Scientists as Writers: Using a content management system to promote

collaborative writing in the sciences (and beyond)

Ken Bolton, Eric Eberhardt, Cristian Opazo

Vassar College

NERCOMP Annual Conference 2006

Project abstract and outline of talk

A team of faculty, technologists, librarians and writing specialists at Vassar explored the use of the Plone content management system as a tool for collaborative writing in a senior-level science course. We present a review of our experience and plans to extend the use of this technology beyond the sciences.

• Project motivation; pedagogical goals (EE)

• Instructional design; team coordination; user’s training (CO)

• CMS identification, implementation and administration (KB)

• Final discussion; future directions (EE)

Project motivation

• Protein Chemistry course at Vassar College– Required for biochemistry majors– elective for chemistry majors– Typically 8-12 students; no laboratory

• Strong primary literature component– Critical evaluation and experiment interpretation

– Strong one-on-one faculty-student interactions

• Fall ’05: Doubling of enrollment (24 students)

• Book contract to write a primer on emerging areas in the chemical and life sciences

• Idea: Why not have students develop preliminary bibliography as part of the course?

Pedagogical goals

• Translate emerging areas in the chemical and life sciences into a classroom activity

• Develop scholarship and writing skills of future generation of researchers

• Create opportunities for students to access and gain ownership in these emerging areas and examine the implications of these emerging areas for disease diagnosis and treatment

Topics: emerging areas in the chemical and life sciences “-omics”

• Genomics

• Transcriptomics

• Proteomics

• Metabolomics

• Pharacogenomics

• Kinome

• Chemical biology

• Systems biology

• Bioinformatics

Case studies: how these emerging areas are being

used in the context of current medical issues Examples of student project choices:

• HIV/AIDS: current targets and strategies, genetic diversity in an area -pharacogenomics

• Cell cycle control and how small molecules impact cell growth and regulation: Chemical biology and cancer therapies, Crohn’s disease

• Metabolomics: protein turnover related to prions or “Mad Cow’s” disease, chronic wasting disease

• Pain Relief: Vioxx

Student-faculty collaboration/mentoring process

• Identification of leading citations

• Identification of leading scholars on each of the emerging fields studied

• Development of specific project outline

• Review of bibliographic elements

While working with students individually, it is important to focus on:

Significant changes in science primary literature search engines and bibliographic tools over the

past decade

Then:

• Science citation index

• Chemical Abstract Service (CAS)/STN

Also considered:

– RefWorks (site license)

– Endnote (expensive)

Now:

• Web of Science

• ACS publications

• Scifinder Scholar (CAS)

• PubMed

Almost all is full text and available online!National Digital Library, commercial search engines,

scholar homepages, Wikipedia

Importance of a dedicated science librarian to train students in these tools

Pedagogical advantages and disadvantages of collaborative writing

Advantages

• Higher quality final product

• Leveling of student skills

• “Real world” experience

• Learning to communicate across disciplines

• Chemist, Biochemist and Biologist in each group

Disadvantages

• Group management

• Student accountability

– Individual grades

• Individual skill development

Teaching and Learning Center to support writing activities

Could technology solve my instructional dilemma?

• Need to maintain the core pedagogical goals

• Given the on-line nature of scientific primary literature, could we compile a bibliography with accessible PDF articles for evaluation of student papers?

• Does an appropriate technology focused on collaborative writing even exist?

• If so, is this technology seamless?

– Students should keep focused on the subject matter and not spend excessive time learning a new software tool

Implementing a pilot project in the college curriculum means high stakes

• A curricular pilot project like this is a golden opportunity to break new ground in the use of technology in the classroom -but stakes are high…there’s no rehearsal possible

• Identify all players; define roles; elaborate plan and stick to it

• Success will come only as a result of full commitment from all parts involved

Instructional technology comes in

Our role as instructional technologists include:

• Identify and clarify the needs of the project

• Identify technologies that meet those needs

• Research the field and determine what has been done and how

• Implement and deliver instruction on the technology tools chosen (workshops, one-on-one sessions)

• Provide leadership and facilitate communication and collective work of various college constituencies that will play a role

A very particular set of needs

• Need for storage, sharing and remote access of documents

• Technology should allow collaborative writing between students as a main feature

• Need for creation and management of a large set of bibliographic references

• Technology should be simple, efficient, customizable and inexpensive

• Technology should facilitate curricular goals, instead of being a hurdle

We need an online system that allows collaboration betweenstudents and instructor, and among students themselves.Specific needs follow:

Academic technology support team

• Two instructional technologists (CO: overall coordination; KB: system administration)

• A science librarian (Flora Grabowska, Vassar Libraries)

• A writing specialist (Natalie Friedman, Learning and Teaching Center)

A team-approach like this requires a continuous process of

coordination and communication

Specific instructional and technical challenges

• Identification, deployment and testing of a Content Management System (CMS)

• Challenges: hardware allocation, system administration, functionality, accessibility, authentication, backup strategies, etc.

• Plan and schedule rollout

• Plan and schedule team and student instruction

Team and student instruction in the use of a Content Management System

• The system was demonstrated to the other members of the team and the faculty member in separate, individual sessions.

