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Calls are held every Thursday at 1 pm eastern time (GMT-5) – convert to your time at – and note that the U.S. is already on daylight savings time

These calls now use WebEx and have no limit on the number of attendees – see the "Call-in Information" at the bottom of this page.

Note that there will be no call at this time next week (April 25) due to the Implementation Fest – we'll be back on the regular schedule on May 2


  • Brown (Ted) – rolled out some changes to templates and the sorting of the browse screens; preparing for the I-Fest
  • Colorado (Stephen) – deployed release 1.5.2 to the staging environment and rolled it out after the data update today – easy with the 3-tier build to deploy to both Colorado Springs and Boulder campuses; so far no issues. Have also releases a new automated harvesting process to testing and working through the various components, but a first successful run yesterday. 
  • Cornell (Tim) – looking at performance of the SPARQL query to bring geographic focus onto a map within the home page; the query is trying to roll up numbers for U.S. states into the total for the U.S. on the world map. Has moved from a data getter to a controller paired with an Ajax call. Working on disambiguation of people based on frequency of last names, and hoping to be able to vary the strictness of matching so that unusual last names can be matched with lower exactness than very common last names.
  • Duke (Richard) – preparing for release; looking at publications and characterizing people based on high, medium, or low publication counts to help with performance.
    • Alex – there's a session next Friday morning on troubleshooting that will touch on performance issues, and will support remote call-in
  • Indiana (Rohan) – Found a concurrency issue and have fixed it – hope to push the source code in a week or so after further testing and code review
    • 20-23 minutes of loading time for the entire University of Florida, after which the Science Map visualizations load almost instantly
    • Jim – would be happy to participate in the code review, as would Chin Hua
  • NYU (Yin) – busy with creating a new summer school course; will be a special NIH study section on grants affected by Sandy; just got their computing cluster back up. Trying to get their Vmware server back up that had VIVO data on it
    • May be able to participate in the Saturday development day remotely
    • Has an algorithm in mind for modifying the search ranking and would like to focus on that and get some feedback
  • Weill Cornell (Paul) – a couple further people to test on publications ingest, and will then be deploying to production as a lookup source f
    • starting to do reports with MeSH terms – using it to look at a community of researchers to see their subject areas in common; looking at MeSH terms in published papers and comparing them to the block of MeSH terms associated with diseases; will also show how people fit into a hierarchy of MeSH terms. Will eventually want to show this for each term on an author's articles
    • Noticing that there are a lot of duplicate terms in UMLS – 3 different hits for HIV, for example, with links to different source vocabularies – had been hoping to use the cleaner hierarchy of Snomed CT but that does not have as broad a coverage as UMLS

Upcoming events

2013 Implementation Fest – April 25-26 at CU Boulder

  • community hands-on development day is planned as an optional additional activity on Saturday the 27th, e.g. working on internationalization
    • We have interest from Costa Rica, Mexico, and France in principle – there's one room choice option that has H.323 videoconferencing
    • Please sign up as an attendee (also can register as a remote attendee) and indicate here whether you plan to be involved in the development day activity
    • Jim – we have a template and a methodology for multi-language support, but we're interested in other topics if people want to explore them
    • Alex – we'll have two rooms available so people could work independently
  • 2013 VIVO Implementation Fest page has information on transportation and hotels
  • Registration page – note that there is no registration fee for the workshop
  • Schedule is available for preview on (including for mobile view) and as a Google Doc
    • If your are attending, please indicate the sessions you intend to attend
    • If you are not, you can still register as a remote attendee and indicate sessions there, or else email Jon or Alex

2013 VIVO Conference Call for Posters and Papers – due May 10

Upcoming Webinars

  • DuraSpace will be organizing and publicizing a series of 3 webinars in May and June focusing on VIVO
  • The first (May 14) will be a general introduction
  • The second (June 4) will include 3 case study presentations on VIVO implementations at Colorado, Brown, and Weill Cornell Medical College
  • The final webinar will be a "technical deep dive" on June 11

VIVO 1.5.2 released 

Update from Jim Blake on the issue discovered by Arve Solland from Griffith last week.

Notable implementation and development list traffic

  • Memory leak requires restarting Tomcat?
    • (Brian L) – looking at what's happening on the VIVO Cornell server
      • taking heap dumps to look for objects that are hanging around across garbage collections
    • (Alex) – we restart MWF with data updates so have not had a problem, but will look for messages
    • Other possible approaches:
      • Verifying that what is being seen is actual memory usage, not just the size of the JVM as reported by top() – check the gc (garbage collection) logs
        • adding a JSP page to force a full garbage collection may verify whether the baseline memory used by Tomcat is in fact increasing
      • Check the possibilities for thread contention that could cause the application to freeze up
      • Make sure your robots.txt blocks access to visualizations and CV generation (if you have that activated, which I think only UF does)
      • What other sites are experiencing this problem? – checking the Cornell VIVO logs this morning
  • Any way to batch convert Ontology URIs?
    • (Brian) A hybrid approach might be workable
      • could use the existing change namespace tool (designed for changing the namespace of the VIVO) to update all the ontology URIs in the instance data graph, if it's all in the main (KB-2) graph and accessible to that tool in its default configuration
      • then you could export the ontology only, use a text editor to modify the URIs, and load it back in
    • make a JIRA issue

Resolved but worth discussing

  • (Mark) Bug in Tomcat 7 for Ubuntu – source of the "There is no <whatever> content in your VIVO" problem from last week
Still open?
  • (Kelly) Harvester duplicates and speed issues for pulling from PubMed

Call-in Information

Topic: VIVO weekly call

Date: Every Thursday, no end date

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

Meeting Number: 641 825 891

To join the online meeting

Go to

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If those links don't work, please visit the Cornell meeting page and look for a VIVO meeting.

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To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code.

Call-in toll-free number (US/Canada): 1-855-244-8681

Call-in toll number (US/Canada): 1-650-479-3207

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Access code:645 873 290

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