Category Archives: VRE

VRE Final Report

As this term comes to an end, so must these reading courses. Below is the report I submitted as the final element of my participation in my Reading Course on Open Source Software and UPEI’s Virtual Research Environment:

Lise’s Final VRE Report

OSS Presentation (March 26, 2008)

You can hear the March 26, 2008 presentation delivered by Zac, Amanda and myself on Open Source Software at the link below:

OSS Presentation in mp3 format

Open Source Issue of Computers in Libraries (March 2008)

De Groff, A. (2008). Using Open Source to Give Patrons WHAT THEY WANT. Computers in Libraries 28(3): 6-10, Retrieved March 13, 2008, from Academic Search Premier database.

(2008). The Community Behind the Code. Computers in Libraries 28(3): , Retrieved March 13, 2008, from Academic Search Premier database.

Balas, J. L. (2008). Open Source Becomes More Accessible. Computers in Libraries 28(3): 32, Retrieved March 13, 2008, from Academic Search Premier database.

Breeding, M. (2008). Making a Business Case for Open Source ILS. Computers in Libraries 28(3): 36-39, Retrieved March 13, 2008, from Academic Search Premier database.

Chudnov, D. (2008). What Librarians Still Don’t Know About Open Source. Computers in Libraries 28(3): 40-43, Retrieved March 13, 2008, from Academic Search Premier database.

Gordon, R. S., & West, J. (2008). What Can Open Source Do for You?. Computers in Libraries 28(3): 44-45, Retrieved March 13, 2008, from Academic Search Premier database.

These recently published articles in Computers in Libraries could be useful to someone in the library community who wishes to get a quick glimpse at some of the uses of OSS in libraries, as well as some of the arguments for and against. The very fact that such a substantial part of this issue is devoted to OSS is indicative of how prevalent at least some of these solutions have become in libraries.

In his aptly called “What Librarians Still Don’t Know About Open Source,” Chudnov graciously alerts us to the one phrase one should be sure to retain from his article: “FLOSS provides the freedom to run, study, adapt, improve, and redistribute software.” I certainly find this description of OSS (or FLOSS) freedom more useful than Gordon & West’s, who assert that the “free” in free software is like in “free kittens”. They do however present a tidy list of OSS offerings that they believe are ripe, or accessible to all libraries. This list includes Firefox add-ins such as Check4Change and Accessibar, OCLC Link Evaluator and Greasemonkey scripts. WordPress, Drupal and Ubuntu also get a nod.

Chudnov, knowing his audience, makes a point of reminding readers that using OSS software does not have to mean doing all the customization in-house. He lists examples of vendors who provide OSS software along with fee-based service. He also recommends understanding the concepts around OSS in order to gain more leverage when negotiating with vendors, even when it comes to proprietary software — i.e. adding a clause that requires the vendor to hand over the code should the product be discontinued.

e-Science and the Life Cycle of Research (Humphrey)

Humphrey, C. (2006), “E-science and the life cycle of research”, available at:

Humphrey has used  the “Life Cycle Model of ResearchKnowledge Creation” (Humphrey and Hamilton) and the “Knowledge Transfer Cucle” within it to illustrate the gaps between the various stages of information production and manipulation that make up the research process, and to draw attention to the loss of information that can so easily happen at the juncture between these phases. He has also described the many “streams of activity” involved throughout the process, the shifts of responsibility, intellectual ownership and “digital custodianship” that are unavoidable and in need of clarification so as to maintain continuity.

His main argument is that research libraries must become familiar with the full spectrum of this life cycle, and customize their services and partnerships with a view to fostering research outcomes and continued data access.

The unacknowledged convergence of open source, open access, and open science (Willinsky)

Willinsky, J. (2005). The unacknowledged convergence of open source, open access, and open science. First Monday 10(8). Retrieved from

It is in the concluding paragraph of this article that Willinsky makes his plea: for universities and faculty members to take a leading role in promoting the “common commitment to a larger public sphere” that he identifies as a common trait of the open source, open access and open science movements. He suggests that just as disparate groups commited to environmental causes had to join forces in order to build a popular environmentatism movement, so should these three groups. The similarities he draws include the important mix of community and competition, people’s motivations for participating and fostering these movement (largely driven by intellectual curiosity and the “addictive economy of ‘cool opportunities'”), “actively rejecting the extension of intellectual property right” (in favour of correct attribution but not of exclusion), an important relationship with patronage (whether at the individual or state level), and support of the Lockian concept of a “commonwealth of learning”.

