From franz at nceas.ucsb.edu Mon Jul 5 12:48:03 2004 From: franz at nceas.ucsb.edu (franz@nceas.ucsb.edu) Date: Mon, 5 Jul 2004 12:48:03 -0700 Subject: [seek-reports] Nico Franz - weekly status report, July 5, 2004 Message-ID: <1089056883.40e9b073f2170@hyperion.nceas.ucsb.edu> Status Report Nico Franz July 5, 2004 Completed Tasks/Bugs Fixed: ----- * None. Current Work and Bugs: ----- * Made a set of tables and figures to express concept relationships; these were sent out for review to our developers at KU and further discussed during a conference call on July 2. More parts will be made available to members of SEEK Taxon soon. Significant Issues ----- * Another issue that came up in the conference calls is the reuse (citing) of concepts. Will work towards a set of rules or guidelines to understand when concept authoring can/should stop, to minimize inflation and the "bubbling" up or down of new concepts through the entire classification hierarchy. At the present this might be more of an internal document, rather than a significant part of the concept relationships paper. ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From Serguei.Krivov at uvm.edu Tue Jul 6 07:32:47 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Tue, 6 Jul 2004 10:32:47 -0400 Subject: [seek-reports] Progress Report 07-06-04 Message-ID: <000001c46366$1b8101f0$3ca6c684@BTS2K3000D5635086B> Progress Report 07-06-04 Serguei Krivov;GrOWL 1) Completed tasks/bugs fixed #1 Bug with display of enumerations #2 Bug with display of data Ranges Metadata dialog design finalized, started work on implementation 2) Current Work and Bugs Metadata Dialog, then icons for toolbox 3) Significant issues Metadata Dialog/Panel design has been finalized by KR-SMS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040706/5f3324bb/attachment.htm From rich at sfsu.edu Tue Jul 6 08:25:15 2004 From: rich at sfsu.edu (Rich Williams) Date: Tue, 6 Jul 2004 08:25:15 -0700 Subject: [seek-reports] (no subject) Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs (a) Lots of ontology design discussion with Shawn (b) Code to save OWL file from GrOWL including dealing with property axioms (c) Added instances to biodiversity ontology 3) Significant issues None From higgins at nceas.ucsb.edu Tue Jul 6 09:12:52 2004 From: higgins at nceas.ucsb.edu (Daniel Higgins) Date: Tue, 06 Jul 2004 09:12:52 -0700 Subject: [seek-reports] Status Report - Dan Higgins, July 6 Message-ID: <40EACF84.5030206@nceas.ucsb.edu> Status Report Dan Higgins July 6, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * (Bug 1606) Updated the head of Kepler CVS to work with the recently released version 4.0 of Ptolemy * Created a preliminary test example of Kepler workflow applet for possible inclusion on web page Current Work and Bugs: ---------------------- * Working on workflow example applets for addition to Kepler web site * Continuing work on various R actor(s) * Fixing some minor issues with Kepler actor tree with Ptolemy 4 Significant Issues ------------------ * None -- --------------------------------- Dan Higgins Software Developer National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Rm 205 Santa Barbara, CA 93101 805-892-2531 higgins at nceas.ucsb.edu --------------------------------- From rgales at eecs.ku.edu Tue Jul 6 09:36:55 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Tue, 6 Jul 2004 11:36:55 -0500 (CDT) Subject: [seek-reports] Status Report 6-28 to 7-2 Message-ID: <3682.129.237.201.101.1089131815.squirrel@129.237.201.101> Status report Robert Gales July 6, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Bug 1577 - Implemented addConcept * Bug 1603 - Implemented addRelationship Current Work and Bugs: ---------------------- * Bug 1618 - Fix current database representation of a taxon concept's rank Significant Issues ------------------ * None From tao at nceas.ucsb.edu Tue Jul 6 09:49:04 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Tue, 6 Jul 2004 09:49:04 -0700 (PDT) Subject: [seek-reports] Status report Message-ID: Status Report Jing Tao 07/06/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Working on data access rules 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 jwang at sdsc.edu Tue Jul 6 10:15:05 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Tue, 6 Jul 2004 10:15:05 -0700 (PDT) Subject: [seek-reports] Weekly report