From jones at nceas.ucsb.edu Tue Jun 8 09:33:08 2004 From: jones at nceas.ucsb.edu (Matt Jones) Date: Tue, 08 Jun 2004 08:33:08 -0800 Subject: [seek-reports] status report - jones - June 7, 2004 Message-ID: <40C5EA44.4060106@nceas.ucsb.edu> Status report Matt Jones June 7, 2004 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 -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- From thau at learningsite.com Tue Jun 8 14:42:35 2004 From: thau at learningsite.com (dave thau) Date: Tue, 8 Jun 2004 14:42:35 -0700 (PDT) Subject: [seek-reports] [Fwd: [seek] instructions for weekly status reports] Message-ID: <28790.64.175.14.219.1086730955.squirrel@64.175.14.219> Report for Dave Thau, May 31 - June 4 1) Completed tasks/bugs fixed Created and vetted initial basic feature set for Taxon LSID server 2) 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 3) 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. From xianhual at email.unc.edu Wed Jun 9 08:15:10 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Wed, 09 Jun 2004 11:15:10 -0400 Subject: [seek-reports] report In-Reply-To: <40C5EB18.3080305@nceas.ucsb.edu> References: <40C5EB18.3080305@nceas.ucsb.edu> Message-ID: <1086794110.40c7297e5b940@webmail7.isis.unc.edu> Status report Xianhua Liu June 9, 2004 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 ------------------------------------------------------------------- ------------------------------------------------------------------- From tao at nceas.ucsb.edu Wed Jun 9 10:54:51 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Wed, 9 Jun 2004 10:54:51 -0700 (PDT) Subject: [seek-reports] Status report Message-ID: Status Report Jing Tao 06/09/2004 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 Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From berkley at nceas.ucsb.edu Wed Jun 9 11:28:49 2004 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Wed, 09 Jun 2004 11:28:49 -0700 Subject: [seek-reports] 6/1-6/4 Message-ID: <40C756E1.6050006@nceas.ucsb.edu> 1) -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 2) Working on getting ready for SSDBM. Mostly working on poster. 3) 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 From rods at ku.edu Fri Jun 11 11:44:02 2004 From: rods at ku.edu (Rod Spears) Date: Fri, 11 Jun 2004 13:44:02 -0500 Subject: [seek-reports] Status Report for 6/7 - 6/11 Message-ID: <40C9FD72.3000806@ku.edu> *Completed Tasks/ Bugs Fixed:* * Bug 1594 - Impl revised Resultset XSD for all 3 platforms * Spent time thinking about the registry and DiGIR and how DiGIR will need to register multiple times. Each time for a different type of data, thus specifying the portal URL and the Consecptual schema namespace *Current Work and Bugs:* * Start on Bug 1595 - Create Advance Query Builder UI o Initial prototyping to understand what parts of Swing can be used directly and what part may need to be extended. Next I should have a detailed summary *Work This Week:* * Start on Bug 1595 - Create Advance Query Builder UI * Important or Outstanding Issues* (of a significant nature) * None -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040611/11e64b8e/attachment.htm From xianhual at email.unc.edu Mon Jun 14 06:25:20 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 14 Jun 2004 09:25:20 -0400 Subject: [seek-reports] (no subject) Message-ID: <1087219520.40cda740d46e4@webmail1.isis.unc.edu> Status report Xianhua Liu June 14, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- * Finished design of Auto-Manager: auto-email, auto-assignment and auto-decision * Implemented 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 ------------------------------------------------------------------- ------------------------------------------------------------------- From Serguei.Krivov at uvm.edu Mon Jun 14 08:13:22 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 14 Jun 2004 11:13:22 -0400 Subject: [seek-reports] status report Message-ID: <000401c45222$225be530$3ca6c684@BTS2K3000D5635086B> Serguei Krivov 6/14/04 1) Completed tasks/bugs fixed -developed toolbox pane (no icons yet) and enabled raw visual editing of simple owl constructs -wrote a small section of growl paper 2) Current Work and Bug -functions for editing relations and links -owl-dl compliance resolution for graphic primitives - enable node property editing - one more section for growl paper 3) Significant issues Should we support owl-full? All who responded seems favor support for owl-dl only -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040614/6c2d5db1/attachment.htm