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Calls are held every Thursday at 1 pm eastern time (GMT–4 in daylight savings, GMT-5 standard time) – convert to your time at

View and edit this page permanently at, or use the temporal Google Doc for collaborative note taking during the call.

VIVO is hiring!

DuraSpace is seeking a dynamic and entrepreneurial Project Director for the open source VIVO project (, a world-wide community focused on creating software tools, ontologies, and services. The VIVO Project Director will have the opportunity to play a major role in a collaborative movement that will shape the future of research.

See full posting – applications are still being accepted -- the sooner the better. Note that there is no requirement to be a U.S. citizen.

Release update –

Last Friday – We have a release candidate! Please take a few minutes to download it, start it up, and look for telltale signs of smoke. Make sure that your favorite fix or improvement is working as desired. Let us know if we have broken anything.

We have created maintenance branches in the repository, and will be using them for the final release. Any bugs found during testing should be committed to the maint-rel-1.6 branch and merged to the develop branch. This is our first release cycle using Git, so let me know if you have questions, and we'll try to figure out the answers. 

The files for the release candidate are here:



Or you can get the latest and greatest directly from the maint-rel-1.6 branches of the repositories on GitHub.

Current blocker issues

Join the release test mailing list if you wish to be informed of release candidates, plus the final distribution -- and we’d love to have help testing -- subscribe here:

Apps and Tools Group

Notes from Tuesday 10/22 (and on YouTube)

Next call is November 5 at 1 pm – look for an announcement from Chris Barnes confirming the time and connection info.

Upcoming Events

  • 1st Annual UCosmic Conference, October 31 in New York
    • Collaborative Software Development to Address Strategic Challenges in Higher Education: Kuali, VIVO and UCosmic 
    • Deep discount for VIVO community members
  • VivoCamp pre-conference at SWIB13 conference, November 25-27 in Hamburg 
    • short presentations and demos on a number of topics by a couple of experienced people, followed by discussion, Q&A, panels etc.
    • Organized by Valeria Pesce, Lambert Heller, and Lukas Koster
    • John Fereira from the U.S. will be attending
  • Duke will be hosting the 2014 VIVO Implementation Fest from March 19-21 – reserve your hotel room today and stay tuned for more information in coming weeks


  • Brown (Ted)

    • working on getting ISSNs for about 3,000 journals mostly in the health/medical field.  Using the NLM API and Google Refine.  With ISSNs we can use a CrossRef API to obtain DOIs.  

    • today - working with testing VIVO 1.6 and submitted a pull request; has not yet looked at how the ontology changes will affect ingest processes. Where should we report issues we encounter? in (using the same account you use for the VIVO wiki). Attaching screenshots or log messages is always helpful

    • Jim -- 23 outstanding JIRA issues, mostly reported through Holly Mistlebauer’s Selenium tests

  • Colorado (Stephen and Alex)

    • Still working on initial publications curation in Elements

    • VIVO 1.6 testing on TODO list

    • Stephen and Alex attended an Open Access Week talk where one of the Nobel laureates on campus spoke on Open Access -- Dr. Thomas Cech was President at the Howard Hughes medical institute when they pushed through an Open Access policy, and this has been influential with NIH/PubMed.  Also a speaker from ImpactStory, an NSF/Sloan-funded non-profit that collects data from various Internet sources (including GitHub) to augment typical profile content for researchers. CU’s INSTAAR Geosciences group helped launch Elementa (“Science of the Anthropocene”), a new open access journal together with other major universities. Interesting to hear from senior faculty/researchers about Open Access and not just from librarians and students.

  • Cornell (Jon, Jim, BrianL, Huda, Tim)

    • Prepping for the 1.6 release has been the major activity

  • Duke (Richard)

    • Progressing on with artistic works (implementing a plan that has been developed with faculty input, and creating a tool to supplement what Elements provides as input screens).  Beyond that, mainly production support for troubleshooting loads and other issues.

  • EPA (Zac)

    • No updates -- just returned from the shutdown and glad to be back.

  • Florida (Chris)

    • Working on a big course ingest to update all courses using a new Python data ingest tool that outputs add and subtract RDF to paste into the VIVO interface. It’s a multi-step process, where it first tries to see if the instructor is in VIVO -- works through the people ingest tool to see if the person exists, and won’t put a course into VIVO unless the instructor is in VIVO.

