Planning for ISMB

1
Planning for ISMB AHM(take 2)

• myGrid AG meeting
• 30 April 2004

2
Agenda

• Review WBS scenario progress
• what did/didn't we show at NeSC?
• progress on issues at previous AG session (16
  Apr)
• do we need to revise or extend the scenario?
• Update on portal meeting (Thursday 29 April)
• visited by Rob Allan (CLRC) to discuss CHEF
  first impressions
• Planning for myGrid tutorial at SEEK workshop
  (led by Mark)
• AOB

3
Review WBS scenario progress

• what did/didn't we show at NeSC?
• progress on issues at previous AG session (16
  Apr)
• do we need to revise or extend the scenario?

4
Review WBS Scenariowhat did/didnt we show at
NeSC (1)

• Our user launches Taverna.
• She uses the find facility to view what workflows
  are available that match her goal.
• She finds an exact match for a workflow and loads
  it into the Taverna editor.
• She enacts the workflow, using a particular BAC.
  this workflow finds a DNA fragment that extends
  into the gap region being investigated. The
  workflow is left to complete. There is a filter
  service at the end of the workflow that checks
  for newly submitted sequences that are suitable
  and not seen before. She is notified that a
  suitable sequence has arrived.
• This notification means that she can carry on
  with her next bioinformatics experiment that
  characterises this new bit of DNA.

• Find facility not cleanly integrated into
  Taverna need a plugin approach to separate
  Taverna DiscoveryView builds
• In progress with Tom and Chris W
• Notification processor implemented but not yet
  used in WBS workflow
• Ananth to assist?

5
Review WBS Scenariowhat did/didnt we show at
NeSC (2)

• She uses the find facility to view what workflows
  are available that match her goal.
• She finds a close enough workflow and loads it
  into the Taverna editor.
• She needs to modify the workflow slightly and
  again uses the find service to add a couple of
  services into the workflow.
• She uses the view mechanism, because shed rather
  have local Manchester services unfortunately,
  Manchester doesnt have what she wants available,
  and she uses a general view of all services and
  finds what she wants.

• Multiple views supported by View Service but no
  interfaces for view selection in Taverna
• Follow on from integrating single view into
  Taverna?
• Support from Southampton?

6
Review WBS Scenariowhat did/didnt we show at
NeSC (3)

• She enacts the workflow, using the output from
  the previous experiment.
• She is again notified that the experiment has
  completed.
• We could have an optional step here of
  correcting a failing workflow, prompted by some
  notification.

• Notification via built-in Taverna/Freefluo
  workflow state monitor
• pluggable notifier in Taverna?
• Correcting the workflow?

7
Review WBS Scenariowhat did/didnt we show at
NeSC (4)

• Also something about ambient text analysis here
  perhaps following links through to documentation
  about disease, genes, proteins, or whatever.

• Text analysis via web service in workflow
• Not integrated with official WBS workflow
• Neil/George and Chris W
• Generality of text service?
• AQL support in progress
• Ambient text support
• Based on Swissprot BLAST reports
• Swing-based viewing components
• Portal? Taverna?

8
Review WBS Scenariowhat did/didnt we show at
NeSC (5)

• This round of experimentation is now complete and
  she wishes to perform a results analysis. She
  launches Haystack to check her results and
  evaluate any new material.
• She first looks at the GenBank record for the
  BAC, to check that it is a legitimate extension
  into the gap.
• She then looks at the results of the gene
  prediction for the fragment and traces through
  the characterisation of each legitimate
  prediction.

• Taverna annotation templates adequate?
• Domain-specific
• Annotations linked to workflow instance?
• General audit trail provenance?
• Chris W refining output not based on templates
• Haystack viewing tools adequate?
• Status of Haystack build

9
Review WBS Scenariowhat did/didnt we show at
NeSC (5)

• She annotates some of the results with opinion
  on the validity of those findings.
• She also annotates the experiment with her
  thoughts on the discoveries she has made.
• She reviews progress on her series of experiments
  by looking back in time on this particular topic.
• Finally, she looks at what comments her
  supervisor has made about her findings,
  conclusions and results.

• Making annotations within Haystack?
• Support for multiple users
• Taverna login
• Tom username/password
• MIR
• Arijit, Nedim info model
• Kevin MIR/Taverna plugin
• Provenance browsing without Haystack?

10
Review WBS Scenariodo we need to revise or
extend the scenario?

• Removing or replacing existing steps?
• Demonstrating new aspects
• Demonstrating more biology
• More WBS workflows
• More GD workflows

11
CHEF first impressions

• Portal framework
• Aggregates output (HTML, XHTML) from one or more
  portlets
• Arranges portlet output in panes in single page
  (under user control)
• Supports users with RBAC
• Workspaces have different subsets of available
  portlets

12
CourseTools
Over 42,000 users at the end of 2003
13
CHEF General Tools

• Announcements
• Chat
• Threaded Discussion
• Calendar
• Schedule
• E-Mail Archive
• Resources (including WebDav)
• Web-Frame
• Worksite Setup
• Profile
• Notifications / Subscriptions
• Public View
• Anonymous Comment

14
Benefits for myGrid

• Ready-made utility portlets (discussion, chat,
  file sharing, ) add value to myGrid-specific
  components
• Framework/portlet split reduces burden on
  developers
• Personalizable
• provided myGrid CHEF have same model of user
• Use of RDF in CHEF?

15
Adding Grid Infrastructure to CHEFThe value of a
component based architecture
Tools
Grid Service API
Jetspeed
Tomcat / Apache
CHEF Grid Service Component
COGs
MyProxy
UserDirectory
UserDirectory Provider
CHEF UserDirectory Service Component
Grid UserDirectory Provider Service
Jetspeed Login
Existing CHEF
New Code
User
IU Portlets LDAP GridFTP Proxy
IU Code
Existing GRID
16
CHEF Evolution

• CHEF 1.2
• available now
• based on Jetspeed 1 (non-JSR-168)
• CHEF 2 Sakai
• available July/August
• based on uPortal (JSR-168)

17
myGrid portals

• Evaluation (Stef)
• CHEF 1.2 vs. Jetspeed 1 vs. uPortal 2.3
• Benefits of CHEF
• Support from Daresbury
• Benefits of uPortal
• Easier path to Sakai?

18
myGrid portals

• Develop Hannahs GAS as portal
• Look for opportunities for generic portlets
• Workflow execution portlet
• Results browser
• MIR browser
• Ambient text portlet