From higgins at nceas.ucsb.edu Mon Jun 14 08:27:39 2004 From: higgins at nceas.ucsb.edu (Dan Higgins) Date: Mon, 14 Jun 2004 08:27:39 -0700 Subject: [seek-reports] Status report - 14 June 2004 (Dan Higgins) Message-ID: <40CDC3EB.40907@nceas.ucsb.edu> Status report Dan Higgins June 14, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Bug 1556 (One Button mouse problems on Macintosh) --- Provided a test of fixes to this problem that have been implemented by the Ptolemy group (Steve Nuendorffer for Version 4. Checked the latest fixes which apparently solve the problem. Current Work and Bugs: ---------------------- * Bug 1342 (need R Actor) --- Created a preliminary version of a simple R actor which runs an R script using the current CommandLine actor. There is still a good deal of work in trying to determine just how to get information from other actors into the R engine. An email discussion of the problem was initiated. * Bug 1579 (Create SubSampling actor) --- Two simple subsampling workflows were created using existing components and checked into CVS. These are simple samples and a complete samples are still needed * Continued getting a better understanding of the details of Ptolemy/Kepler and R. Significant Issues ------------------ * A primary issue that effects any of our work on Kepler is the need to upgrade to the Ptolemy 4.0 base from 3.0.2. The beta indicates a number of useful additions in version 4.0 that we may want to use in Kepler. From rich at sfsu.edu Mon Jun 14 08:43:47 2004 From: rich at sfsu.edu (Rich Williams) Date: Mon, 14 Jun 2004 08:43:47 -0700 Subject: [seek-reports] (no subject) Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs a) Developing an ontology for biodiversity indices, extending existing ontologies to accommodate this, and adding instances for the biodiversity indices and related concepts. This includes a general model for properties computed in terms of other properties. b) Review/comment on paper that Shawn is lead author on, about the inter-ant parasitism semantic mediation prototype. c) GrOWL editor: updating of the OWL model when the user edits the displayed graph 3) Significant issues I looked into existing work on the semantics of mathematics, potentially for use when defining quantities in terms of other measured quantities. A useful initiative is www.openmath.org, an emerging standard for representing the semantics of mathematical objects. From tao at nceas.ucsb.edu Mon Jun 14 07:29:43 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 14 Jun 2004 07:29:43 -0700 (PDT) Subject: [seek-reports] Status report Message-ID: Status Report Jing Tao 06/09/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Finished the collaboration and class diagram draft design for bug 1584 and 1586 * Installed and evaluated both windows and linux SAS as sql engine * Resinstalled and tested Metacat ecogrid server in my local machine after Rod changed the code according to the change of resultset Current Work and Bugs: ---------------------- * Continue to find a good sql engine for data query * Probably start to code after finding a good sql engine * Fix some bugs in ecogrid client after the resultset change Significant Issues ------------------ * None Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From berkley at nceas.ucsb.edu Mon Jun 14 09:01:38 2004 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Mon, 14 Jun 2004 09:01:38 -0700 Subject: [seek-reports] 6/7-6/11 Message-ID: <40CDCBE2.4050306@nceas.ucsb.edu> Last Week: * Worked on the Kepler poster for SSDBM * Worked on nightly build systems for kepler * Began preperation to go to SSDBM This Week: * Hopefully get a nightly build system working * Leave for Greece From astewart at ku.edu Mon Jun 14 09:21:01 2004 From: astewart at ku.edu (Stewart, Aimee Marian) Date: Mon, 14 Jun 2004 11:21:01 -0500 Subject: [seek-reports] Weekly report Message-ID: <743DD2FE4C085D45B1EA9114C3044085012CBBA3@meadowlark2.home.ku.edu> 1) Completed tasks/bugs fixed * Bug 1602 - Moved the Taxonomic Object Service SOAP service to http://seek.ittc.ku.edu:9080/TaxObjServ . The WSDL is available from the link there (http://seek.ittc.ku.edu:9080/TaxObjServ/services/TaxonomicObjectService?wsdl). 2) Current Work and Bugs * Working on Bug 1576 - Implement EnterProviderData. This includes modifying the architecture somewhat to separate database modification methods from database query methods into separate classes. Also adding a database connection class which will be used by both DB classes. * Described (in an email to Seek-Taxon) the difficulties we are encountering with the assumption that a GUID-bearing Taxonomic Concept is defined by the current Taxon Exchange Schema. 