March-April 06 Workplan

This page is acting as a temporary list of jobs allocated to people until a medium term project plan has been completed.

The tasks are in no particular order. SAxxx tasks refer to actions from the OMII-UK f2f meeting, and can be found on the OMII-UK website. http://www.omii.ac.uk/Wiki.jsp?page=PrivateSTAFFOperations&null

David

Builds, integration, OMII, data storage, GUI

Scheduled activities

1. Code refactor Due for completion on tues 4th July

Background tasks

1. Maven build for taverna and plugins This is complete for all the streams of Taverna on sourceforge. However, the plugins are not done due to a problem with Mac builds. Possibly 1 day work remaining to resolve this plugin/Mac issue. Other work to do on this point: is to batch tests so that continuum only runs a basic set as part of the build process and doesn't fail. Need to update the build to integrate the Mac release as well
2. Continuum (for continuous integration) This is complete except for the issue that the build always fails due to the test set. Further work to be done on this: Issues with continuum sending massive log files as much of the code outputs loggin to stdout. The refactor should assist with this.
3. JIRA (for bug tracking and task management) _Initial investigation has proved that this could be a useful tool. It provides some roadmapping features over bugzilla. We have a license and you can import bugzilla bugs in to start up. Maybe a couple of hours work to get it rolling. Pencilled in the convert for the 1.5 release. Will have to migrate Sourceforge bugs/feature requests over at this time. _
4. myGrid Properties GUI for Taverna (This is useful because, because of constant irritation caused by the fact that the current properties file is hard to read/edit.) _Initial investigation done. This is a large piece of work and has been adopted as an OMIIUK requirement SA003 - being investigated there. Will be part of the GUi rework. _
5. Consider integrating Maven-generated documentation with current Taverna documentation.

1. Lined up future work: GUI rework.
2. Lined up future work: biomart 0.5 support.

Stian

_Hard problems, biology services understanding and integration, T2, Grid, Tomcat and Phoebus management, Learning to support Daniele on Security and Metadata _

Scheduled tasks

1. Functional tests (understanding of bioinformatics services) test harness in place. Just need to define the list of missing gaps in our testing. Stian to forward list to Katy to help in idenifying gaps in the testing. Has to be complete in time for the 1.5 release
2. Provenance debugging/modification support for Daniele.
3. Mirror of Matt to understand outstanding status of annotation tool
4. Analysis of Workflow Repository. Ideas to Taverna-Users on 28th June. Estimates for work involved on 3rd July.

Katy

Workflows, biology, requirements, website management

_ effectively out of the development project on other commitments until w/c 10th July._

Scheduled tasks

1. Help Stian with tests. Will probably require Katy to write some new tests to fill the gaps - or find workflows that plug the gaps. 2. Phoebus Consider replcement for Phoebus. Main things here are the wiki, website, some services for Paul.
2. Investigate existing/new use cases for provenance searching._

Background tasks

1. "How to write a workflow" Started investigating this and pulling resources together.
2. rationalisation of website Started to investigate the two websites with a view to merging.

Background tasks

1. Requirements/features/impact/scenario activity
   • User_requirements_summaries.doc
2. Management of the website "in general".
3. Biology "101" workflow to be created
4. Define a standard demonstration environment that can work out of the box.
5. "Systematic training and documentation" for users to be developed.

Stuart

Architecture, T2, complex coding

Scheduled tasks

2. Analysis of Long running workflows "group" of requirements. To produce a breakdown of the steps involved and estimates. 1. Code refactor (see David's schedule - pairwise work)

Background tasks

1. Architecture and Design of T2 (with Tom and Stian)

Matt

GUI, metadata browsers

Scheduled tasks

1. FETA/Pedro GUI redesign with incorporation of (redesigned) BioMoby features _ Currently working on tool for the annotationathon - due for prototype at end of w/c 27th June. Possibly a further 2 weeks work remaining at that point._

Background tasks

1. Hardening of Provenance Browser Bug fixing only now_

Daniele

Semantics, metadata, security

Scheduled tasks

1. Provenance changes. _Ongoing bug fixing/maintenance

Background tasks

1. FETA backend redesign Not started yet (will be started once intermediate data storgae bug fixed)
2. Security Large task. Not currently working on this.
   • MetadataSecurityAuthentication
3. SA021 - review of OMII3 authority.
4. Working on T2 semantics.

Tom

Taverna 2 core, workflow language, next gen ui design

Scheduled tasks

1. Metainfrastructure Release structure for Taverna 2.is ready - approx 1 calendar week to integrate with code after code refactor.
2. Interface definitions. Scheduled for completion 2nd June.
3. T2 workflow language(s), formal specification, architecture and capabilities. Mostly documentation at this point, I'm happy with the actual designs. There is about 2 man months worth of work to complete the new enactor (including design of the new workflow object). Work has begun .

Background tasks

1. Evangelism, teaching, talking and the like
2. T2 data layer design and impl

James

User/task oriented GUI for directly interacting with workflows from within UTOPIA

1. Build dynamic graph rendering component for UTOPIA in C++/OpenGL.
2. Investigate its possible uses:
   • pathways
   • provenance data
   • workflows
   • ontologies
   • UTOPIA data model