• Students were trained in out-of-class mandatory sessions (4 sessions during first two weeks; 2 more sessions later on)

• Just basics (creating documents, uploading external files, basic editing)

• First assignments were simple 1-page literature reviews by groups of three students with the goal of testing their response to the new system

Goals for technical outcomes

• User Authentication

– LDAP, User Groups

• Collaborative Writing

– Blog, Wiki, Change Tracking, Version Tracking

• Client Application Integration

– PDF, MS Word -- how cool if students could search inside files stored in the site?!

• Bibliographies

– Web, journal, book references

Possible solutions

• Blackboard

• Moodle

• MovableType

• Drupal

• Plone

We chose Plone

• maturity, with a polished user interface

• stability, running on Linux and legacy hardware

• flexibility, speaks standards

• low total cost of ownership

• scalability, with Zope Enterprise Objects (ZEO)

• add-on products that met our needs

Plone is a Content Management System (CMS) built on the

Zope Object Publishing Environment that has:

Also, we had some in-house knowledge and experience in

the use of Plone

Implementation

• Initial Plone/Zope instance lived on a x86 Linux desktop.

• Used out-of-the-box user and group tools to manage account creation and secure the system.

• Installed add-on products to extend functionality:

– CMFBibliograhyAT & ATBiblioList; add/edit/import/export/organize

– PloneExFile; file that

– PloneArticle

• Added accounts and groups

The main page

The main page presents tab navigation, a navigation portlet, and a content area. In this case, the content area is made up of content panels, including an RSS feed of recent changes.

Adding an article (authoring a new page)

Users can add several types of objects to the site

Editing an article

The WYSIWYG Kupu editor provides a familiar word-processing experience

A bibliographic reference

A full bibliography

Individual (group) bibliographies are being automatically collected into a single combined project bibliography

Integration with external files; e.g. PDF

Previewing text content from anexternal PDF document

Searching for content

Start typing in the search field and the results come up immediately

Successes

• Massive, concise bibliography

• User’s difficulties with the system were mostly related to performance of back end (speed) rather than front-end functionality

• One instance of questionable academic integrity was successfully detected (automatic time-stamps)

• Ability to search text through all site objects, including external PDF and MS Word documents

Shortcomings

• Speed was an issue (when you run on rusty iron, expect tetanus)

• Blogs and wiki tools went mostly unused, though they were available

• No document history, though recently installed CMFEditions tool resolves this

Some stats

• 14 weeks

• 24 students

• 1 instructor, 1 librarian, 1 writing specialist, 2 technologists

• 1184 total items in the database

• 496 bibliographic references

• 252 MS Word & PDF files uploaded

• 201 image files uploaded

• 78 pages & articles authored

• 14 link objects created

Other CMS uses we are exploring

• ePortfolio prototyping

• In-house CMS/portal

• Prototyping environment

• Group workspace

• Place to put older websites that need updating

• Giving presentations!

A view of a finished article

• HIV-1 Protease: Research at the Edge of Chemical Biology and Enzymology

by Emily Bruce, Adam Goldman-Yassen and Philipose Mulugeta

http://mcload.vassar.edu/protein_chem/CBE/hiv-1-protease-paper/plonearticle.2005-11-21.3393415847/

Some lessons learned

• Choice of CMS an appropriate one for our specific needs

• When encountering some missing functionality or a process that does not work as expected, it can be modified! (The system is not broken, but rather set differently to user’s expectations)

• Deal with user's expectations (e.g. using a CMS is different than using a tool like MS Word, and team-writing adds to the sense of difference)

Student’s opinions

• Plone was indispensable with our group project mainly because it allowed us to work on a joint paper on our own time. Apart from eliminating hours spent on sending out .doc files with various edits around, it allowed us to review what an author did at last login and add comments as well as content on the fly.

• The killer application was the combined bibliography. It allowed us to avoid duplicated efforts at finding references. In my opinion, without this feature it would have been a nightmare to write our paper.

• I think Plone was a great communication resource, especially when I was away from campus and had no other means of sharing information with my group colleagues. In fact, without Plone it would have been impossible for me to keep up with the work on both group and individual parts of the project when I had to leave campus.

Why was all this worth the effort?

• Some outstanding papers came as result of student work

• Big advantage for time management:

– Students: ease in collaborative writing (avoid conflict in different versions of a document by having a single one at all times)

– Faculty: ease in grading group vs. individual student papers

• Benefit of having a single web location where all these materials reside -which translates in easier evaluation and grading of student work

Future directions

• Reimplementation with include full assessment in order to measure educational effectiveness

– A challenge: to identify a source of funding to implement a full assessment

• This project served the purpose of building a concrete bibliographic database that will be used in the writing of a textbook in emerging areas of the chemical and life sciences

Acknowledgements

• Steve Taylor (Director, Academic Computing Services)

• Natalie Friedman (Writing Specialist, Vassar College Teaching and Learning Center)

• Flora Grabowska (Science Librarian, VC Libraries)

• Vassar College