3) Significant issues * Taxon Exchange Schema and GUIDs described in seek-taxon email. This may warrant a Seek-Taxon teleconference, preferably by polycom. Aimee Stewart Taxon group From franz at nceas.ucsb.edu Mon Jun 14 09:43:42 2004 From: franz at nceas.ucsb.edu (Nico M. Franz) Date: Mon, 14 Jun 2004 09:43:42 -0700 Subject: [seek-reports] Nico Franz - weekly status reports In-Reply-To: <40C5EB18.3080305@nceas.ucsb.edu> Message-ID: <5.2.1.1.2.20040614093147.017cdb50@hyperion.nceas.ucsb.edu> Status Report Nico Franz June 14, 2004 Completed Tasks/ Bugs Fixed: ----- * None, really. Current Work and Bugs: ----- * Since SEEK Edinburgh, has been writing on a substantial manuscript (with R. Peet as co-author) for the journal Taxon, which deals with concepts and relationships among them. * The manuscript is about half-way completed; will take another 2-4 weeks to be ready for internal review. * This work is seen as a precursor to the GUID development, i.e. it's trying to answer the question when/what (something) should get a GUID. Significant Issues ----- * There's been a bit of a quiet in SEEK Taxon after the Edinburgh meetings, but apparently that just ended today, with KU sending out an update/request. * As the TDWG New Zealand planning is moving ahead, would like to make sure that the concept/relation paper is part of our SEEK Taxon presentation package there. From dpennington at lternet.edu Mon Jun 14 12:10:32 2004 From: dpennington at lternet.edu (Deana Pennington) Date: Mon, 14 Jun 2004 13:10:32 -0600 Subject: [seek-reports] June 14 report Message-ID: <40CDF828.5050605@lternet.edu> 1) Completed tasks/bugs fixed --completed specs for IPCC climate data processing as kepler design workflow and accompanying document --completed specs for sampling actor --sent notes on Kepler (user feedback) to Rod --sent GARP output schema to Shawn 2) Current Work and Bugs --planning for new BEAM working group on diversity/productivity --getting all relevant data for ecological niche modeling project into the SRB --thinking about user interface design and testing approaches 3) Significant issues --will have to create EML for all of the IPCC data --need a decision on the useability engineer slot (LOTS of discussion on the lists about the UI & testing) Deana -- ******** Deana D. Pennington, PhD Long-term Ecological Research Network Office UNM Biology Department MSC03 2020 1 University of New Mexico Albuquerque, NM 87131-0001 505-272-7288 (office) 505 272-7080 (fax) From sroman at lternet.edu Mon Jun 14 12:43:26 2004 From: sroman at lternet.edu (Samantha J Romanello) Date: Mon, 14 Jun 2004 13:43:26 -0600 Subject: [seek-reports] weekly status report for EOT Message-ID: <40CDFFDE.1000605@lternet.edu> ** Hi ya Matt I thought you were out this week?!?! Here is what EOT came up with this week... Have a good one :-) sam *Completed tasks and Bugs fixed* 1. Finalized agenda for upcoming Data Management Tools Workshop 2. Finalized GIS agenda for RCN training *Current Work and Bugs* _Website: _ 1. Working on copy for education section of website; attaching links to presentations of former and current trainings. _Trainings: _ 1. Need to finalize ecoinformatics agenda for RCN training October 18- 30: 2. Composing email for Monthly SEEK Seminar _Conferences and Events: _ 1. In contact with Sandy re moprho tutorial for upcoming ESA August 1 - 7: Workshop; Evening Session 2. Working on poster presentation for ESA * * *Significant issues * 1. Finalize participant and trainer numbers for September KNB Data Management Tools training -- conference call scheduled for June 22. 2. Finalize ecoinformatics agenda and logistics for RCN training October 18- 30 * * From jwang at sdsc.edu Mon Jun 14 14:41:52 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Mon, 14 Jun 2004 14:41:52 -0700 (PDT) Subject: [seek-reports] Weekly report In-Reply-To: <40C5EB18.3080305@nceas.ucsb.edu> Message-ID: Weekly report "Jenny" Guilian Wang June 14, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Analyzed our schema matching tool user interface design * Fixed one of the bugs for improving its UI: the windows for 2 schema trees were changed to be individually scrollable in order to be able to visually handle the mappings between very large schemas Current Work and Bugs: ---------------------- * Work on 