Message-ID: Weekly report "Jenny" Guilian Wang July 6, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Have made data type and cardinality information of schema nodes accessible from the GUI of our schema matching tool. Current Work and Bugs: ---------------------- * Work on 2 paper drafts * Fix more bugs of the tool: 1) correctly handle union types of matches in the GUI, 2) consistently highlight where user attention is needed * 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 Tue Jul 6 15:37:13 2004 From: astewart at ku.edu (Stewart, Aimee Marian) Date: Tue, 6 Jul 2004 17:37:13 -0500 Subject: [seek-reports] Weekly Status Report Message-ID: <743DD2FE4C085D45B1EA9114C3044085012CBBED@meadowlark2.home.ku.edu> 1) Completed tasks/bugs fixed None 2) Current Work and Bugs -- Working on making the Taxonomic Exchange Schema parser multi-threaded so that it can resolve references as it encounters them, rather than holding the entire document in memory until the references are resolved at the end of the document. Created a new ReferenceParser and two ContentHandlers - one for Publication references (bug 1619) and one for Vouchers references (bug 1620). 3) Significant issues -- Nothing new. From rods at ku.edu Mon Jul 12 08:38:00 2004 From: rods at ku.edu (Rod Spears) Date: Mon, 12 Jul 2004 10:38:00 -0500 Subject: [seek-reports] Status 7/5 - 7/9 Message-ID: <40F2B058.3000703@ku.edu> Completed Tasks/ Bugs Fixed: * Working on converting prototype to production code for Advanced version of the Query Builder * Almost completed the "where" clause builder for the Advanced tab * Last week I attended the GRIDs conference in Madison. * Most significant thing was that they have finally gotten the message that your average scientist cannot easily deal with certificate based security. * The Earth Web project wrote some code on top of Globus and MyProxy to enable scientist to sign up for a user name and password that behind the scenes translates into a certificate that is managed by MyProxy. Then whenever they submit jobs or makes requests, the certs are obtained and the everything happens seamlessly. * This part of the project is being broken out and made "generic" for all consumers. This will be the perfect solution for us. * Was out two days last week. Current Work and Bugs: * Continued on Bug 1595 - Create Advance Query Builder UI Important or Outstanding Issues (of a significant nature) * None Work This Week: * Continue work on Bug 1595 - Create Advance Query Builder UI * Finish Trip Report for Madison From berkley at nceas.ucsb.edu Mon Jul 12 09:17:04 2004 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Mon, 12 Jul 2004 09:17:04 -0700 Subject: [seek-reports] 6/06-6/09/04 Message-ID: <40F2B980.40100@nceas.ucsb.edu> 1) Completed tasks/bugs fixed -fixed eml parser for eml 2.0.1 release (no bug number) -reinstalled eml parser on ecoinfo -tested eml 2.0.1 validity with parser 2) Current Work and Bugs -working on bug 1546, integrating sparrow into kepler for use in organizing the actor library -trying to determine what we need to do to moml to allow us to encapsulate this information. -conference call with matt, shawn, mark and dan about this. -created screen shots for discussion about the ontological interface in kepler -working on getting eml 2.0.1 released. reviewed schemas. checked the eml parser for 2.0.1 compliance. found one bug and fixed it. also updated the parser so the namespaces are no longer hardcoded into the java code. 3) Significant issues From higgins at nceas.ucsb.edu Mon Jul 12 09:25:29 2004 From: higgins at nceas.ucsb.edu (Daniel Higgins) Date: Mon, 12 Jul 2004 09:25:29 -0700 Subject: [seek-reports] Status Report - Dan Higgins, July 12 Message-ID: <40F2BB79.5020201@nceas.ucsb.edu> Status Report Dan Higgins July 12, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Checked in an interactive Command Line actor that allows one to interactively issues commands to systems like 'R' that can operate with command line I/O through standard streams. Current Work and Bugs: ---------------------- * Working on workflow example applets for addition to Kepler web site; also investigating use of WebStart for distribution of example workflows * Continuing work on various R actor(s) * Working on actor which calculates a variety of Biodiversity indices Significant Issues ------------------ * None -- -- --------------------------------- Dan Higgins Software Developer National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Rm 205 Santa Barbara, CA 93101 805-892-2531 higgins at nceas.ucsb.edu --------------------------------- From bowers at sdsc.edu Mon Jul 12 09:55:57 2004 From: bowers at sdsc.edu (Shawn Bowers) Date: Mon, 12 Jul 2004 09:55:57 -0700 Subject: [seek-reports] Status Report (July 5-9) Message-ID: <40F2C29D.3000709@sdsc.edu> 1) Completed tasks/bugs fixed -- Didn't complete or fix anything. 