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Please add additional agenda items or updates --

Rethinking VIVO calls

Discussion last week:

  • Keep this call but describe it as what it is – a blend of implementation and development; reduce overlap with implementation call so that people focused on implementation don't have to attend both
  • Arrange focused calls on topics that might be about either implementation or development, or that bring in experts from related semantic web projects such as Fuseki
  • It may be hard for people to justify attending more than one call per week, so be clear on what the topic of each supplementary call would be__

Suggested special topics so far

Effective use of Git

  • what's a good workflow as a core developer, and how do you fully integrate with the Git model?
  • if on the implementation side, how to contribute
  • are we going to use GitFlow?

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OpenSocial and http://www.orng.info Open Researcher Networking Gadgets,]

Using the three-tiered build (Vitro + VIVO + your local modifications)

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VIVO custom forms – in two parts, introduction and a walkthrough of modifying an existing form for a new property and/or role

An Environment call – a set of short presentations on VIVO development, test, and production environments

Office hours about adoption questions

Wiki move

Since Jim is on vacation for a few days, we can feel free to praise his work – thank him without embarrassing him in person – it was a lot more work than expected and is

Updates

  • Weill – 
  • UCSF – 
  • Penn – 
  • NYU --
  • Johns Hopkins --
  • Indiana --
  • Florida --
  • Duke --
  • Cornell – 
  • Colorado – 
  • Brown – 
  • other

Notable development list traffic

it's great to be able to continue right where we left off, with some nice new features.

What would help this wiki going forward?

  • more use, and more consistent use of tagging
  • more navigation
  • putting in placeholders for pages that should be there
  • encouraging everyone to do some documentation and some correction/updating/removal of older content

Issues?

  • speed
  • can we be other than the last entry on
  • can we have a search that by default is limited
  • can we block search of the old wiki, so that Google over time points only to the new one
    • can put a meta element on each page – on the page template, perhaps?
  • do we all have permission to edit

Updates

  • Weill – (Eliza) – working to improve the performance of the site, by exploring Memcached and Squid. Brian Caruso is working with a dump of the database to see if he can replicate some of the performance issues on a server. Otherwise getting feedback from a small pilot group of faculty members to try out the site and get feedback – responses so far are saying something different, but people have not interacted with the forms that much yet.
  • UCSF – (Eric) – last week mentioned Elda on this call, and are using for RDF to JSON conversion but the way they do it is different than the standard JSON-LD – do we have any personal contacts at Elda? (no) – will try to make a contact
  • Penn – (John Mark) – trying to make sure the site can handle a big onslaught of editors when launch – separating MySQL. Florida is using replication of the Amazon RDS database to support a public sparql endpoint.  Also trying 1.5.1 with some of the visualizations turned off.  Noticed that in some of the list views, things get put at the end in outdented form – most likely the inferences did not happen because the process was interrupted. At Weill, will say "research article" but manual triggering of inferences by making a change that forces inferences to be computed for that individual.  Brian – may be pushing some of the inference processing until after the ingest is completed to try and finish the ingest; in 1.4 there was a tradeoff where it would take longer to get the data ingested and show the new assertions, but complete the inferencing; now in 1.5 the inferencing happens after the new assertions.
  • NYU – (Yin) – excited about the  move to GitHub and has forked a copy of the code to start entering in his changes for the search. There are so many different branch versions – 1.5.1 stable? Stephen – best to work off of Master. Develop is where the features that are finished are committed to. Can look for the 1.5.1 tag for the maintenance release and cherry pick a later commit into his version if necessary. Master will become version 1.6.  Yin doesn't have changes yet to commit back, but will likely have some in the future – the rewriting of the ranking algorithms.  At that time, there's a way to refresh from develop and create a pull request against the develop branch.
  • Stony Brook – (Erich) – two accomplishments recently, in a 2nd VIVO implementation for Stony Brook alone and trying to make it cover the full campus by next April to replace a Lotus Notes product called Faculty Addendum.  Were able to hook this to CAS authentication using a module from Rob Fox at Notre Dame.  In meetings around campus around where can share the VIVO data around campus.  Are investigating adding WebID capability, the public key portion, to VIVO so can become an identity provider as well for verification by a remote authentication  service? The goal is to be able to provide WebID for authentication in other web applications elsewhere, and to build up on a grass roots basis the provision of WebID so that more sites accept it for authentication. Work is underway to link WebID and OpenID.
  • Johns Hopkins – 
  • Indiana --
  • Florida --
  • Duke --
  • Cornell – 
  • Colorado – 
  • Brown – 
  • other

Notable development list traffic

  • Performance issues at Brown with self-editing presentations – update on whether Tim's improved sparql queries solved the problem
  • Strange behavior when editing ORCID ids and Scopus ids, and a workaround
  • Deploying VIVO with Git
  • Building with Ant WAR
  • VIVO/MySQL deployment
  • Image issue with 1.5.1 VIVO
  • removing "Person" from the browse list on the home page (not the People menu page, where the Person class can be unchecked via page management – requires changes to the browseClassGroups.js file_(Weill, Stony Brook)_
  • upgrade halted in FileGraphSetup (Northeastern) – Jim suggests rebuilding the search index, which when there's no content in the system should only take a couple seconds
  • optionally creating role in EditConfigurationGenerator – Melbourne is doing advanced custom forms development
  • solution to missing inverse property (Brown) – They introduced a local sub property of bibo:performer that has the desired inverse to link the performances from people pages
  • VIVO-Fuseki-Elda – making Fuseki accept sparql updates, and working with VIVO, Fuseki, and Elda Epimorphics Linked Data implementation. Michael from the LASP lab at Boulder will keep working the the latest Fuseki code and see if anyone in that community can explain its failure to update, and bring back anything he learns.
  • WebID in VIVO? (Stony Brook) – anyone interested in WebID should contact Erich Bremer
  • Dbpedia countries showing up in search results – Alex suggest the option of a three-tiered or more modular build approach for the ontology, too, which fits with the modularity that the CTSAconnect project is developing
  • VIVO and CAS authentication (Stony Brook and Notre Dame) – Tammy reports this is working
  • what's (still) up with http://vivo.vivoweb.org? – still in transit, somewhat delayed by other deadlines; primarily just need to transfer the domain name
  • anything else?Joe Mancino would like to hear from others about how they are doing load testing, especially for simultaneous editing. Jim has done load testing in fairly simplistic ways as part of our release preparations, but considers it still rudimentary.

Still pending

  • map of science and temporal graph visualizations – 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 in December

Call-in Information

Topic: VIVO weekly developer call

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Meeting Number: 645 873 290

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