2 paper drafts * Fix more bugs of the tool: 1) make details of nodes accessible from the GUI, 2) look for solutions for the conflicted requirements on java version from running multiple threads on windows and the XQuery engine with Kepler. Significant Issues ------------------ The second bug is related to making easier connection of our tool with Kepler. From thau at learningsite.com Mon Jun 14 15:36:44 2004 From: thau at learningsite.com (dave thau) Date: Mon, 14 Jun 2004 15:36:44 -0700 (PDT) Subject: [seek-reports] report for dave thau, June 7 - June 11 Message-ID: <28844.64.175.14.219.1087252604.squirrel@64.175.14.219> Report for Dave Thau, May 31 - June 4 1) Completed tasks/bugs fixed Got local version of the taxon server set up in my IDE and running on my home machine. 2) Current Work and Bugs Working on bug #1597 - the intial user management for the taxon server. Wrote initial tests and some of the code for logging in / logging out and editing user information. Probably will finish this part by Wednesday. Working on paper with Shawn Bowers for the Semantic Web and Databases conference. 3) Significant issues None. From bowers at sdsc.edu Mon Jun 14 15:56:33 2004 From: bowers at sdsc.edu (Shawn Bowers) Date: Mon, 14 Jun 2004 15:56:33 -0700 Subject: [seek-reports] Status Report, Week 2 Message-ID: <40CE2D21.30609@sdsc.edu> My "status" report for last week. -shawn 1) Completed tasks/bugs fixed -- Worked mainly on Bug 1592 "describe Sparrow toolkit interface". In particular, defined a preliminary draft of a Java API for accessing ontological information via Sparrow to support Bug 1546 "dynamic data and actor views using ontologies". I also defined a simple extension to the API (set of derived classes) for Bug 1546, which would take a single concept from an ontology and return a tree-structure representing the appropriate Kepler tree-view for browsing (that is, the result is a data structure that could be used to populate a tree-view, however that would work). Still need to add to the API to fully support bug 1546, since it requires access to information about actors. I'll "release" a stable version of the APIs soon, as Javadocs and UML diagrams. Want to prototype it first. -- Worked on a paper with Dave Thau and Rich Williams to describe the Ant Parasitism SMS prototype. It is due on the 21st. 2) Current Work and Bugs -- Need to start working on implementing the API, which means writing the java code and connecting it to the Sparrow code (this work is situated in bug 1592 and 1546). -- Extend API (see 1 above). -- Need to finish writing the paper -- Need to prepare slides for SSDBM paper -- I leave Friday. 3) Significant issues -- none From rgales at ku.edu Mon Jun 14 16:14:51 2004 From: rgales at ku.edu (Robert Gales) Date: Mon, 14 Jun 2004 18:14:51 -0500 (CDT) Subject: [seek-reports] Report for 6-7 to 6-11 2004 Message-ID: <3616.192.168.1.1.1087254891.squirrel@192.168.1.1> Completed Tasks/ Bugs Fixed: ---------------------------- * Split the taxonomic object service into two interfaces, ITOSQueryable for handling queries to the Taxon cache and ITOSModifiable for adding information to the Taxon cache * Created a facade object CTOSFacade that implements both interfaces and exposes the taxonomic object service through SOAP. * Moved the previous CMainTOS to CTOSQueryEngine implementing the ITOSQueryable interface and created the stub class CTOSModEngine implementing the ITOSModifiable interface. * Implemented the CDetailedName class for handling the complex atomized names * Moved all classes that are parts of a concept from the tree package to the concept package. Current Work and Bugs: ---------------------- * Bug 1577 - Implement AddRelationship * Bug 1603 - Implement AddConcept * Bug 1604 - Convert ITIS database dump to TES Significant Issues: ------------------- None Cheers, Robert From Saritha.Bhandarkar at asu.edu Fri Jun 18 16:49:24 2004 From: Saritha.Bhandarkar at asu.edu (Saritha Bhandarkar) Date: Fri, 18 Jun 2004 16:49:24 -0700 Subject: [seek-reports] Xanthoria-weekly report Message-ID: <002401c4558e$e244e760$2ecaa995@virga> Hi, I am sending herewith a very brief till date report on development of Xanthoria for EcoGrid. I shall send more specific details next week. Thank you, Saritha 1. Completed task: tested Xanthoria EcoGrid codes on Axis, without globus on windows machine. It works fine. 2. Current work: a. Currently, I am working on two things: i. Making changes to existing codes to make it compatible with latest resultset schema (getting rid of AnyRecordType) ii. 