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- Taxon group
- Considering whether relationships should have global identifiers, and implications for how taxonomists use the system
- Mammal data from ITIS put into the exchange standard, waiting on hickory data
- Kepler group
- Substantial discussions on user interface design and ability for semantic abstraction of workflows
- Preliminary actor for running R scripts in Kepler completed
- EcoGrid group
- Almost complete with new resultset format on all four platforms (Metacat, SRB, DiGIR, Xanthoria)
- EOT group
- New website prototype ready, will be placed in production next week (replacing the existing SEEK web site). Comments appreciated, see the prototype web site
 .
Completed tasks
- tested Xanthoria EcoGrid codes on Axis, without globus on windows machine. It works fine.
Current work:
- Currently, I am working on two things:
- Making changes to existing codes to make it compatible with latest resultset schema (getting rid of AnyRecordType)
- Trying to install and configure GT3.2 on a development machine (linux box), so that I can test Xanthoria and then maybe check in the codes to seek cvs.
Significant issues
- Currently I am interested in the following issues:
- Configuring GT version 3.2-how to use the certificates? Will the older ones work or do we need to create again? What’s the procedure for installing and configuring GT 3.2?
- Is anybody working on setting up GIIS and MDS? What is the current status with this respect?
Completed Tasks/ Bugs Fixed:
- Contributed to the SEEK/Kepler UI discussion.
- Highlights: There is consensus building that a higher level conceptual design tool will be needed that more closely represents how models are constructed by the scientists.
- Dan constructed several screen shots for talking points at http://www.nceas.ucsb.edu/~higgins/BoxesAndArrows
- The filling of the usability engineering position is key to future progress on all UI issues (although there is a lot of progress yet to be made).
Current Work and Bugs:
- Start on Bug 1595 - Create Advance Query Builder UI
- Continued investigation into which Swing features can be leveraged to create the UI.
- In general, the top level of components makes it easy to quickly prototype the general window. But as always the devil is in the details. Here is a small sample of some of the issues:
- The JDesktopPane was not made to expand and shrink as elements are placed "off screen", and items "off-screen to do paint correctly when dragged back
- Painting is problematic in the desktop because of clipping issues
- Hardest: Because Swing uses a single delegate to do all the rendering into a buffer, there are no "real" visual "frames" for each item in the JList that represent a field in a table. This makes it extremely difficult to track the scrolling of table and make the "connection lines" between the tables scroll appropriately.
Significant Issues
Completed Tasks/ Bugs Fixed:
- Attended design & implementation meeting at Chapel Hill about the Concept Review System
- reported current status
- presented a demo
- discussed revision & next-step developemnt
- Tested and revised auto-email function
Current Work and Bugs:
- developing Auto-Manager for Concept Review System to automatically complete some system administration tasks, such as sending emails,assigning proposals to peer-viewers.
Significant Issues
Completed tasks/bugs fixed
Current Work and Bugs (In order of time/effort)
- GrOWL editor: integrated new version of OWLAPI, redesigned and began re-implementing OWL file saving.
- Continued working on the ontology for biodiversity indices.
- Review/comment on the inter-ant parasitism semantic mediation prototype paper. Paper is now submitted.
Significant issues
Completed tasks/bugs fixed
Current Work and Bugs
- working on Bug 1576 - implement enterProviderData. Robert has converted some ITIS data to the current Taxonomic Exchange Schema (still waiting on hickory data) to test parsing the TES.
Significant issues
- Still concerned with the definition of a GUID-bearing concept as containing relationships. This seems to reduce the utility of our service to scientists wishing to markup or search on datasets with a name string.
Completed Tasks/ Bugs Fixed:
- Revised the collaboration and class diagram draft design for bug 1584 and 1586
- Started to code for data query engnie with hsql
Current Work and Bugs:
- Working on the code for data query
Significant Issues
Completed Tasks/Bugs Fixed:
Current Work and Bugs:
- Continuing to work on the concept relationships manuscript, now turning to final sections; the work is directly related to discussions between KU and Napier last week.