2) Current Work and Bugs -- Started working on a manual for the main components of the ontology Rich has been developing. This involved trying to clearly understand what is in the ontology (one of my main goals of writing the manual), discussing the contents with Rich, and providing feedback, etc. I am writing the manual using the new wiki. I think in doing this, we have come up with a more robust notion of observations / measurement, which is at the heart of the ontology. My goal is to keep plugging away at this "on the side." -- We are also experimenting with the use of higher-level modeling constructs to make it easier for extending the ontology by, e.g., domain scientists or metadata experts; allowing them to move to a higher semantic level than direct owl syntax. The jury is still out on the approach, though. -- Worked on a tool to convert owl dl to sparrow. This tool is taking a bit longer than expected; mainly due to some problems/complexities in owl itself and the tools that exist for working with owl. Once this tool is finished, hopefully this week, the rest of the sparrow api should go very quickly. -- Helping to arrange a three day meeting in San Diego for the KR/SMS and BEAM group for September. -- Looking into the use of binding patterns to help specify common transformations between otherwise incompatible concepts within an ontology. For example, for converting between UTM and Lat/Lon coordinates and so on. -- Participated in a phone meeting concerning the interface design for ontology-based actor browsing in Kepler. -- Started looking closely at the biodiversity datasets and metadata. 3) Significant issues -- I think an issue that is surfacing is the need for identifiers in Kepler for actors, workflows, and datasets. Some questions that come up in this regard are: Who is responsible for assigning and maintaining identifiers? What identifier scheme should be used and how? Given an identifier, how do we locate the associated actor, workflow, or dataset? There are probably more issues than these. -- Another issue, that as far as I can tell has been shelved, is how to explicitly represent the input/output port types of actors used in Ptolemy/Kepler. Is someone working on this that is part of the Kepler group? What is the progress? (I think Efrat has been looking at somewhat similar issues, but more for understanding how actors are connected within a workflow.) From franz at nceas.ucsb.edu Mon Jul 12 10:00:34 2004 From: franz at nceas.ucsb.edu (Nico Franz) Date: Mon, 12 Jul 2004 10:00:34 -0700 Subject: [seek-reports] Nico Franz - weekly status report, July 12, 2004 Message-ID: <5.2.1.1.2.20040712095151.0181c7f0@hyperion.nceas.ucsb.edu> Status Report Nico Franz July 12, 2004 Completed Tasks/Bugs Fixed: ----- * First draft of concept relationship paper sent to co-author (Peet). Current Work and Bugs: ----- * Still finishing up certain sections of the paper. Will inquire about placing it on the list of talks presented at TDWG 2004. Significant Issues ----- * Manuscript will soon be distributed more widely. Issues that came up during a recent conference call (with KU/Napier, etc.) will be worked mostly into another paper (with Thau) about GUIDs, which I'll start once the current project is ready for submission. Nico M. Franz National Center for Ecological Analysis and Synthesis 735 State Street, Suite 300 Santa Barbara, CA 93101 Phone: (805) 966-1677; Fax: (805) 892-2510; E-mail: franz at nceas.ucsb.edu Website: http://www.cals.cornell.edu/dept/entomology/wheeler/Franz/Nico.