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  • Brown (Ted) -- Meeting with faculty departments to get feedback, e.g. faculty might want to upload a full CV and link to that from VIVO profile

    • the pairtree-derived file system set to store arbitrary files -- we happen to use it only for images so far

    • in the ontology is related to the person’s URI via a mainImage property and has a MIME type

    • but have never tried to store anything but

    • could also explore uploading to Fedora Commons (the repository, not the Linux OS)

    • Faculty are also interested in linking to full text of their publications.    

  • Colorado (Alex and LIz) -- starting publications work. Stephen has been working on replacing a Selenium-based ingest with a Harvester-based approach; this week the results matched up when run in parallel so are ready to start the switchover. The Harvester-based approach is much faster because it does not work through the UI.  Starting to work on visualizations showing collaboration around research interests, not just co-authors and co-investigators. This should be valuable for institutions not ready to undertake collecting publications data.

    • Using D3.js -- iDevice friendly visualizations

    • Example is a new college being created around media, technology, and art -- trying to find where those connections already exist on campus

  • Cornell (Jon and Jim)

    • working on 1.6 ontology changes, trying to keep migration patterns for context nodes like Positions and Advising Relationships

    • Jon and Jim at Implementation Fest

    • Jim looking into caching issue with help from Arve at Griffith and Ted from Brown

    • IFest internationalization work is being shared by JohnF at a UN meeting on collab of international agriculture researchers

  • Duke (Patrick and Sherri)

    • May 13 School of Medicine go live -- finalizing / curating data as needed, majority of faculty so a big group

  • Johns Hopkins

  • Indiana -- should we schedule a code review?

    • Jim has been iterating with Rohan et. al. based on their pull request

  • Memorial (Lisa)

    • back from the I-Fest safely and looking forward to the conference

  • NYU (Yin)

    • tried to join IFest code sprint, would still like to connect with some VIVO devs interactively to review his approach, use of VIVO GitHub, etc

    • Maybe see 

    • Alex: is there a use case for submitting changes back to VIVO even if they are options that not all sites may want? A community branch? but that may get forked, and someone will need to integrate the changes back into the branch they originated from

  • Stony Brook (Erich and Tammy)

    • new university wide VIVO instance work starting

    • question about generating distinct URIs in a way consistent with VIVO’s approach (Brian Lowe: IndividualDaoJena code calls URI generation code)

  • UCSF (Eric)

    • next release of Profiles on their plate

    • ORNG gadgets ( for adding multimedia to Profile pages, considering Cornell’s VIVO and ontology they see “media contributions” meta data but they can’t see the media itself, ex. a video clip of a faculty interview on Channel 7 or a press release

    • ORNG understanding RDF on page?

  • Weill Cornell (Paul)

    • Eliza more productive when Paul’s in Boulder :)
    • working on automating publication ingest process to free up devs
    • met with Grad School Office interested in tracking pubs by current students, question about alumni pubs
    • Jon discussed use case of monitoring compliance with NIH public access mandate on a grant with 1,000+ co-investigators – PI could receive 115 notices from NIH system for investigators who have not uploaded copies of their NIH-funded publications to PubMed. NIH tracks by grant and Weill can track by publication to notify the correct authors

 I-Fest outcomes and feedback

Apologies to those who tried to remote in --

For those who attended, what did you find most useful? What did you learn? What impressed you about other VIVO implementations?

Report on Saturday coding activities

  • Ted, Stephen and Jim working on internationalization -- documented on the wiki (search “multiple language support”)
  • Stephen ran into an issue after upgrading to Java 1.7 with Tomcat 6 -- resolved by upgrading to Tomcat 7
  • Jon and Alex working on setting up Jon’s Mac and start of wiki page (
  • Pedro from USC working with Michael and Bill from PennState on using Karma to get data in
  • will be trying Google Hangouts for small group coding and/or implementation support activities

If you haven't yet, please provide feedback (anonymously if desired) at 

Twitter stream: 

Slides and other materials are shared on SourceForge file repository -- also there were some notes captured as Google Docs (how do we collect these)

2013 VIVO Conference Call for Papers and Posters due May 10

  • Apps due July 31 

Upcoming VIVO Webinars (all Tuesdays at 11)

  • May 14 -- Overview of VIVO

  • June 4 -- Case Studies: VIVO at Colorado, Brown, Duke and Weill Cornell Medical College

  • June 11 -- VIVO Technical Deep Dive

Notable implementation and development list issues

  • Harvester transfer dying unexpectedly (Giuseppe)

    • on a 64-bit machine I experience this strange issue of the harvester-transfer reporting

    • "killed". Here's the extract of the log.

      • 2013-04-26 18:08:51.747 TRACE [o.v.h.u.r.JenaConnect] loading record: publication/75007

      • 2013-04-26 18:08:53.570 TRACE [o.v.h.u.r.JenaConnect] loading record: publication/75008

      • /root/vivo/harvester/bin/harvester-transfer: line 29:  1328

      • Killed java $OPTS -Dprocess-task=Transfer org.vivoweb.harvester.transfer.Transfer "$@"

    • Note that this happens after hundreds of publications have been loaded.

  • Search in Chinese (Jianwei) – a local fix that will be added to VIVO 1.6

    • Locate the file vitro-core/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/

    • In this file, search for the two occurrences of "ISO-8859-1" and replace them with "UTF-8"

    • Rerun "ant all" to rebuild VIVO

    • After restarting Tomcat, the links on the right side of the search results should work properly with Chinese characters

  • SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object (Tom T.)

    • related to MySQL max_connections configuration? – seems unlikely

    • checking vivo e 'show processlist' while performing a reindex if possible

    • may relate to the shift in connection pool libraries between VIVO 1.4 and VIVO 1.5

    • Alex will follow up with Tom to see if someone from Symplectic is in the loop

Call-in Information

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