JW/LG/RJ
−
| [http://www.biotnet.org/training-materials/das-servers 10 minute introduction to DAS servers], [http://code.google.com/p/mydas/wiki/Tutorials MyDAS] -or- [http://www.biotnet.org/training-materials/bio-das-proserver-tutorial ProServer]
+
| [http://code.google.com/p/mydas/wiki/Tutorials MyDAS] -or- [http://www.ebi.ac.uk/~aj/das_workshop_2012/proserver/tutorial1.html ProServer]
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
−
| 12:15 - 13:15
+
| 12:30
 
| colspan="3" | Lunch break
 
| colspan="3" | Lunch break
 
|-
 
|-
−
|  
+
| 13:30
 
| Tutorial - DAS servers continued
 
| Tutorial - DAS servers continued
−
|  
+
| AJ/JW/LG/RJ
−
| Perl(ProServer) and Java(MyDAS)
+
|
 
|-
 
|-
−
|
+
| 14:50
−
| Hands on Tutorial The DAS registry: Short introduction talk then hands on tutorial
+
| Introduction and hands-on: The DAS registry
−
|
+
| JW
 
| [http://www.biotnet.org/training-materials/short-das-registry-tutorial-basic-knowledge DAS Registry Tutorial]  
 
| [http://www.biotnet.org/training-materials/short-das-registry-tutorial-basic-knowledge DAS Registry Tutorial]  
 
|-style="background:#ffdead;"
 
|-style="background:#ffdead;"
−
| 15:10 - 15:30
+
| 15:10
−
| colspan="3" | Cofee Break
+
| colspan="3" | Coffee Break
 
|-
 
|-
−
|  
+
| 15:30
−
| Hands-on programming tutorial: DAS client libraries, 10 minute introduction
+
| Introduction to DAS client libraries
−
|  
+
| LG
−
| [http://www.biotnet.org/training-materials/bio-das-lite-tutorial Bio::Das::Lite]-or- [http://www.biotnet.org/training-materials/jdas JDAS] -or- [http://code.google.com/p/jsdas/wiki/tutorial JSDAS]. Each will cover sources, sequence & features using the same examples
+
| [http://www.biotnet.org/sites/biotnet.org/files/documents/40/clientlibraries_das_ws_2012.ppt Introduction to client libraries]
 +
|-
 +
| 15:40
 +
| Hands-on programming tutorial: DAS client libraries
 +
| AJ/JW/LG/RJ
 +
| [http://www.ebi.ac.uk/~aj/das_workshop_2012/daslite/tutorial.html Bio::Das::Lite]-or- [http://code.google.com/p/jdas/wiki/dasWorkshop2012 JDAS] -or- [http://code.google.com/p/jsdas/wiki/tutorial JSDAS]. Each will cover sources, sequence & features using the same examples
 
|-   
 
|-   
 
|17:30
 
|17:30
−
| colspan="3" |Departure from Campus to Whittlesford Station/Holiday Inn at circa 17:30 hrs.
+
| colspan="3" | Departure from Campus to Whittlesford Station/Holiday Inn at circa 17:30 hrs.
 
|- style="background:#ffdead;"
 
|- style="background:#ffdead;"
 
|19:00
 
|19:00
−
|Dinner at the Red Lion Whittlesford 7.00 pm for 7.30 pm sit down.
+
| colspan="3" | Dinner at the Red Lion Whittlesford 7.00 pm for 7.30 pm sit down.
−
|
+
 
−
|
 
 
|-
 
|-
 
|}
 
|}
  
−
==Day 2 Develpers Hackathon==
+
==Day 2 and Day 3: Developer Hackathon==
−
DAS developers day
+
This year we will not have a day of talks as in previous years. Instead, both day 2 and day 3 will be "DAS developers' days". This may include some updates on progress since the last workshop, discussions, and a code hackathon. The exact format is yet to be decided.
 +
 
 
===Recent developments since the last workshop===
 
===Recent developments since the last workshop===
−
DAS writeback, DAS search, Registry CRUD via web service (get, post, put, delete), Registry supports JSON for all requests and responses,
+
 