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040712/41d82667/attachment.htm From rich at sfsu.edu Mon Jul 12 10:29:55 2004 From: rich at sfsu.edu (Rich Williams) Date: Mon, 12 Jul 2004 10:29:55 -0700 Subject: [seek-reports] (no subject) Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs (a) Continued ontology design discussion with Shawn, made some changes to MeasurementBase.owl (b) Continued work debugging code to save OWL file from GrOWL 3) Significant issues None From jwang at sdsc.edu Mon Jul 12 11:57:24 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Mon, 12 Jul 2004 11:57:24 -0700 (PDT) Subject: [seek-reports] Weekly report Message-ID: Weekly report "Jenny" Guilian Wang July 12, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Correctly handle union types of matches from the GUI of our schema matching tool. * Partially implemented the abstract schema interface and devoloped a translator that imports DTDs into the schema matching tool as Abstract Schemas. But the "OR" case in DTDs is not handled in an appropriate way yet. Also it may require changes to the abstract schema interface when going further on the design and implementation of schema morphisms. Current Work and Bugs: ---------------------- * Work on 2 paper drafts * Fix more bugs of the tool: 1) Modify the GUI to include an arrow panel for indicating where it is working on, 2) correctly handle union types of matches identified during matching process, 3) consistently highlight where user attention is needed * Implement abstract schemas and abstract schema morphisms to make the tool more general: develope another translator for importing XML Schemas into the tool as Abstract Schemas, and design a schema morphism interface. Significant Issues: ------------------- The implementation of abstract schemas and schema morphisms will help the tool handle constraints to some extent. From rgales at eecs.ku.edu Mon Jul 12 15:09:05 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 12 Jul 2004 17:09:05 -0500 Subject: [seek-reports] Status report Jul 5 - Jul 9 2004 Message-ID: <000001c4685c$d949d130$0801a8c0@shiris> Status Report Robert Gales July 12, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Bug 1618 - Fix rank representation in DB to support the schema and entry of taxonomic concepts Significant Issues ------------------ * None From tao at nceas.ucsb.edu Mon Jul 12 16:24:25 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 12 Jul 2004 16:24:25 -0700 (PDT) Subject: [seek-reports] Status report Message-ID: Status Report Jing Tao 07/06/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Working on data access rules 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 bzhu at sdsc.edu Mon Jul 12 16:44:42 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 12 Jul 2004 16:44:42 -0700 Subject: [seek-reports] status report from Bing Zhu - July 12 Message-ID: Completed Tasks/Bugs Fixed: - Developed a Perl script to upload 'whywhere' data along with their metadata into SRB. Whywhere data was successfully uploaded into SRB storage place. This completed the initial task for SEEK bug 1596. - Developed an initial implementation within SRB for Niche Modeling to retrieve partial images. With this implementation, Niche Modeling applications successfully get partial images and Metadata in a distributed environment. Current Work and Bugs: - continue work on an Ecogrid solution for Niche Modeling. The prospective approach will have a generic approach which can be applied to other applications who request partial data transfer. (Bug 1596) Significant Issues: - The initial prototype designed by Raja and Bing for Ecogrid will extend the SRB capability into Ecogrid to allow partial data retrieval within Ecogrid. From astewart at ku.edu Tue Jul 13 07:17:26 2004 From: astewart at ku.edu (Aimee Stewart) Date: Tue, 13 Jul 2004 09:17:26 -0500 Subject: [seek-reports] Weekly status report from Aimee Stewart Message-ID: <40F3EEF6.4080102@ku.edu> 1) Completed tasks/bugs fixed -- Finished initial work on multi-threaded parser (bug 1617) for taxonomic exchange schema. This encompasses a reference parser for parsing Vouchers (bug 1620) and Publications (bug 1619). Testing still needs to be completed on these objects though, so the bugs are not resolved yet. Made other modifications to concept objects to handle additional fields in the schema. 