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Calls are held every Thursday at 1 pm eastern daylight time (GMT-5) – convert to your time at

There will be no development call next Thursday, November 22nd – Happy Thanksgiving

These calls now use WebEx – see the "Call-in Information" at the bottom of this page.

Please add additional agenda items or updates --

Jon Corson-Rikert will be leading this week's call.


  • Brown
  • Colorado (Alex and Stephen) – about to push 1.5.1. changes to test instance. Working on a Git deploy script to push out new changes and roll them out into production; will share the script and once the wiki is moved will put together the article for the 3-tier build for Jim to review. A meeting with the Library today to talk about VIVO.
  • Cornell
  • Duke (Richard) – loading a large majority of publications into their Symplectic Elements instance and loading that into a test VIVO instance. There is a connector that Elements provides, but are submitting the data through Jena directly. Takes a while, but then can ask for incremental changes. Data partly from Reach NC, a state-wide SciVal experts, but also harvested some out of a Duke legacy system.
  • EPA
  • Florida (Matt) – have 1.5.1 on development server and are testing it. Vincent will be moving to another project in January. Nicholas is doing data cleanup and having trouble getting SPARQL queries to complete – tried through Fuseki but getting 502 errors, even though connecting to the 3030 port directly.
  • Indiana
  • Johns Hopkins
  • NYU
  • Penn – _attended DLF last week – 2 sessions, one on "transcending silos and using LOD and image interoperability" and another on "global open knowledge base" – see
    Also a session about using the principles of Github (or GitHub itself) for data management.
    • have a lot of faculty and an existing system where publications have been gathered – are trying to correlate with PubMed and disambiguate co-author relationships
    • indexing seems to be fast with 1.5.1 but the visualizations don't seem to be working – a specific error message. In 1.4 works, if very slowly, but now the Java and MySQL processes spin up. But with 1.5.1, Java spins up for a few minutes and stops, and a warning message in the logs and never finishes. Temporal and Map of Science not working on individual pages, but co-author visualizations do work.
    • Michaleen just loaded 26,000 pages of publications in a 1.5.1 test server – came back in an hour after asking for a Map of Science and had been generated. Did found that some of the publications weren't mapping, and verified that the journal name was in Thomson ISI format. Katy referred her to Robert Preston at IU. Also a question where it was trying to map a dissertation, which wouldn't be linked to a journal anyway, so should be excluded from the visualization – confusing.
  • UCSF
  • Weill - 1) Set up Red Cloud and ran Harvester publication ingests successfully. 2) Upgraded dev to VIVO 1.5.1

Wiki Move Prep

Jim Blake has started on the wiki move and extracted a list of the 549 pages in the wiki, sorted by major category – 69 pages on adoption and outreach, 3 on the conference, 85 on implementation, 41 on the ontology, 143 on the harvester, 54 on development in general, 21 on user stories, and 135 pages of meeting agendas and notes. The plan is to move all this content (preserving as much of the current format as possible) and work from that as a base for the DuraSpace Confluence wiki as soon as that becomes available. We expect the page tags to carry across and to have a similar search functionality.

Jim – any opinions on whether he should try to bring over the history?
Stephen – if it's easy, can be helpful, but if it's a pain, maybe not

The Move to Git/GitHub, continued

Stephen moved the linked data index builder from the tools repository to its own repository. Wondering whether the link for the VIVO search Drupal module has changed – is milesw, not milesworthington

VIVO search is very much on the front burner with DuraSpace

Development Tasks for VIVO 1.6 and Beyond

There is more information being collected on the VIVO v1.6 release planning page – and more work there already than can possibly be accomplished for the VIVO 1.6 release.

Feedback is welcome on what's still missing, priorities, and areas where people think they can help with requirements, design, implementation, and/or testing.

Notable Development List Traffic

  • what's up with's being moved from an Amazon EC2 instance at UF to a virtual machine at Cornell. We hope to get it back in service next week
  • map of science and temporal graph visualizations not completing at Penn with 1.5.1, when they did with 1.4.1 (200K publications) – Chin Hua from the visualization team at Indiana University wrote to say he is working on another project but will get back to improving the visualization caching work next month
  • multi-server and data swapping setup requirements at Penn – currently swapping between a staging server and a production server. Have noticed that Florida's installation does a split between Apache and MySQL, without having to make changes other than to specify the location of MySQL on the other machine. Also want to change in another database – what would have to swap? Are pulling images from another source. They do not allow any editing. What about the display model and the ontology tbox. Would have to be restarting Tomcat anyway, so it should reload the display model.
    • would be a nice option for the future to be able to hot swap without having to restart your tomcat
  • overriding Javascript in themes – the fix on the list did work – actually have to change where it points to, because doesn't by default look in the theme directory for JavaScript
  • Question – if you put replace template in the same place in the theme directory, it should find it.
    • John Mark – might have to wait a few minutes for the Freemarker cache to be refreshed
    • Jim – an undocumented flag where can turn off Freemarker caching for development purposes – so you can make repeated changes and not have to wait

Call-in Information

Topic: VIVO weekly developer call

Date: Every Thursday, no end date

Time: 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)

Meeting Number: 645 873 290

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