wiki:LEGACY - Integration phase 20101112

LEGACY - Integration phase 20101112


Email from Nick

Chris and I spent some time today trying to clarify the technical tasks we need to accomplish between now and next March. The attached file is a planner document, which identifies the tasks, and our respective time allocations to them. It is an early draft, which is just as well, since Jeff and I appear to be about 120% committed for all of December and January.

Can you identify tasks I have missed, or any resource allocations you think are wrong? Once we've got a definite set of tasks and allocations, we will be able to discuss with Tim whether to reschedule some of the work, or bring in additional resources.


Number of VMs Available

I've not really started to go through the document in detail. But it dawned upon me that if we have a target of test deployment of i2b2 on the UHLT side by February, then we are currently severely constrained by the lack of test VM's. Jeff.

Infrastructure – Development Environments

My understanding is that this would cover:

  • A project within svn for each.
  • Built artifacts within a maven repository.
  • Some explanatory documentation on the wiki and probably notes within the projects themselves.
  • Install procedures held within svn.

What is not covered so far in the planner:

  • Labels Webapp (has a project in svn),
  • UIDGEN (has a project in svn)
  • The ability to design label formats. Knowledge of the latter is restricted to Vasil working in a Windows environment. There is no project within svn covering this.

Project updates / issues for BRICCS tech meeting, 11 January 2011

Note: Following the Oxford / NIHR conference, work streams relating to C3PR have been postponed pending review of EDGE as platofrm for research unit management data


  • Development environments (Dave) Current status: Have server resources within UoL dedicated to BRICCS development, with four virtual servers enabling us to test various configurations of software A more flexible approach has been taken, with servers currently being used to create and test 'deployment' and 'upgrade' routines. These resources will also be used for testing modifications to software.
  • Establish 'test' and 'training' versions (Dave, Nick, Jeff) A test+training version of Onyx is now working on UHL's servers A test+training version of caTissue is to be deployed on UoL servers very soon A test+training version on i2b2 will be deployed on UHL's servers soon
  • Development tools (Dave) Trac is in use for documentation and technical issue tracking Subversion and Maven in use for storing programs under development
  • Backup / restore (Dave) System restore routines being tested on development servers Data backup for UoL is handled by RCS Data backup for UHL (Onyx) is currently within BRICCS (Nick) Data backup for UHL (i2b2) will be handled by UHL IMT
  • Test scripts (Dave) Development of test routines underway
  • System security review (Dave) Not yet underway

Onyx (Nick)

Note: a new version of Onyx, including an easier questionnaire creation tool, will be released shortly

  • Questionnaire review ongoing
  • feedback from teleconference with Philippe / Vincent re audit and validation options ? decisions ?
  • data export trials being undertaken (Jeff) ? progress ? what data goes to i2b2? what (if any) goes anywhere else, e.g. for reporting?
  • report.php chart functions (Vasil) ongoing, including interview/notes data correlation ? timetable? integrate with reports generated from exported data?

caTissue (Nick currently)

  • caTissue now in its (semi-)permanent home on briccs-3
  • caTissue upgrade to v1.2 temporarily delayed due to delay in release of v1.2
  • exploration of API for script / bar code reader / multiple data entry (Jeff) ? progress ?

i2b2 (Jeff)

  • Discussions with i2b2 developers regarding ontologies has resulted in us working with a team at Stanford developing a cell for i2b2 which enables us to 'pull' ontologies from a library (likely including SNOMED CT) when needed for specific data loading into i2b2. Progress expected during early months of 2011, and therefore fits our timetable.
  • Successful deployment of a test i2b2 installation complete
  • Next step is to deploy i2b2 on UHL test server, and attempt load of test data from Onyx, mapping data to SNOMED CT codes en route.
  • Ongoing discussion with UHL IMT regarding greater use of Jason to support data aggregation from UHL systems.

Clinical informatics / registry

  • Outline discussions with Trevor Howlett scoping objectives complete
  • Although PATS, Workstation, etc., all offer some valuable data, none offer a full systematic EPR without major strategic input by UHL. ? decisions ?

Management tool (Nick)

  • Amendments being made to collect OPD recruitment data

Genomics data

  • Deferred for now.

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