2) Current Work and Bugs -- Working on the API for enterProviderData (bug 1576). The next step in this process will be to thoroughly test the parsers and handlers with our available data. Since the schema is not yet in final form, I will concentrate on testing elements of the TES parsing for which we have data. 3) Significant issues -- none From berkley at nceas.ucsb.edu Fri Jul 16 15:28:27 2004 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Fri, 16 Jul 2004 15:28:27 -0700 Subject: [seek-reports] 7/12-7/16 Message-ID: <40F8568B.2000003@nceas.ucsb.edu> 1) Completed tasks/bugs fixed -fixed bug introduced into junit tests from fixing the parser -wrote a templating system for creating junit tests -installed and configured AnthillPro nightly build system for kepler 2) Current Work and Bugs -rework screenshots for bug 1546 -participating in the seek-dev discussion of kepler UI issues 3) Significant issues From xianhual at email.unc.edu Mon Jul 19 07:13:44 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 19 Jul 2004 10:13:44 -0400 Subject: [seek-reports] report Message-ID: <1090246424.40fbd718a12c2@webmail0.isis.unc.edu> Status report Xianhua Liu July 19, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- * Finished dynamic PDF generation of revision proposals * Designed concept revision online proceedings Current Work and Bugs: ------------------------------------------------------------------- * developing concept revision online proceedings Significant Issues ------------------------------------------------------------------- ------------------------------------------------------------------- From Serguei.Krivov at uvm.edu Mon Jul 19 07:30:00 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 19 Jul 2004 10:30:00 -0400 Subject: [seek-reports] growl progress report Message-ID: <000001c46d9c$dfe63bb0$3ca6c684@BTS2K3000D5635086B> Serguei Krivov 7-19-2004 1) Completed tasks/bugs fixed - Added static/manual layout mode (!!!). Layout engine can be turned on and off as user desires. This is very usefull during editing . - Created icons for editing toolbox and for the toolbar. Growl looks better now (see screenshot attached) - Several enhansements to owl-dl compliance function, that facilitate faster graphic editing 2) Current Work and Bugs -Still workning on owl-dl compliance function, specifically on handling relations "are same", "are equvalent", "are different", etc. - Need to finish metadata panel 3) Significant issues - Icons in editing toolbox/ editing operations should be sufficiently intuitive for domain expert users and perhaps the icons should be more artistic. For this end feedback is requred and this week I am planing to send around the alpha version of growl with preliminary editing functionality. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040719/de2b37b0/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: growl.jpg Type: image/jpeg Size: 191525 bytes Desc: not available Url : http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040719/de2b37b0/growl.jpg From higgins at nceas.ucsb.edu Mon Jul 19 08:38:36 2004 From: higgins at nceas.ucsb.edu (Daniel Higgins) Date: Mon, 19 Jul 2004 08:38:36 -0700 Subject: [seek-reports] Status Report -- Dan Higgins, July 19, 2004 Message-ID: <40FBEAFC.7060108@nceas.ucsb.edu> Status Report Dan Higgins July 19, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Example workflow which calculates a variety of biodiversity indices was checked in with bug fixes and simplified workflow. Also checked in a example which used a new actor which reads string tables to provide input for the biodiversity index calculator actor. * Checked out the new Mac fixes provided by Christopher Brooks (Works for me!) Current Work and Bugs: ---------------------- * Continuing work on various R actor(s) * Looking into GIS (Grass?) integration Significant Issues ------------------ * None -- --------------------------------- Dan Higgins Software Developer National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Rm 205 Santa Barbara, CA 93101 805-892-2531 higgins at nceas.ucsb.edu --------------------------------- From tao at nceas.ucsb.edu Mon Jul 19 10:55:02 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 19 Jul 2004 10:55:02 -0700 (PDT) Subject: [seek-reports] Status report Message-ID: Status Report Jing Tao 07/19/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Installing metacat ecogrid semi-production node in NCEAS * Implementaion of data query in kepler. Significant Issues ------------------ * None -- Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From jwang at sdsc.edu Mon Jul 19 11:34:30 2004 From: jwang at sdsc.edu (Jenny Wang) Date: