[seek-dev] suggested Ecogrid tasks

Matt Jones jones at nceas.ucsb.edu
Thu Apr 7 09:35:12 PDT 2005

Sure, I think that's a great model for development.  But we don't even 
have the beginnings of a semantic annotation tool for users to test. 
That seems like a first step to me, and it is one of the main areas of 
development for Kepler (e.g., it is a whole session at the May 
developers meeting, see 
  For more traditional (non-semantic) collections building and metadata 
authoring we have Morpho and other tools like Specify in the museum 
community, and we are in the continual process of letting users use 
these and trying to improve them for their needs.  Are you suggesting 
that SEEK should provide developer resources to improve Morpho and other 
collection building tools in use in the community?


Arcot Rajasekar wrote:
> Matt
> 	I agree that our primary aim should be to build tools. But
> building tools in vacuum is going to create problems downstream. I am of
> the school that tools should be built incrementally with feedback from
> real users. If the feedback loop is not there,  some small roadblock can
> jeopardize several years of developmental work.  Hence, my mntra: throw it
> to the users and let them throw brickbats at it :-)
> 	raja
> On Thu, 7 Apr 2005, Matt Jones wrote:
>>Well, we have already started this process of building collections in
>>the community, and are well aware of the problems that could and have
>>cropped up.  We have data registry and repository initiatives going with
>>all of the LTER sites, the OBFS network, the NRS network, groups like
>>PISCO, individual labs, Kruger Nat Park in South Africa, and others.
>>All of these are collection building activities.  We certainly need more
>>funding for it, but I'm not sure what SEEK's role should be in advancing
>>this.  Right now I would be happy if SEEK could provide the tools and
>>guidance to do, for example, semantic annotation of data sets, and test
>>these tools on our case studies alone.  Once we develop the semantics
>>tools, we can make these available to our other partners who are trying
>>to build collections.
>>Arcot Rajasekar wrote:
>>>	I agree. But we need to take steps to find out what problems can
>>>occur when we start building the SEEK holdings. I have seen problems crop
>>>up in bizzare fashion when we try to do that: political, technical,
>>>usability, etc. It will  be a good idea to make a start at this. Once we
>>>have some collections that we can open to SEEK community, that is the time
>>>when we can go and ask for more money to enlarge the collection.
>>>	 my2cw
>>>	raja
>>>On Thu, 7 Apr 2005, Deana D. Pennington wrote:
>>>>Re: your 3rd item, building the eco digital library, this is indeed a huge job,
>>>>especially if all of the data have to have EML.  I think we should try to get
>>>>some funding (perhaps BDI?) to hire a few people to work just on this.  I could
>>>>see, for instance, a BDI proposal to find data and tools, get them described for
>>>>use on the system, semantically tag them, and get them on the system.  The
>>>>research objective would be developing the KR needed to do the semantic tagging.
>>>>Mark and I noted the need for a bigger KR effort at the meeting in Davis in March.
>>>>Quoting Bing Zhu <bzhu at sdsc.edu>:
>>>>>After talked with Raja, we suggested the following tasks for
>>>>>Ecogrid development.
>>>>>1. Ecogrid web page development for
>>>>>    - upload Eco-data into SEEK data repositories (Metacat, SRB,
>>>>>    - search and view SEEK Eco-data
>>>>>    - submit computational jobs in Ecogrid
>>>>>1. Deployment of Condor to Ecogrid for distributed job submission.
>>>>>    This is a feedback from Raja's talk in SEEK workshop in Jan.
>>>>>    Most probably we will use the approach of Minigrid from UK.
>>>>>    We are aware of the similar R&D work by you and Ilkay for a
>>>>>    solution. I didn't see the conflict between these two efforts.
>>>>>3. Build SEEK digital library -- This is a huge job and will
>>>>>    be very useful for SEEK project and Eco-scientists in general.
>>>>>    Basically we would find any public Eco data and mine those data
>>>>>    Metacat (if XML documents) or SRB (if a file, e.g. image,
>>>>>    data, etc).
>>>>>    And also the data collected in our Ecogrid can provide useful info
>>>>>    other SEEK groups such as Taxonomy and modeling.
>>>>>    Actually there are a lot of Eco data just at SDSC. We need to
>>>>>    talk to those domain scientists and mine their data into SEEK
>>>>>    data repositories. It is conceivable that collecting eco-data can
>>>>>    our big useful task.
>>>>>Ecogrid Team
>>>>>SEEK project
>>>>>Bing Zhu
>>>>>Programmer/Analyst III
>>>>>San Diego Supercomputer Center
>>>>>bzhu at sdsc.edu
>>>>>Seek-dev mailing list
>>>>>Seek-dev at ecoinformatics.org
>>>>Dr. Deana D. Pennington
>>>>Long-term Ecological Research Network Office
>>>>UNM Biology Department
>>>>MSC03  2020
>>>>1 University of New Mexico
>>>>Albuquerque, NM  87131-0001
>>>>505-277-2595 (office)
>>>>505 272-7080 (fax)
>>>>Seek-dev mailing list
>>>>Seek-dev at ecoinformatics.org
>>>Seek-dev mailing list
>>>Seek-dev at ecoinformatics.org

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

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