    • Will be producing an N3 file of all UF VIVO data for use in testing mapping from VIVO to CERIF, the European research information standard

    • Mike Conlon is creating JSON files from the UF VIVO SPARQL endpoint and using the d3.js JavaScript visualization library to create network graph visualizations of connections between organizations at UF. Uses the JSON resultSet from the SPARQL query.  Did have to do some transformations in the JSON to make the arrays hierarchical for the particular visualization he wanted.

  • Memorial (Max)

    • Has been in contact with Stella, who will be giving the team at Memorial some help. Lisa and colleagues are finalizing the Knowledge Mobilization ontology. John is working on the front end, and Max himself is working with the Harvester

    • Jon CR from Cornell and Jennifer Adams from Memorial gave a joint talk at the CASRAI conference last week in Ottawa.

  • Stony Brook (Tammy)

    • Erich Bremer presented at CEWIT conference this week (Center of Excellence in Wireless and Information Technology)

      • Talk about webid4vivo, explaining what VIVO is and why it’s important, semantic web, public key encryption, etc

    • Tammy & Erich planning on attending the UCosmic conference next week, together with Bill Barnett from Indiana, Michele Kimpton from DuraSpace, and Jon and Dean from Cornell

    • Continuing work on, aggregating and transforming data

      • Upgraded to Java 1.7 and having trouble with Harvester finding paths; Stephen is running on Java 1.7 at CU Boulder and suggests that Tammy send him any error messages

  • UCSF (Eric)

    • Still working on the cross-linking project to be able to add the home institution URI for authors.  Dave Eichmann thinks he can put together a SPARQL endpoint to jumpstart that process using the data he has aggregated from 17 institutions for CTSAsearch

    • Looked at overlap between UCSF and USC and found that 18% of the USC authors had co-authored with a researcher at UCSF, and look forward to being able to directly cross-link the research networking systems

    • Paul -- did an analysis at the article level and found 10% of the articles from the Hospital for Special Surgery had co-authored with researchers at Weill Cornell.  Shared publications are a great metric for collaboration in general.

  • Weill Cornell (Paul)

    • Large Pilot launches October 30 for about a week with 50 or 60 people testing VIVO

    • Have in place a reconciliation process of pubs from faculty evaluation versus ingested pubs: 99% precision, 86% recall (low due to 2 factors -- lingering issues in process and articles that are not in Scopus -- both addressable

  • University of Florida (Chris)

    • Working on a course ingest. Written new Python-based tool to do so.

    • Courses won’t be ingested if the tool can’t find the instructor

    • Next Apps and Tool call on November 5

    • Intends to publish all UF triples as an N3 data set

Notable list traffic

See the vivo-dev-all archive and vivo-imp-issues archive for complete email threads

  • Eclipse issue after Mac OS X Mavericks (10.9) upgrade (Alex, Tammy)

    • Upgraded Mac OS X and found that Eclipse was not working well with Java 1.7

    • There’s a few links to workarounds in the message he sent out

    • Tammy has an upgrade in process ...

  • Password for VIVO 1.4.1 virtual box – see VIVO v1.4.1 virtual appliance on this wiki

    • Update download page and sync with the wiki page that it points to

    • Follow up on Chris’s suggestion to check out Vagrant-based alternative to older virtual appliances -- can create a shell script to create a virtual machine

      • have to install Vagrant, and then check out Ted’s repository at GitHub and issue a command called “vagrant up”

      • took 14 minutes from doing a Git clone to logging into VIVO

      • you can modify that configuration to your own needs and check into your clone of the repository

      • or you can issue a pull request for Ted to add to his repository for everyone to use -- for example, to add sample data that could be shipped and installed optionally

    • Check out the catalogue of apps and tools in the Apps & Tools section of the wiki 

    • Vagrant Virtual Machine: Give it a shot. 

  • Any relevance here? 

    • Maybe a good place for Erich to share his WEBID story?

    • Can share a story and clone and extend -- something like the WebId work at Stony Brook

  • Javascript which renders the result of SPARQL SELECT queries into charts or HTML elements 

    • related: UF SPARQL endpoint outputs JSON, which Mike and team are using to generate a D3 viz org chart -- Chris would like to have Mike demo this in Apps & Tools call, also Eric Meeks on OpenSocial container demo

Call-in Information

  • Date: Every Thursday, no end date
  • Time: 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)
  • Meeting Number: 641 825 891

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