Mon, 19 Jul 2004 11:34:30 -0700 (PDT) Subject: [seek-reports] Weekly report Message-ID: Weekly report "Jenny" Guilian Wang July 19, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Devoloped a translator that imports XML Schemas into the schema matching tool as Abstract Schemas. But the "Sequence" case in is not handled in an appropriate way yet. Also it may require changes to the abstract schema interface when going further on the design and implementation of schema morphisms. * Modified the GUI to include an arrow panel for indicating where it is working on. Current Work and Bugs: ---------------------- * Work on 2 paper drafts * Fix more bugs of the tool: 1) polish the arrow panel for indicating where it is working on in the GUI: adjustable as GUI changes, etc. 2) correctly handle union types of matches identified during matching process. 3) consistently highlight where user attention is needed. * Implement abstract schemas and abstract schema morphisms to make the tool more general: focus on designing a schema morphism interface and implementing it. Significant Issues: ------------------- To include the path context in types emerges as a problem when designing and implementing schema morphism interface. This may require significant change to the abstract schema definition and its interface. From rgales at eecs.ku.edu Mon Jul 19 14:35:42 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 19 Jul 2004 16:35:42 -0500 Subject: [seek-reports] Status Report 7-12 to 7-16 2004 Message-ID: <40FC3EAE.2040306@eecs.ku.edu> Status report Robert Gales July 19, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Bug 1618 - Fix current database representation of a taxon concept's rank - Database model designed - Currently, fixing the database related code to incorporate the changes Significant Issues ------------------ * None From astewart at ku.edu Mon Jul 19 15:18:43 2004 From: astewart at ku.edu (Aimee Stewart) Date: Mon, 19 Jul 2004 17:18:43 -0500 Subject: [seek-reports] Weekly Status Report from Aimee Stewart Message-ID: <40FC48C3.6020206@ku.edu> An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040719/995acf77/attachment.htm From franz at nceas.ucsb.edu Mon Jul 19 15:45:07 2004 From: franz at nceas.ucsb.edu (Nico Franz) Date: Mon, 19 Jul 2004 15:45:07 -0700 Subject: [seek-reports] Nico Franz - weekly status report, July 19, 2004 Message-ID: <5.2.1.1.2.20040719153438.017f0e88@hyperion.nceas.ucsb.edu> Status Report Nico Franz July 19, 2004 Completed Tasks/Bugs Fixed: ----- * None. Current Work and Bugs: ----- * Completing manuscript with co-author (Peet). It's in principle available (should anyone care already). Significant Issues ----- * None. From bzhu at sdsc.edu Mon Jul 19 19:01:40 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 19 Jul 2004 19:01:40 -0700 Subject: [seek-reports] status report from Bing Zhu - July 17 Message-ID: Completed Tasks/Bugs Fixed: none Current Work and Bugs: - re-read the design document of Ecogrid's put API. - working on the gwsdl for Ecogfrid's put operation. Significant Issues: I am not sure if I need to continue my data integration work for Niche Modeling data. I uploaded Niche Modeling data into SRB and created a SRB version of pgm_cut which works very well. Unfortunately there are different opinions about moving the approach into ecogrid level. I personally think it is worth thinking as how we split workloads to server side and client side (especially Kepler actors). From rods at ku.edu Tue Jul 20 07:47:44 2004 From: rods at ku.edu (Rod Spears) Date: Tue, 20 Jul 2004 09:47:44 -0500 Subject: [seek-reports] Status 7/12 - 7/16 Message-ID: <40FD3090.9040403@ku.edu> Completed Tasks/ Bugs Fixed: * Put up alpha version of the Query Builder for comment * http://129.237.201.166:8080/ogsa/qb/QueryBuilder.html Current Work and Bugs: * Continued on Bug 1595 - Create Advance Query Builder UI Important or Outstanding Issues (of a significant nature) * None Work This Week: * Continue work on Bug 1595 - Create Advance Query Builder UI * Work on the generation of SQL -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040720/a975e1ac/attachment.htm From T.Paterson at napier.ac.uk Fri Jul 23 08:23:51 2004 From: T.Paterson at napier.ac.uk (Paterson, Trevor) Date: Fri, 23 Jul 2004 16:23:51 +0100 Subject: [seek-reports] report Message-ID: <735F04A99D358E468A16EDB64FC0455519A321@EVS1.napier-mail.napier.ac.uk> Hi Matt - here's a report - not much to it I'm afraid, I'm still feeling my way around looking for something meaty to get stuck into !!Trevor Paterson Completed Tasks/ Bugs Fixed: Current Work and Bugs: * examining and documenting some of the issues surrounding the Concept Transfer Schema * examining how character circumscriptions may be incorporated into the notion of taxonomic concept * examining relationship of Concept Schema in relation to other standards Significant Issues: Trevor Paterson PhD t.paterson at napier.ac.uk School of Computing Napier University Merchiston Campus 10 Colinton Road Edinburgh Scotland EH10 5DT tel: +44 (0)131 455-2752 www.dcs.napier.ac.uk/~cs175 www.prometheusdb.org Napier University Open Day for full and part time programmes, Craighouse Campus and Merchiston Campus, Wednesday 15th September 11.00am - 7.00pm -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040723/ff4fdf35/attachment.htm From Serguei.Krivov at uvm.edu Mon Jul 26 07:34:57 2004 From: Serguei.Krivov at uvm.edu (Serguei Krivov) Date: Mon, 26 Jul 2004 10:34:57 -0400 Subject: [seek-reports] growl progress report Message-ID: <000001c4731d$b9a8a6a0$3ca6c684@BTS2K3000D5635086B> seek-reports at ecoinformatics.org Progress Report Serguei Krivov 07-26-2004 1) Completed tasks/bugs fixed -Developed a toolbox (with icons) for editing relation hierarchy (RBox) and enabled all required editing features; Added option for editing "one of" relation. I hope that by now growl is not missing any owl semantic construct. We can edit all owl -dl things with no gaps whatsoever. -Fixed inconsistent rendering of areEqual relation -Fixed several minor bugs/inconsistencies in OWLDLCompliance function 2) Current Work and Bugs -I need to rewrite a few search related functions that query OWLOntology object which will not exist in runtime as from now , since we decided to changed the way how ontology is stored and saved - Preparing for the first alpha release of GrOWL editor, hope it will happen this week 3) Significant issues The list of questions/issues will come with alpha release -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040726/b9eade13/attachment.htm From rich at sfsu.edu Mon Jul 26 08:36:02 2004 From: rich at sfsu.edu (Rich Williams) Date: Mon, 26 Jul 2004 08:36:02 -0700 Subject: [seek-reports] (no subject) Message-ID: 1) Completed tasks/bugs fixed None 2) Current Work and Bugs (a) Working on GrOWL metadata panel and save to OWL file. Extending OWLAPI code to handle saving imports. (b) Changing the OWL ontologies to reflect the work on the upper ontology done by Shawn and I. Common properties (such as Whole-Part) expressed as subclasses of classes defined in the upper ontology rather than as properties that are restricted in lower classes 3) Significant issues None From xianhual at email.unc.edu Mon Jul 26 09:45:59 2004 From: xianhual at email.unc.edu (xianhual@email.unc.edu) Date: Mon, 26 Jul 2004 12:45:59 -0400 Subject: [seek-reports] report Message-ID: <1090860359.4105354722389@webmail0.isis.unc.edu> Status report Xianhua Liu July 26, 2004 Completed Tasks/ Bugs Fixed: -------------------------------------------------------------------- Current Work and Bugs: ------------------------------------------------------------------- * Tested and revised dynamic PDF generation of revision proposals Significant Issues ------------------------------------------------------------------- ------------------------------------------------------------------- From franz at nceas.ucsb.edu Mon Jul 26 10:09:15 2004 From: franz at nceas.ucsb.edu (Nico Franz) Date: Mon, 26 Jul 2004 10:09:15 -0700 Subject: [seek-reports] Nico Franz - weekly status report, July 26, 2004 Message-ID: <5.2.1.1.2.20040726100214.00baf198@hyperion.nceas.ucsb.edu> Status Report Nico Franz July 26, 2004 Completed Tasks/Bugs Fixed: ----- * None. Current Work and Bugs: ----- * Discussion/revision of concept relations manuscript with co-author and other members of SEEK Taxon. * Starting to work on next project (with D. Thau, eventually): "what gets a GUID and when to stop?" (a.k.a. GUID paper). Significant Issues ----- * Still not sure about TDWG New Zealand, i.e. what SEEK's (TES group in particular) role is and how to place our concept relations paper within that framework. Friday's conference call will hopefully