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. 3. Significant issues: currently I am interested in the following issues: a. 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? b. Is anybody working on setting up GIIS and MDS? What is the current status with this respect? Saritha Bhandarkar Research Assistant Center for Environmental Studies ASU-Tempe AZ saritha.bhand arkar at asu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040618/0c28cdf0/attachment.htm From rods at ku.edu Mon Jun 21 06:08:02 2004 From: rods at ku.edu (Rod Spears) Date: Mon, 21 Jun 2004 08:08:02 -0500 Subject: [seek-reports] Status 6/14 - 6/18 Message-ID: <40D6DDB2.9050600@ku.edu> *Completed Tasks/ Bugs Fixed:* * Contributed to the SEEK/Kepler UI discussion. o /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. o Dan constructed several screen shots for talking points at http://www.nceas.ucsb.edu/~higgins/BoxesAndArrows o 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 o Continued investigation into which Swing features can be leveraged to create the UI. o 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. *Work This Week:* * Start on Bug 1595 - Create Advance Query Builder UI * Important or Outstanding Issues* (of a significant nature) * None -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040621/0d42aeac/attachment.htm From xianhual at email.unc.edu Mon Jun 21 06:43:23 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 21 Jun 2004 09:43:23 -0400 Subject: [seek-reports] (no subject) Message-ID: <1087825403.40d6e5fba60f2@webmail0.isis.unc.edu> Status report Xianhua Liu June 14, 2004 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 ------------------------------------------------------------------- ------------------------------------------------------------------- From rich at sfsu.edu Mon Jun 21 08:47:09 2004 From: rich at sfsu.edu (Rich Williams) Date: Mon, 21 Jun 2004 08:47:09 -0700 Subject: [seek-reports] (no subject) Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs (In order of time/effort) a) GrOWL editor: integrated new version of OWLAPI, redesigned and began re-implementing OWL file saving. b) Continued working on the ontology for biodiversity indices. c) Review/comment on the inter-ant parasitism semantic mediation prototype paper. Paper is now submitted. 3) Significant issues None From astewart at ku.edu Mon Jun 21 09:02:17 2004 From: astewart at ku.edu (Stewart, Aimee Marian) Date: Mon, 21 Jun 2004 11:02:17 -0500 Subject: [seek-reports] Weekly Status Report Message-ID: <743DD2FE4C085D45B1EA9114C3044085012CBBB9@meadowlark2.home.ku.edu> 1) Completed tasks/bugs fixed None 2) 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. 3) 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. From tao at nceas.ucsb.edu Mon Jun 21 09:53:34 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 21 Jun 2004 09:53:34 -0700 (PDT) Subject: [seek-reports] Status report In-Reply-To: Message-ID: Status Report Jing Tao 06/21/2004 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 ------------------ * None -- Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From franz at nceas.ucsb.edu Mon Jun 21 10:01:45 2004 From: franz at nceas.ucsb.edu (Nico M. Franz) Date: Mon, 21 Jun 2004 10:01:45 -0700 Subject: [seek-reports] Nico Franz - weekly status report, June 21, 2004 Message-ID: <5.2.1.1.2.20040621095240.017c9820@hyperion.nceas.ucsb.edu> Status Report Nico Franz June 21, 2004 Completed Tasks/Bugs Fixed: ----- * None. 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. From higgins at nceas.ucsb.edu Mon Jun 21 11:36:36 2004 From: higgins at nceas.ucsb.edu (Dan Higgins) Date: Mon, 21 Jun 2004 11:36:36 -0700 Subject: [seek-reports] Status report -21 June 2004 Message-ID: <40D72AB4.50000@nceas.ucsb.edu> Status Report Dan Higgins June 21, 2004 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 * None From Serguei.Krivov at uvm.edu Mon Jun 21 13:23:09 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 21 Jun 2004 16:23:09 -0400 Subject: [seek-reports] status report Message-ID: <000001c457cd$91d0f800$3ca6c684@BTS2K3000D5635086B> Status Report Serguei Krivov 6-21-04 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 rising an exception) check if a string is a valid URI without using external java libraries???!!! (this problem slows down my work on editing properties) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040621/84a718f5/attachment.htm From rgales at eecs.ku.edu Mon Jun 21 15:14:53 