2012Apr04

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Etherpad for meeting notes: http://firuta.huh.harvard.edu:9000/FP-2012Apr04

Agenda

  • AOD manuscript
  • Report from iDigBio cyberinfrastructure workshop
  • Collaborations/Potential Collaborations
    • GNA
    • Symbiota
    • SCAN
  • VM/Appliance Resource offer by iDigBio
  • SPNHC
  • State of Ecosystem components
    • Client helper: Annotation generation.
    • Firuta configuration.
    • Integration with Morphbank.
    • AnnotationProcessor: Specify Driver.
    • FP Access point API and FP Network Nodes.
  • Pending non-tech issues
    • Discussion of potential grant proposals.
    • Collaborations
    • SPNHC (two computers/projectors should be feasible).
    • iDigBio symposium and workshop at Botany 2012 (July).
  • Pending Tech Issues
    • Packaging Structure
    • API For Query and Cluster Finding
    • Tech group needs to make a decision on or set a date for decision for the query language for pub-sub for Apple Pie.
    • Tech group needs to decide on or set a date for decision for the scope, composition, and implementation of the "global cache."
    • Tech group needs to document the use, roles, and rationales for identifiers.
      • Who is responsible for MessageIDs and what purposes do they serve.
      • Identifiers in messages
      • Identifiers in annotations

Reports

  • Paul
    • At iDigBio cyberinfrastructure workshop last week.
    • Began construction of a new Georeference annotation
  • David
    • Set up Access Point enterprise project in Eclipse with glassfish, added maven support.
    • Finished documentation of the Rdf_Handler
    • Documenting access point Javaee project and client helper web service deployment
    • Working on getting Symbiota to invoke client helper web service
  • Bob
    • Manuscript submitted
    • At iDigBio workshop last week

Notes

FilteredPush Team Meeting 2012 Apr 4

Present: Jim, James, Lei, Bob, David, Paul, Maureen

Agenda:

  • AOD manuscript

Bob: Submitted. Will circulate to authors version of MS as submitted.

  • Report from iDigBio cyberinfrastructure workshop

Bob: iDigBio collecting knowledgable input on cyberinfrastructure goals. TCNs have highly varying beliefs in what iDigBio will provide. Profiles for minimum information needed to meet particular science goals on table.

  • Collaborations/Potential Collaborations
    • GNA

Exploring Proposal with GNA team providing FP functionality for them.

    • Symbiota

Exploring proposal for tighter Specify-Symbiota-FP integration.

    • SCAN
  • VM/Appliance Resource offer by iDigBio

Discuusion: Conclusions: VM Access, yes follow up. Appliance: Begin conversation on what it might do.

  • SPNHC

Abstracts. James: Due in week and a half. (1) an abstract for the demonstration - straightforward. (2) Discussion ? AO/AOD/OA Bob: Not sure that this helps the SPNHC community. Not a great deal of message there for that community. James: Important but simple point. James: There will be an AppleCore talk. Bob: The domain practictioners who embrace XML almost never want to study the XML schema in which their statements are expressed, they find the example documents to be more relevant. James: Not enough of a QC story yet. Could discuss ApplePie, duplicate finding, and generalize duplicates. Bob: Definitely time to say hello to the people who wlll be ApplePie nodes. James: We didn't choose people. We have 5 nodes, but didn't say who they would be. Bob: All the more reason to start a list. Maureen: Do we have a statement about what it would mean to be a node? Bob: They have botanical collections, they have a substantive number of duplicates. Maureen: You need to host this machine, keep it updated, etc, the machine provides these services, etc. Bob: Will take on drafting such a statement. Need to discuss: Defining 'node', and what it means to participate in a FilteredPush network instance. Paul: Will start framing some abstract text.

  • Pending non-tech issues
    • Discussion of potential grant proposals.

Jim: Fast need to make some decisions about potential collaborations for ABI. Do we want to put in our own, need to discuss with Bertram. Will need to make decisions within this month.

    • iDigBio symposium and workshop at Botany 2012 (July).

James: Thanks for the help with the abstract. Will be be able to have someone else go to show off network or have other mechanism for demonstration. Date is: July 12.for workshop, July 11 for talk.

    • FP All Hands Meeting

Jim: Paul to look at SPNHC schedule, suggest travel dates, meeting date in Cambridge. Paul: Will put out this afternoon.

  • State of Ecosystem components
    • Client helper: Annotation generation.
    • Firuta configuration.
    • Integration with Morphbank.

Forms in Morphbank for submitting new determinations - backing code invokes a webservice in tomcat along with morphbank to build an annotation, this creates rdf/xml and submits it to a filtered push webservice access point. Bob: Some low hanging fruit: We let people who ask nicely have a sandbox that lets them use this on the web, annotations are delivered to a triple store with a sparqul endpoint. Maureen: Hard part being removing data from Morphbank. About a week's work to get such a sandbox set up. Could convince morphbank to add our changes to their test site. Paul: Might be easier to demonstrate this with Symbiota. Bob: Morphbank might be amenable to doing this in their development infrastructure. Maureen: Nice encapsulated project for a student? Bob: Simple project for Swami for a couple weeks? James: Desire setting up Morphbank instance there. Keen on image management.

    • AnnotationProcessor: Specify Driver.

Maureen: Work on driver, no recent new work on annotation processor. Maureen: Driver takes static configuration and can insert a collection object record as represented in key-value pairs, can do inserts, not yet links to existing objects.

    • FP Access point API and FP Network Nodes.

Paul: Glassfish with EJB triage, implementation of jobs, implementation of messaging using JMS and a MySQL store and forward that looks like JMS.

Next steps for Lei?

Maurren: Need instructions on how to get Glassfish pieces installed and running. Next step to add in unit tests. Data into symbiota, then David to hook in anntation generation. Good to have data set shared between specify/symbiota (more complex morphbank). Going from david's annotation generation to a triple store. Need to define where things go into the SVN repository. Start with a separate project for David's Glassfish project bits.

Friday tech meeting to focus on defining projects and pulling disparate pieces together. (Packaging structure).

Short term focus bits: (1) Get developers on same page for deployment (document glassfish deployment), organize repository. Add morphbank/symbiota patches into svn. (2) Integration testing framework. (3) Maureen: Specify Driver David: Annotations from symbiota, triple store in annotation generation. Lei: Annotation Procesor (4) Maureen: SPARQL Push David: Annotation store in glassfish network capability Lei: Kepler engine in glassfish network capability.

  • Pending Tech Issues
    • Packaging Structure
    • API For Query and Cluster Finding
    • Tech group needs to make a decision on or set a date for decision for the query language for pub-sub for Apple Pie.
    • Tech group needs to decide on or set a date for decision for the scope, composition, and implementation of the "global cache."
    • Tech group needs to document the use, roles, and rationales for identifiers.
      • Who is responsible for MessageIDs and what purposes do they serve.
      • Identifiers in messages
      • Identifiers in annotations