clear this up. From higgins at nceas.ucsb.edu Mon Jul 26 12:32:43 2004 From: higgins at nceas.ucsb.edu (Dan Higgins) Date: Mon, 26 Jul 2004 12:32:43 -0700 Subject: [seek-reports] Weekly statrus report - Dan Higgins - July 26, 2004 Message-ID: <41055C5B.4090005@nceas.ucsb.edu> Status Report Dan Higgins July 26, 2004 Completed Tasks/Bugs Fixed: ---------------------------- * Tracked down bug in CommandLine Actor on Linux/Unix systems that resulted in redirection to output file to not work properly. Fix enabled the R data reader example to work properly on Linux Current Work and Bugs: ---------------------- * Continuing work on intergrating R into Kepler in a more direct manner (API interface rather than as a string-based subprocess) * Reviewing emlDataSource actor for modifications and possible connection R for data display. Significant Issues ------------------ * None From rods at ku.edu Mon Jul 26 13:16:26 2004 From: rods at ku.edu (Rod Spears) Date: Mon, 26 Jul 2004 15:16:26 -0500 Subject: [seek-reports] Status 7/19 - 7/23 Message-ID: <4105669A.6080701@ku.edu> Completed Tasks/ Bugs Fixed: * Started on serialization and an object that encapsulates the query Current Work and Bugs: * Continued on Bug 1595 - Create Advance Query Builder UI Important or Outstanding Issues (of a significant nature) * None Work This Week: * Continue work on Bug 1595 - Create Advance Query Builder UI * Work on the query object (the output of the query builder) From rgales at eecs.ku.edu Mon Jul 26 15:30:50 2004 From: rgales at eecs.ku.edu (Robert Gales) Date: Mon, 26 Jul 2004 17:30:50 -0500 Subject: [seek-reports] Status Report 7-19 to 7-23 2004 Message-ID: <4105861A.4050206@eecs.ku.edu> Status Report Robert Gales July 26, 2004 Completed Tasks/ Bugs Fixed: ---------------------------- * Attended meetings regarding the issues that have been presented regarding the Taxonomic Exchange Schema and the possible modifications to the schema and/or data model to solve the issues in the most flexible manner. Current Work and Bugs: ---------------------- * Making the modifications to the schema and data model as discussed in the the above meetings Significant Issues ------------------ * None From tao at nceas.ucsb.edu Mon Jul 26 17:15:15 2004 From: tao at nceas.ucsb.edu (Jing Tao) Date: Mon, 26 Jul 2004 17:15:15 -0700 (PDT) Subject: [seek-reports] status report Message-ID: Status Report Jing Tao 07/19/2004 Completed Tasks/ Bugs Fixed: ---------------------------- * None Current Work and Bugs: ---------------------- * Installing metacat ecogrid semi-production node in NCEAS Significant Issues ------------------ * Resultset java object deserializer couldn't be load successfully. -- Jing Tao National Center for Ecological Analysis and Synthesis (NCEAS) 735 State St. Suite 204 Santa Barbara, CA 93101 From bzhu at sdsc.edu Mon Jul 26 18:15:18 2004 From: bzhu at sdsc.edu (Bing Zhu) Date: Mon, 26 Jul 2004 18:15:18 -0700 Subject: [seek-reports] status report from Bing Zhu - July 26 Message-ID: Completed Tasks/Bugs Fixed: - initial design of the gwsdl for ecogrid's 'put' - installed ecogrid client in the whywhere machine and built two query examples for whywhere data - had a meeting with Bertram and Raja for the future work of SRB actors Current Work and Bugs: - revise the 'put' gwsdl - Implement pgm_cut algorithm into ecogrid's SRB implementation for whywhere data Significant Issues: - none From astewart at ku.edu Tue Jul 27 07:16:21 2004 From: astewart at ku.edu (Aimee Stewart) Date: Tue, 27 Jul 2004 09:16:21 -0500 Subject: [seek-reports] Weekly Status Report from Aimee Stewart Message-ID: <410663B5.8050807@ku.edu> An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-reports/attachments/20040727/9a91aef6/attachment.htm From berkley at nceas.ucsb.edu Tue Jul 27 11:05:09 2004 From: berkley at nceas.ucsb.edu (Chad Berkley) Date: Tue, 27 Jul 2004 11:05:09 -0700 Subject: [seek-reports] 7/19-7/23 Message-ID: <41069955.10804@nceas.ucsb.edu> 1) Completed tasks/bugs fixed -got scrollbars partially working in the kepler canvas 2) Current Work and Bugs -working on vergil gui issues -keep working on scrolling -start work on adding the quick search area to the actor library pane 3) Significant issues -need to figure out if we should add the scrollbar/navigation code to diva, or keep doing what i have been doing and add the code to vergil itself.