Science Environment for Ecological Knowledge
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Science Environment for Ecological Knowledge




Status Report 08 June 2004


  • Kepler User Interface meeting in Santa Barbara, meeting notes in CVS
  • EcoGrid group revamping resultset format, adding new dynamic data query methods based on EML
  • Kepler group working on
    • ontology-driven data and actor browsing
    • integrated EcoGrid data discovery and access
    • Presenting Kepler demo paper at SSDBM in Greece
  • EOT working on
    • Upcoming RCN and KNB Metadata Tools training sessions
    • New website based on wiki about to come online, waiting on LDAP issues and final graphics tuning
  • Taxon group focusing on LSID and user management issues and finishing the name server prototype

Individual reports

Rod Spears

Completed Tasks/ Bugs Fixed:
  • Attended the Kepler UI design meeting in Santa Barbara

Current Work and Bugs:

  • Bug 1594 - Impl revised Resultset XSD for all 3 platforms o The XSD has been changed and the resultset java classes have been generated o I have all 3 platforms converted over to use the new classes o DiGIR Resultset parser has been tested o Currently working on the generic transform from the Resultset to HTML for display purposes. At this time it doesn't look like the an XSLT transform will work due to the complexity of the new resultset set definition. I am sure it can be done, for now I think a simple DOM parser will be easier to maintain considering this will more than likely not be used in the final production mode.

Work This Week:

  • Hopefully complete Bug 1594
  • Start on Bug 1595 - Create Advance Query Builder UI

Important or Outstanding Issues (of a significant nature)

  • Globus has moved on to version 3.2, this means it will be difficult to get support for 3.0.2 o They have deprecated the PersisentGridServiceImpl class and replaced it with GridServiceImpl o The have included a "simple CA" which I was able to generate a local certificate and get it working
  • When we move to the next version of the Resultset we should consider moving to 3.2

Robert Gales

Unfortunately I don't have much to report about last week. I looked a little bit into customized serialization of objects in Axis with little luck, but spent the majority of the week doing a burst of development for the other projects funding my salary.

I'll be devoting this entire week to SEEK as Aimee and I are undergoing some minor changes to the architecture and I'd like to get started on creating a more permanent web presence for the Taxon WG.

Aimee Stewart

Last week I worked on integrating the schema changes into WSDL, SOAP, and the tests. I am still getting some failures in the client tests, so I have not yet checked them back into CVS.

EnterProviderData is the next task on my list. Robert and I have met to discuss how best to implement data entry and modification and will expand our data model just slightly to accomodate this fundamentally different process (modifying as opposed to querying). Documentation will be created as we begin this API.

Samantha Romanello

Completed tasks and Bugs fixed
  • Poster for NSF/ITR completed

Current Work and Bugs

  • Website:
  • Trainings:
    • RCN training October 18- 30: need to send out advertisement of events
      • SEEK Post-doc training Jan 05: need to finalize topics to be covered
    • Conferences and Events:
      • NSF ITR meeting June 10-11
      • ESA August 1 - 7: Workshop; Evening Session and poster presentation

Significant issues

  • Finalize schedule and participant and trainer numbers for September KNB Data Management Tools training -- conference call scheduled for Friday.
  • Monthly SEEK Seminar: trying to developing a virtual SEEK monthly brown-bag seminar to provide mechanism for collaboration of SEEK team. Tentative format: 1 hour presentation/ status report from development and/or working group teams where issues can be resolved or discussed. Need to know:
    • which SEEK sites can link through access grid; and
    • the possibility of video taping for archiving/ on website.

Matt Jones

Completed Tasks/ Bugs Fixed:
  • Attended the Kepler UI design meeting in Santa Barbara

Current Work and Bugs:

  • Bug 1339, 1343: ecogrid/eml support in kepler
  • Continuing work on web site, helping tekell with ldap issues
  • Planning training meeting in September
  • Will revise JIIS manuscript and Frontiers manuscript

Significant Issues

  • None

Bing Zhu

  • Had a meeting with David Stockwell and Raja to discuss the data integration of Niche Modeling in Ecogrid system. Has been working on the setting up the SRB accounts and choosing physical storage for those niche modeling images. A SEEK new task was created for this data integration in SEEK’ Bugzilla.

  • Evaluated the schema and architecture of Ontology Server developed by STAR Lab ( and discussed it with SEEK SDSC team in a UCSD SEEK meeting. Exchanged ideas with SEEK and GEON researchers about establishing ontology registry, search for ontology (what does this mean) and issues about future usage of ontology registry.

Xianhua Liu

Completed Tasks/ Bugs Fixed:

  • Revised National Vegetation Classification Revision System (NVCRS)
    • Revised nvcrs database structure
    • Revised the first jsp pages for all 3 roles: author, peer-viewer and manager
    • Implemented uploading function for supporting documents.

Current Work and Bugs:

  • Designing and developing Auto-Manager for nvcrs to automatically complete some system administration tasks, such as sending emails,assigning proposals to peer-viewers.

Significant Issues

  • None

Jing Tao

Completed Tasks/ Bugs Fixed:

  • Attended the Kepler meeting in Santa Barbara and identify the tasks/bugs for next couple months.

Current Work and Bugs:

  • Bug 1584(loading data into relation db) and 1586 (Data query engine implementation in Kepler)
    • Design for those bugs(Collaboration diagram and class diagram design).
    • Try to install and paly with SAS which is a candidate SQL engine for data query.

Significant Issues

  • SAS is complicated and probably the learning curve is high.
  • Need to identify which SQL engine we should use to loading data. Some criteria about this engine
    • Ease to install it in both Windows and Linux
    • DDL is simple
    • Good performance

Chad Berkley

Completed Tasks/ Bugs Fixed

  • researched ontology integration for kepler (bug 1591)
  • worked on bug 1579 with dan
  • helped debug the mac issues in kepler
  • attended the 2 day kepler meeting

Current Work and Bugs

  • Working on getting ready for SSDBM. Mostly working on poster.

Significant Issues

  • Need to have conf. call with matt and shawn about sparrow/ontology issues in kepler. we decided to hold the call after my return from greece

Dave Thau

Completed tasks/bugs fixed

  • Created and vetted initial basic feature set for Taxon LSID server

Current Work and Bugs

  • Working on bug #1597 - the intial user management for the taxon server.
  • Getting current taxon server to work on my local box for testing purposes

Significant issues

Is there any centralization of user management across SEEK, or any standard information about users we want to maintain? Should I use LDAP, or something like that, or just maintain taxon server specific user information. Seems like the latter is fine - people contributing taxonomic concepts may not care about the rest of SEEK, so shouldn't necessarily be burdened by a SEEK-wide user management system. However, it'd be good to collect and name contact information similarly across SEEK. I'm going to start with the sorts of contact information used in the Darwin Core.

Other Status Reports

You can see the status reports for other time periods as well.

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This page last changed on 09-Jun-2004 12:32:02 PDT by jones.