−
===Suggestions for discussions on Developers Days===
+
* DAS writeback
−
JSON roll out to other servers and clients? (jw)
+
* DAS search
−
Firming up of the authentication DAS standard so the registry and writeback are consistent (jw)
+
* Registry CRUD via a web service (get, post, put, delete) (JW)
−
Add support for conditional get (If-Modified-Since - reply only if modified since the modified since header) ? (jw)
+
* Alternative content negotiation (e.g. the Registry supports JSON for all requests and responses) (AJ/JW)
 +
* Authentication/encryption in ProServer (AJ)
 +
 
 +
===Suggestions for topics on Developers Days===
 +
 
 +
Please feel free to add suggestions for discussions or code sprints.
 +
 
 +
* JSON roll out to other servers and clients? (JW)
 +
* Firming up of the authentication DAS standard so the registry and writeback are consistent (JW)
 +
* Add support for conditional get (If-Modified-Since - reply only if modified since the modified since header) or ETags? (JW)
 +
* High density simple features such as SNPs - vcf format or simple json format without method and stop? (JW)
 +
 
 
===Possible DAS related Talks===
 
===Possible DAS related Talks===
−
DAS Registry - new architecture and capabilities (jw)
 
  
−
==Day 3 DAS Developers Day Hackathon==
+
* DAS Registry - new architecture and capabilities (JW)
−
DAS Developers Hackathon
+
* DAS in personal genomics (MC/JW/BG)
−
Location is the EBI Training Room
+
* Secure DAS trial (David Martin, Jim Procter, Thomas Down)
 +
 
 +
===Useful links===
 +
DAS 1.6 specification [http://www.biodas.org/documents/spec-1.6.html spec]
 +
 
 +
RelaxNG document for validation of features: [http://www.dasregistry.org/validation1.6/features.rng relaxng]
 +
 
 +
6 easy steps to setting up a [http://biodasman.wordpress.com/2012/01/12/easy-deployment-of-das-server-for-personal-genotype-data-to-the-amazon-cloud/'MyDAS genotype data source in the cloud/tomcat server']
 +
 
 +
['Sanger Proserver Adapters' https://sangeradaptors.svn.sourceforge.net/svnroot/sangeradaptors/Bio/Das/ProServer/SourceAdaptor/]
 +
 
 +
 
 +
===Images===
 +
 
 +
Pictures, mostly from day 2 are here [[http://www.flickr.com/photos/davidmam/sets/72157629110016398/]]
 +
 
 +
=Outcomes from workshop 2012=
 +
 
 +
A Ruby server is in development that implement the sources, sequence, features, types and soon entry_points request/responses : [https://github.com/alexkalderimis/RubyDAS https://github.com/alexkalderimis/RubyDAS] Bastian Greshaek and Alex Kalderimis
 +
 
 +
Mixed mode authentication for DAS servers specification [http://www.biodas.org/wiki/DAS1.6E#Authentication http://www.biodas.org/wiki/DAS1.6E#Authentication]. David Martin, Jim Proctor, Thomas Down, Andy Jenkinson.
 +
 
 +
SOLR based MyDAS gff current svn repository version of MyDAS. Rafael Jimenez
 +
 
 +
Firming up of the DAS JSON format (decided on "real" JSON rather than a convert from xml). Thomas Down, Andy Jenkinson, Jonathan warren.
 +
 
 +
DAS server code is being added to the Intermine project (MyDAS based). Alex Kalderimis
 +
 
 +
DAS support in the VectorNTI Genome Bench software is being updated. Ajish A Kahar
 +
 
 +
Additions to the JDAS (Java DAS library) code including authentication mixed mode mentioned above. Jim Procter, Leyla Garcia, Jonathan Warren.

Latest revision as of 10:08, 13 March 2012

The 2012 DAS Workshop will be held on 27-29 Feb at the EBI Hinxton campus.


DAS Workshop 2012 Schedule

All 3 days will be held in the EBI training room.

Day 1

Some knowledge/experience of PERL or Java and or Javascript would be beneficial for the hands on training day.

Example DAS commands can be found here as a DAS quick reference guide: DAS examples

The draft schedule for Day 1 is below. Please note that session times are a rough indication only and will vary according to progress on the day.

