Deprecated. This material represents early efforts and may be of interest to historians. It doe not describe current VIVO efforts.


We are talking about changing the site of VIVO's web-presence, and the tools used to maintain VIVO in the community.

There is some urgency to parts of this discussion, since SourceForge will soon discontinue support for MediaWiki. Other changes might happen at the same time, but are not directly related or time-constrained.

We should discuss these things at the VIVO Conference. This page is to act as a basis for that discussion.

The issues


We have been using MediaWiki on SourceForge.

SourceForge is about to discontinue support for MediaWiki. We must find another Wiki, but where and using what tool?

  • "We had originally slated this to happen on September 1st. We are electing to delay this service shutdown to later in 2012Q4."

DuraSpace will provide us with Confluence, if we want it.

  • Jon Corson-Rikert has said that he likes the tree-structure of Confluence. Pages have parents and children, instead of an unstructured web of pages.
  • Graham Triggs says: Also, for the Wiki transition, iirc DSpace performed an automated migration of content from a MediaWiki instance to the Duraspace confluence.

Source Control

We have been using Subversion on SourceForge. Some developers have expressed a preference for Git. Git seems to be gaining market share over Subversion. GitHub seems to be gaining market share over SourceForge.

About a year ago, the Harvester moved to GitHub, but the Cornell team said: "let's not move the core VIVO code now". Well, what about now?

SourceForge supports Git repositories, but GitHub also supports the process of tracking pull requests, which might be very useful as we become more community-oriented.

Issue Tracking

We have been using JIRA, hosted by Cornell.

Duraspace will provide us with JIRA, if we want it.

  • Jon Corson-Rikert has pointed out that the Cornell team has invested a lot of time to find an effective methodology for planning with JIRA, including scripts that manipulate JIRA data.

One of the features that the Cornellians like about JIRA is that it can poll Subversion to find commits that have JIRA issue IDs in the commit message and show them on the page for that issue.

Mailing Lists

SourceForge is the site of 6 mailing lists:

  • vivo-outreach
  • vivo-ontology
  • vivo-contact
  • vivo-imp-issues
  • vivo-announce
  • vivo-dev-all

Are these all still active?

Do we have a reason to move these to a different host? (GitHub or elsewhere)

  • Jim Blake says that the archives are really difficult to search. Or perhaps he hasn't learned the secret.
  • Graham Triggs says: We (DSpace) are currently still using Sourceforge for the mailing lists, although there has been some discussion about moving these to Google Groups, due to various issues with SourceForge mailing server.
  • Jim Blake recently created another list called vivo-release-testing

Chat room

Is this still active?

  • Nicholas Skaggs says that the participation is sparse, but there are a few regulars and occasional seekers after truth.

Do we have a reason to move it to a different host? (GitHub or elsewhere)

Web presence

Our "home page" is somewhat distributed, including:

In part, this stems from a desire to have both a curated site (like vivoweb) and a crowd-sourced site (like the wiki).

Random questions

I have heard that GitHub is more oriented toward "social networking". Is this true? Are there ways that we should be taking advantage of this?

Are any of these tools or sites branded with NIH-VIVO? Does the change to DuraSpace provide a reason to move or change our tools?

When can we meet?

Is there a time at the Conference when we can discuss this?

  • We are schedule for a BOF session, but I don't know which day.
  • No labels


  1. VIVO, Vitro, and VIVO Harvester sources are all on GitHub now. Can this discussion page be archived or deleted?

  2. The roadmap task force addressed all the issues on this page.  See their report for recommendations.