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  • Day: Tuesday, 17th June 2008
  • Time: 10.00
  • Room: Atlas 2


Carole, Stuart, Katy

Attending and Minuting

  • Stian

Ondex updates

Robert Stevens talk about Ondex.

There will be an ondex meeting in Newcastle in July/August and they would like a myGrid developer to be there.

There are two pieces of work, getting Taverna to talk to Ondex (to populate Ondex), and building some Taverna workflows.

Some perl scripts already exists for doing some gathering, cleansing and filtering, but it would probably be more flexible to do this using (fairly trivial) workflows.

ISMB demoes? Taverna 2 can be shown as a demo to highlight the speed improvements. There'll also be a myExperiment stand. Marco will be there as well, he's there as a PAL and will joinj David, Katy, Paul, Roberts, George, Jits.

Actions from previous meetings

  • Stuart: wiki page to list T1 artifacts and comment "clean, unclean, old mygrid, external" - ongoing, see T2 artifacts license status
  • Stuart: arrange beanshell / localworker meeting. ongoing - on Thursday

OMII Operations and Management

Neither Stuart or Tom is present.

T2 progress update

Activity palette is filling up, wsdl, soaplab, etc.  Finished the dragging bit that can pop up a view on drop. What about Biomoby? There are both BioMoby objects and BioMoby services.  Stuart has been thinking about it.

David has been working on the diagram so everything is clickable - or at least the things that are clickable. Heavily nested workflows can't really be edited inside, you have to open it. Coming along. When you click something, it selects it, and then more information about that will be shown in the "contextual view" where you can configure it - and also the tree view would show the selection. The menues should be the same when you click in the tree or the diagram.

Stian has done simple file handling, adding t1 translation (can only handle t2 dataflows currently), "Save All" , "Open recent".

Report back/Upcoming from Team A

Visitted people who cured cancer.

Report back/Upcoming from Team B


BioCatalogue updates - a meeting on Friday last week. Looking at semantic annotation work, Khalid, Steve Pettifer, myGrid.

Discussed the annotation model, silver, gold, platinium. 

Meeting with Cambridge people who want to adopt BioCatalogue. Discussion with Alex on security. 

Issue from Jits: Scalability for backend. Java or Ruby?  Using Java might take more time to get something (1 year), with Ruby we could have something quickly. Frontend and backend as a distinction, but we still want backend. But we want the backend to be a bit more stronger and "enterprise". Jits have a main concern on this, the plan is to have the two pieces - and for the pilot they want to build almost a new social networking site for services. 

Franck says there will be a Biocatalogue frontend and a myExperient frontend. Backend exposed as an REST interface.

They think it will be more productive to do a rapid prototype first instead of spending 1 year on building "the perfect backend". (very rough estimates: an alpha for September and beta for December). 


New intern: Sergej working on eLabs and myExperiment.

Three hour chats on packs - attachments and packs. Files and presentations that are interesting on their own, but sample data are directly attached to a workflow.

Working on a Taverna plugin. Identifier a few things with WHIP for the ISMB demo. Four tabs, "Latest workflows", "", "", "".  Click on a whip and start Taverna.

Report back/Upcoming from Team C

Alex showed how you can build a Taverna workflow that can invoke a secure service without requiring magic config files on the classpath - although currently the parameters are hard coded.

A form or tick box to say which and how services should be accessed in a secure way.

Set up a few secured services for testing.

We're using different frameworks for our tests: Axis 2, xfire, axis 1.

Working on annotating workflows. 

Tom points out there are two levels of Security APIs. A higher level one with more like "Can you do this for me?" and the more lower-level API is what Alex has done so far.

UI for how to say a service is secure, some right click thing, or contextual view? We've said that t2 "can  

Report back/Upcoming from Team Frog

Southampton says we have not signed off yet.

Test it, checks the documentaiton, sign off, put in the security, sign off, update docs, sign off, etc.  Jits will do a plugin for myExperiment.

We're not quite sure where we'll host the service for myExperiment - on a myExperiment machine?

InstantSOAP - no more news from the InstantSOAP front. Phil sent out some document.

Soaplab2 did have documentation - but the menus on their web page were difficult to find.

Changes on the Frog web page, content is going in now. Agreed hierarchy for the tools. (Taverna, myExperiment, InstantSOAP, Soaplab, something else, things we use: Protege, PELLET, etc) - each tool have description,

Report back/Upcoming from Training, Outreach and Curation

Training from 9-17.

Some OMII-thing, Simon and Ally are coming.

A discussion about how a REST service can be annotated, including some from EBI.

Report back/Upcoming from Team Tom

See Tom's progress reports to taverna-hackers. 

gLite integration talk should go to taverna-hackers, not the mygrid list.

Writing a "Getting started with t2references" guide.

Within OMII we have various grid plugins for commons-vfs (GridFTP and SRB?) that we can refer to.

Stuart and Tom said in the ops meeting that it would be great to get those plugins packed up as Maven artifacts so we can build External references that uses them.

Might be interesting to try with mySQL instead of Derby, but performance with Derby seems also quite decent.

Report back/Upcoming from BioAssist

A good meeting, two-tier system for provenance.

Machiel: Grid integration - we would like to have some contact person

Tom: Grid integration is key to the design of t2.

  1. Write an activity that can access the services
  2. Write an external reference implementation that can access the data
  3. Security agent plumbing

First of all - propose on taverna-hackers what you are going to do.

Round-table from Floating Team Members

Upcoming Milestones/Cross Team Scheduling Issues

Support Hat and JIRA Review (alternate weeks)

Upcoming Meetings

Digital 60 this Friday. Stian is going.

Friday Franck is going to the caBIG meeting.

Funding News

myGrid platform grant proposal sent

Any Other Business (AOB)

Discussion regarding Machiel's question for Taverna and GLite integration.

Minuting for the Next Meeting

New actions

Previous/Next Minutes

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