Time Title Speaker Resources
9:15 Welcome and Information JW
9:20 DAS - Introduction/Overview AJ DAS Introduction
9:40 The DAS Game LG The DAS Game
10:00 DAS - Technical Introduction AJ DAS Technical Introduction
10:20 Coffee break
10:40 Using DAS software, an introduction to some DAS implementations RJ Implementations Introduction
11:00 Demo: creating a DAS source from a file with EasyDAS RJ easyDAS tutorial
11:10 Hands-on: viewing DAS sources with Ensembl AJ DAS in Ensembl
11:20 Introduction to DAS server frameworks JW 10 minute introduction to DAS servers
11:30 Hands-on programming tutorial: Creating a custom DAS source AJ/JW/LG/RJ MyDAS -or- ProServer
12:30 Lunch break
13:30 Tutorial - DAS servers continued AJ/JW/LG/RJ
14:50 Introduction and hands-on: The DAS registry JW DAS Registry Tutorial
15:10 Coffee Break
15:30 Introduction to DAS client libraries LG Introduction to client libraries
15:40 Hands-on programming tutorial: DAS client libraries AJ/JW/LG/RJ Bio::Das::Lite-or- JDAS -or- JSDAS. Each will cover sources, sequence & features using the same examples
17:30 Departure from Campus to Whittlesford Station/Holiday Inn at circa 17:30 hrs.
19:00 Dinner at the Red Lion Whittlesford 7.00 pm for 7.30 pm sit down.

Day 2 and Day 3: Developer Hackathon

This year we will not have a day of talks as in previous years. Instead, both day 2 and day 3 will be "DAS developers' days". This may include some updates on progress since the last workshop, discussions, and a code hackathon. The exact format is yet to be decided.

Recent developments since the last workshop

  • DAS writeback
  • DAS search
  • Registry CRUD via a web service (get, post, put, delete) (JW)
  • Alternative content negotiation (e.g. the Registry supports JSON for all requests and responses) (AJ/JW)
  • Authentication/encryption in ProServer (AJ)

Suggestions for topics on Developers Days

Please feel free to add suggestions for discussions or code sprints.

  • JSON roll out to other servers and clients? (JW)
  • Firming up of the authentication DAS standard so the registry and writeback are consistent (JW)
  • Add support for conditional get (If-Modified-Since - reply only if modified since the modified since header) or ETags? (JW)
  • High density simple features such as SNPs - vcf format or simple json format without method and stop? (JW)

Possible DAS related Talks

  • DAS Registry - new architecture and capabilities (JW)
  • DAS in personal genomics (MC/JW/BG)
  • Secure DAS trial (David Martin, Jim Procter, Thomas Down)

Useful links

DAS 1.6 specification spec

RelaxNG document for validation of features: relaxng

6 easy steps to setting up a genotype data source in the cloud/tomcat server'

['Sanger Proserver Adapters' https://sangeradaptors.svn.sourceforge.net/svnroot/sangeradaptors/Bio/Das/ProServer/SourceAdaptor/]


Images

Pictures, mostly from day 2 are here [[1]]

Outcomes from workshop 2012

A Ruby server is in development that implement the sources, sequence, features, types and soon entry_points request/responses : https://github.com/alexkalderimis/RubyDAS Bastian Greshaek and Alex Kalderimis

Mixed mode authentication for DAS servers specification http://www.biodas.org/wiki/DAS1.6E#Authentication. David Martin, Jim Proctor, Thomas Down, Andy Jenkinson.

SOLR based MyDAS gff current svn repository version of MyDAS. Rafael Jimenez

Firming up of the DAS JSON format (decided on "real" JSON rather than a convert from xml). Thomas Down, Andy Jenkinson, Jonathan warren.

DAS server code is being added to the Intermine project (MyDAS based). Alex Kalderimis

DAS support in the VectorNTI Genome Bench software is being updated. Ajish A Kahar

Additions to the JDAS (Java DAS library) code including authentication mixed mode mentioned above. Jim Procter, Leyla Garcia, Jonathan Warren.

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