Introduction

Notes on the myGrid tutorial NeSC, 13 May 2004. The tutorial was part of workshop organised by SEEK project. For details see LinkUp#NeSC_workshop_May_2004

The tutorial concentrated on those aspects of myGrid of most interest to SEEK and friends. As part of LinkUp it aimed to get people interested in trying out myGrid and giving feedback.

Agenda and Material

Most of this material is also available on the NeSC web pages for the

1 Overview

• Overview Talk http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/myGridSEEK_1intro.pptmyGridSEEK_1intro.ppt: myGrid introduction and overview

(based on Carole"s Life Science VCG Symposium talk (see PresentationStore), and Chris Greenhalgh"s revision)

2a Taverna (myGrid workflow) "hands on" session

• 2a (based on Peter"s

2b Service Description session

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/servicedescriptionanddiscovery.pptservicedescriptionanddiscovery.ppt: semantic tutorial slides

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/query-workflow.aviquery-workflow.avi: simple text query for workflow
• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/pedro-blast.avipedro-blast.avi: quick look at blast service details in pedro

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/blast-wsdl.docblast-wsdl.doc: example blast wsdl document
• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/interpro-wsdl.docinterpro-wsdl.doc: sample InterPro^? WSDL file

3 Results Management

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/myGridSEEK_2resultmgmt.pptmyGridSEEK_2resultmgmt.ppt: result management

This was only covered quickly due to time constraints. Additional material:

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/DataRegistration.pptDataRegistration.ppt: use of LSIDs and provenance to manage data
• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/lsid-launchpad.avilsid-launchpad.avi: using lsid launchpad to browse provenance
• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/provenance-generation.aviprovenance-generation.avi: Shows how to set up some context for workflow run

4 Wrapup session

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/myGridSEEK_3current.pptmyGridSEEK_3current.ppt: current status and plans

Expected issues included

• computationally intensive services
• large data volumes
• security

Most people who want should be able to get some "hands on" experience, and a chance to talk to people in smallish groups. This concentrates on WorkFlow and semantics as the focus of the tutorial.

Thanks

The tutorial was well received by the people at the workshop. Thanks to: Peter Li and Justin Ferris for their work on the Taverna tutorial, Phil Lord and Chris Wroe for delivering the same semantics talk back to back, Duncan Hull, Jun Zhao, and Pinar Alper for helping out in the "hands on" sessions and making sure things went smoothly.

Additional Preparation Information

Risks

• Hands on session problems
  • need ratio 4/5 users to 1 presenter, perhaps users working in pairs
  • careful tested script with no deviation
  • backup of lecture rather than 2nd demo session
  • examples accessible to SEEK ecologists - not a lot of biology to explain

• Problems accessing remote services
  • video backups
  • dummy services on local machines

myGrid component coverage

There is obviously a limit to what we can cover in 3 hours, so we will not cover all the myGrid components in depth. Taking the

• General - covered by overview and wrapup talks
• BioServices - part of hands on and demos
• DQP - mentioned, not included
• eScience Layer - Taverna (and Haystack demo video)
• Framework - not included, not part of current prototypes
• Notifications - mentioned, not included
• Ontologies - demo(s) on semantics
• Provenance - Haystack demo video, Taverna + Ouzo demo
• Repositories - information model part of overview and wrapup talks
• Service Directory - demo(s) on semantics and registries
• Text Extraction - mentioned, demo not included due to time
• Use Cases - demos, mentioned in overview
• Workbench - prototype 1, not included (now Taverna and Portal)
• Workflow -

Components can be classified in several ways:

• historical - varying prototypes (myGrid timeline)
• lifecycle - making and registering, discovering, running, managing and analysing
• applications (Portal/Taverna), integrating (DQP, Freefluo)

-- MarkGreenwood - 29 Apr 2004

Service Description session materials

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/servicedescriptionanddiscovery.pptservicedescriptionanddiscovery.ppt: semantic tutorial slides

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/query-workflow.aviquery-workflow.avi: simple text query for workflow

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/pedro-blast.avipedro-blast.avi: quick look at blast service details in pedro

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/blast-wsdl.docblast-wsdl.doc: example blast wsdl document

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/interpro-wsdl.docinterpro-wsdl.doc: sample InterPro^? WSDL file

-- ChrisWroe - 12 May 2004

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/myGridSEEK_1intro.pptmyGridSEEK_1intro.ppt: myGrid introduction

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/myGridSEEK_2resultmgmt.pptmyGridSEEK_2resultmgmt.ppt: result management

• http://www.mygrid.org.uk/wiki/pub/Mygrid/NeSCmyGridTutorial/myGridSEEK_3current.pptmyGridSEEK_3current.ppt: current status and plans