One of the most interesting aspects of this article is Willinsky’s description of these movements and the factors that influence them in economic terms. He reminds us of the importance of free sharing of information between science clubs in the 17th century, and reminds us that computer software did not start out as a proprietary model, but only becaume thus in the 1980’s. He describes the current intellectual property rules as economically imposed, and places both open source software and open access in clear opposition to this system. Finally, he portrays these movements as means of resistance in the ongoing shift in how we approach and develop knowledge by calling them “practical and proven means of resisting that constant capitalization of knowledge work that marks this economy.”

Jumping on the Linux Bandwagon

Joining the VRE team has heightened in a very urgent way my need for a computer that can speak 2.0. My current G3 iBook has been a wonderful little friend these past years, but despite its ability to surf and help me write papers, it is barely supporting the OS 10.3.9 that is installed on it, and more often than not new versions of software I want to install need more than it can offer. (Not to mention its inability to burn CDs, play DVDs, access streamed video or run Skype, and last but not necessary least, its 12″-screen.)

So it is with much eagerness that I am about to transform my friend Kiley’s old PC (with the assistance of my OSS-Reading-Course teammate Zac) into a Linux machine (where I can be FREE to try out a variety of Open Source software), which will hopefully fill the gaps where my Mac can’t  oblige. I will keep you posted on its progress.

My VRE Glossary

Ajax (Asynchronous JavaScript and XML): supports web based applications in the interchange of data between server and client

Audience (in Drupal): with Communication Tools (e.g. forums) allows to select which groups will see a particular post or thread

Canarie: Canada’s Advanced Network / Le réseau évolué du Canada; non-profit membership-based organization devoted to supporting advanced web projects

Community of interest: a community of people who share a common interest, although they may differ greatly in other ways

Content types (in Drupal): basic means for organizing the content in Drupal, using pre-defined or user-specified terminology

DDI: Data Documentation Initiative — “an international project to create a standard for information describing social science data” (from DDI Wikipedia entry)

Disposable screencasts: quickly (and cheaply) produced screencasts that can be tailored to specific and immediate needs, then disposed of once the technology/needs change

DotProject: web-based Open Source project management software

Drupal: Open Source content management software (CMS) with active user community

Eating our own dogfood: VRE Dev Team speak; being sure to pay attention to work/changes we ask for (is that right?)

EML: Ecological Metadata Language; XML standard developed by and for the ecology discipline (could be used for Critter DB)

Fedora: digital repository system, known for supporting a variety of types of objects

Forums (in Drupal): based on Organic Groups

FoXML: Fedora Object XML — a simple XML format for storing Fedora digital objects, as well as for ingesting and exporting diigital objects into and out of Fedora

Ingesting: Fedora-speak; appears to mean something slightly different from “importing”

Jing – software for creating screencast learning tools

LDAP: Lightweight Directory Access Protocol — an Internet protocol that email and other programs use to look up information from a server

LOR: Learning Object Repository — online databases of learning content (many of these exist)

Lucene: information retrieval library used in full-text indexing and searching of the Web, wither local or Internet-wide

METS: Metadata Encoding and Transmission Standard

MODS: Metadata Object Description Schema (standard maintained by the Library of Congress)

Modules (in Drupal): optional software components that make up Drupal ;designed for specific purposes; can be global or local; similar to FaceBook apps except typically more complex?

Muradora: repository application that supports federated identity (via Shibboleth authentication) and flexible authorization (using XACML); compatibe with Fedora

NEP: either Network Entry Point or Network Equipment Provider (or Needle Exchange Program?)

NeuroDyn: Canadian biotechnology company, PEI-based

Open Conference Systems (OCS): OS system for creating full-service website for conferences

Open Journal Systems (OJS): OS system for publishing and archiving an electronic journal

Pid: (most likely Process ID — or PID tuning software? or pelvic inflammatory disease?)

Regurgitating our own dowgfood: ?

Schema: document that defines the content and structure of a document or group of documents (often referring to XML schema)

Screencast: digital object that uses screen captured video, often with voice-over audio (usually referring to a learning tool = web tutorial); webcast

Script: piece of code written to control a specific aspect of a piece of computer software (often by the end user) but distinct from the application source code

Shibboleth: OS project devoted to federated identity-based authentication and authorization infrastructure — information about users in one security domain can be provided to other organizations in a common federation (also a notable West Wing episode)

Sliced-Book Navigation: Drupal module that creates a menu sub-item in menu structure when a child item is created in the site

Taxonomy: hierarchically structured classification system designed to organize and provide a systematic categories for a specific area (in the case of the VRE, these can be preexisting field-defined systems in XML that can be imported into applicable VREs)

TinyMCE: type of WYSIWYG (or WYSIWYAG) editor

Type ahead: software feature that allows users to continue typing at whatever speed, and if the receiving software is busy at the time it will be called to handle this later

Vertical application: software defined for a very narrow, specific market