- In exchange with KU and Napier about these issues (see e.g. http://tdwg.napier.ac.uk/phpwiki/index.php/What%20Gets%20a%20Guid and http://tdwg.napier.ac.uk/phpwiki/index.php/RelationshipTypes).
Significant Issues
- It seems like we're converging on a consensus that concept relationships may be authored (as an option) without also authoring concepts. KU made this a requirement, in essence, and Napier is now working on ways to accommodate it within the taxonomic exchange schema.
Completed Tasks/ Bugs Fixed:
- Completed some additional examples of ecology specific pipeline (Predetor/Prey detailed model) --- Bug 1336
- Completed a Simple R actor using the existing CommandLine Actor and and input script file (Bug 1342). R creates an image file which is then displayed by existing Ptolemy actors.
- Created a web page comparing various 'box and arrow' systems
Current Work and Bugs:
- Continuing work on a more general R-actor system. I have succeeded in getting a java system for running interactive command line systems like R running. This should make it easier to create customized actors from command line systems without having to write system specific jni code for every case.
- Working on updating to a Kepler system based on Ptolemy 4.
Significant Issues
Completed tasks/bugs fixed
- Growl
- Sketch of owlDLCompliance function
- Enabled editing of class/instances properties save for uri base
- Replaced ascii text for math symbol by respective standard math symbols from Unicode, which enhances look and feel
Current Work and Bugs
- Redesigning property panes and enabling the editing for constraints , properties, and other things on the toolbox
Significant issues
- Does anyone know how to gracefully (without raising an exception) check if a string is a valid URI without using external java libraries???!!! (this problem slows down my work on editing properties)
Completed Tasks/ Bugs Fixed:
- Bug 1604 - Convert ITIS database dump to TES
- Converted ITIS mammals only, as the requirements were to have a testing instance of the TES for implementation of enterProviderData
Current Work and Bugs:
- Minor data model changes to incorporate the schema fully
- Bug 1603 - Implementation of addConcept
- Bug 1604 - Implementation of addRelationship
Significant Issues
Completed Tasks/ Bugs Fixed:
- fixed the second bug mentioned in the last week report: the previous conflicted requirements on java version from running multiple threads on windows and the XQuery engine being used in our schema matching tool.
Current Work and Bugs:
- Work on 2 paper drafts
- Fix more bugs of the tool:
- make details of nodes accessible from the GUI,
- correctly handle union types of matches in the GUI,
- input domain thesauri from user specified text files instead of builtin ones
- Implement abstract schemas and abstract schema morphisms to make the tool more general.
Significant Issues:
- Regarding connecting the schema matching tool with Kepler, there is no problems of java version and performance on Windows machines any more.
Completed tasks/bugs fixed
- Working on user management of taxon server. Logging in and out works fine in struts on tomcat with mysql.
Current Work and Bugs
- Working on bug #1597 - Logging in and out works fine. I sent a note to Steve about what I'm doing, but haven't heard back yet - I emailed him not too long ago. He mentioned using the hibernate persistance layer in one of his emails a while ago, so I'm incorporating that into the server. It's slowing me down a bit, but I should be over the hump tomorrow.
- Finished the paper with Shawn Bowers for the Semantic Web and Databases conference.
Significant issues
- Wondering if there's any kind of unified authentication system for SEEK? I'm using struts for the authentication stuff I'm doing, so there's going to be a clean division between the view and the model. Who's the best ecogrid person to ask about authentication from the ecogrid perspecitve?
Completed Tasks/ Bugs Fixed:
- Working Version of Web Site
- with LDAP Authentication via new JAAS login module
- with "official" seek logo and layout
- running at "/" rather than "/seekwiki"
- fixed problem with attachments
Current Work and Bugs:
- Converting old wiki content
- Clean up, minor enhancements to login module and web app
- installing in production with Tomcat 5.0.25
Significant Issues
- Tomcat 5.0.25 in production?
You can see the status reports for other time periods as well.
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