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 21 Jun 2004 17:14:53 -0500 (CDT) Subject: [seek-reports] Weekly report for 6-14 to 6-18 2004 Message-ID: <50703.192.168.1.7.1087856093.squirrel@192.168.1.7> Status report Robert Gales June 21, 2004 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: ------------------- None From jwang at sdsc.edu Mon Jun 21 15:26:37 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Mon, 21 Jun 2004 15:26:37 -0700 (PDT) Subject: [seek-reports] Weekly report In-Reply-To: Message-ID: Weekly report "Jenny" Guilian Wang June 21, 2004 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: 1) make details of nodes accessible from the GUI, 2) correctly handle union types of matches in the GUI, 3) 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. From thau at learningsite.com Mon Jun 21 19:36:43 2004 From: thau at learningsite.com (dave thau) Date: Mon, 21 Jun 2004 19:36:43 -0700 (PDT) Subject: [seek-reports] report for dave thau june 15 - june 21 Message-ID: <29424.64.175.14.219.1087871803.squirrel@64.175.14.219> Report for Dave Thau, May 31 - June 4 1) Completed tasks/bugs fixed Working on user management of taxon server. Logging in and out works fine in struts on tomcat with mysql. 2) 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. 3) 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? From rich at sfsu.edu Sun Jun 27 22:29:35 2004 From: rich at sfsu.edu (Rich Williams) Date: Sun, 27 Jun 2004 22:29:35 -0700 Subject: [seek-reports] (no subject) Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs (In order of time/effort) a) GrOWL editor: worked on building an OWLOntology model from the OntoBrowser graph to allow saving to RDF/OWL. b) Various improvements to eml2rdf in response to feedback from Manu Juyal. Output now correctly imports the underlying ontology and is re-formatted to be vastly more readable. 3) Significant issues None From xianhual at email.unc.edu Mon Jun 28 06:53:27 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 28 Jun 2004 09:53:27 -0400 Subject: [seek-reports] (no subject) Message-ID: <1088430807.40e022d79281c@webmail7.isis.unc.edu> Status report Xianhua Liu June 28, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- * Tested and revised auto-email function * Designed dynamic PDF generation of revision proposals Current Work and Bugs: ------------------------------------------------------------------- * developing dynamic PDF function Significant Issues ------------------------------------------------------------------- ------------------------------------------------------------------- From rods at ku.edu Mon Jun 28 08:29:15 2004 From: rods at ku.edu (Rod Spears) Date: Mon, 28 Jun 2004 10:29:15 -0500 Subject: [seek-reports] Status for 6/21 - 6/25 Message-ID: <40E0394B.5060305@ku.edu> Matt, Once again I included the "Work This Week", this is important because it lets folks know I am going to a conference and they may wish to speak with me about it. We may still want to consider adding this section to future reports. Completed Tasks/ Bugs Fixed: * Completed initial prototype (Proof of concept) * Has both Novice and Advanced tab * This gives us a starting place for a discussion on a full featured version * Notiable Features (Advanced Pane): * Drop and Drop (D&D) from table field to table field to create "joins" * D&D from table field to lower pane for expressing the "where" clause Current Work and Bugs: * Start on Bug 1595 - Create Advance Query Builder UI * Continue to refine the prototype Important or Outstanding Issues (of a significant nature) * None Work This Week: * Attending the Globus/Grid Conference in Madison 6/30-7/1 * Start on Bug 1595 - Create Advance Query Builder UI From higgins at nceas.ucsb.edu Mon Jun 28 09:10:06 2004 From: higgins at nceas.ucsb.edu (Dan Higgins) Date: Mon, 28 Jun 2004 09:10:06 -0700 Subject: [seek-reports] Status report - 28 June Message-ID: <40E042DE.2010107@nceas.ucsb.edu> Status report Dan Higgins June 28, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Bug 1606 - Update Kepler to work with version 4.0 of Ptolemy Managed to get all of the current Kepler 3.02 code to compile with Ptolemy Beta 4.0. There are still some questions regarding whether the code actually executes properly and time was spent investigating that issue. * Bug 1342 - R Actor Continued work on more complex R actor. Began ivestigating the reading of data tables using R * Starting building a ReScaling actor from from existing Plolemny actors as an example Significant Issues ------------------ * None From tao at nceas.ucsb.edu Mon Jun 28 09:55:09 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 28 Jun 2004 09:55:09 -0700 (PDT) Subject: [seek-reports] Status Report Message-ID: Status Report Jing Tao 06/28/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Evaluating sql engines. * Working on the code for data query engine * Working on access issues in ecogrid metacat. Significant Issues ------------------ * None -- Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From Serguei.Krivov at uvm.edu Mon Jun 28 11:54:34 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 28 Jun 2004 14:54:34 -0400 Subject: [seek-reports] Progress Report-growl Message-ID: <000001c45d41$5a3a15b0$3ca6c684@BTS2K3000D5635086B> Progress Report Serguei Krivov 6-28-04 1) Completed tasks/bugs fixed None. Many minor solutions for editing, and also deleting the graphic constructs, but none global task was accomplished 2) Current Work and Bugs Continue working on enabling editing of major owl constructs. Plan to draw (27) icons for toolbox. Plan to make tabbed pane to accommodate global properties (???) 3) Significant issues How to edit global properties of ontologies in growl? What to use-popup dialog or tabbed panel? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040628/637245b8/attachment.htm From rgales at eecs.ku.edu Mon Jun 28 14:49:46 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 28 Jun 2004 16:49:46 -0500 (CDT) Subject: [seek-reports] Weekly Report 6-21 to 6-25 2004 Message-ID: <3469.129.237.201.26.1088459386.squirrel@129.237.201.26> Status report Robert Gales June 28 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Redesigned the taxon cache database * Modified all DB relevant code to incorporate the redesign * Moved all DB related code out of concept classes to prevent any future database changes from affecting the higher layers of the architecture Current Work and Bugs: ---------------------- * Bug 1603: Implement addConcept * Adding name, detailed name, according to, detailed according to, publication, detailed publication and concept records have been implemented and tested * Currently implementing adding specimen and character circumscription * Bug 1577: Implement addRelationship Significant Issues ------------------ None From jwang at sdsc.edu Mon Jun 28 15:01:08 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Mon, 28 Jun 2004 15:01:08 -0700 (PDT) Subject: [seek-reports] Weekly report Message-ID: Weekly report "Jenny" Guilian Wang June 21, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * fixed the 3rd bug mentioned in the last week report: input domain thesauri from user specified text files instead of builtin ones Current Work and Bugs: ---------------------- * Work on 2 paper drafts * Fix more bugs of the tool: 1) make details of nodes accessible from the GUI, 2) correctly handle union types of matches in the GUI * Implement abstract schemas and abstract schema morphisms to make the tool more general. Significant Issues: ------------------- The implementation of abstract schemas and schema morphisms will help the tool handle constraints to some extent. From astewart at ku.edu Mon Jun 28 15:09:11 2004 From: astewart at ku.edu (Stewart, Aimee Marian) Date: Mon, 28 Jun 2004 17:09:11 -0500 Subject: [seek-reports] Weekly Status Report Message-ID: <743DD2FE4C085D45B1EA9114C3044085012CBBD8@meadowlark2.home.ku.edu> 1) Completed tasks/bugs fixed -- None 2) Current Work and Bugs -- working on parser for Taxonomic Exchange Schema as part of enterProviderData (Bug 1576) 3) Significant issues -- None From thau at learningsite.com Mon Jun 28 17:44:26 2004 From: thau at learningsite.com (dave thau) Date: Mon, 28 Jun 2004 17:44:26 -0700 (PDT) Subject: [seek-reports] report for dave thau june 22 - june 28 Message-ID: <29203.64.175.14.219.1088469866.squirrel@64.175.14.219> Report for Dave Thau, June 22 - June 28 1) Completed tasks/bugs fixed Got Steve's LDAP authenticator working. 2) Current Work and Bugs Working on bug #1597 - Now that I've gotten Steve's thing working, it needs to be integrated with the taxon server, and with the LSID system. I've written to the Kansas folks about either helping install that stuff, or providing good directions on how to do so. 3) Significant issues I'm taking a month off, starting on Thursday - except for a conference call with the SEEK group, which I'll do whenever it is. I'll be contactable via email intermittently during July, and I'll be back in the swing of things on August 1st.