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Scientists as writers
by
Ken Bolton, Eric Eberhardt and Cristian Opazo
—
last modified
2006-03-27 16:58
Contributors:
Ken Bolton, Eric Eberhardt, Cristian Opazo
Copyright Ken Bolton, Eric Eberhardt, and Cristian Opazo, 2006. This work is the intellectual property of the authors. Permission is granted for this material to be shared for non-commercial, educational purposes, provided that this copyright statement appears on the reproduced materials and notice is given that the copying is by permission of the author. To disseminate otherwise or to republish requires written permission from the author.
Using a content management system to promote collaborative writing in the sciences (and beyond)
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 training (CO)
- Identification, implementation and administration of system (KB)
- Final discussion; future directions (EE)
Project motivation for course redesign
- The course
- Protein Chemistry: required for biochemistry majors, elective for chemistry majors (no laboratory)
- Strong primary literature component
- critical evaluation and experiment interpretation
- strong one-on-one faculty-student interaction
- The field has evolved since I first taught the course
- Enrollment: typically 8-12 students
- Fall '05: doubling of enrollment (24 students)
- Book contract to write a primer on emerging areas in the chemical and life sciences
Pedagogical goals
- To bring these emerging areas in the chemical and life sciences into a classroom activity
- To develop scholarship and writing skills of a future generation of researchers
- To create opportunities for students to access and gain ownership in these emerging areas in order to examine the implications of these areas in their future careers
Student project: write a collaborative scholarly review article
- Online bibliography
- Select a specific disease or case study
- Emphasis on new technologies driving the research in these emerging areas
Topics: emerging areas in the chemical and life sciences ("-omics")
- Genomics
- Transcriptomics
- Proteomics
- Metabolomics
- Pharmacogenomics
- 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:
- Pharmacogenomics- HIV/AIDS: current targets and strategies, genetic diversity in an area
- Chemical biology- Cell
cycle control: how small molecules impact cell growth and regulation;
Chemical biology and cancer therapies; Crohn's disease
- Metabolomics- Mad Cow disease: chronic wasting disease protein; turnover related to prions
- Proteome- Vioxx: pain relief
Student-faculty collaboration/mentoring process
Individual project development:
- Identification of leading citations
- Identification of leading scholars on each of the emerging fields studied
- Development of specific project outline
- Review of bibliography
Student skills development:
- Conducting citation searches
- Writing skills
- Scope of the field
Significant changes in science primary literature search tools over the past decade
| 10 years ago: | Now: |
|---|---|
|
|
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 | Disadvantages |
|
|
Learning and Teaching Center to support writing activities
Could technology solve my instructional dilemma?
- Need to maintain the core pedagogical goals
- Compile an online
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; develop 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
We
need an online system that allows collaboration between students and
instructor, and among students themselves.
- 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
Academic support team
- Two academic computing technologists (CO: overall coordination; KB: system development and 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 CMS
- 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 single-page literature reviews by groups of three students with the goal of testing their response to the new system
Technical requirements
- 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 through the content of documents stored in the site?
- Bibliographies
- Web, journal, book references
Solutions considered
- Blackboard
- Moodle
- MovableType
- Drupal
- CVS / Subversion
- Plone
We chose Plone
Plone is a content management system built on the Zope Object Publishing Environment that has:
- maturity, with a polished user interface
- stability, running on multiple platforms and legacy hardware
- flexibility, speaks and presents standards
- low total cost of ownership
- scalability, with Zope Enterprise Objects (ZEO)
- add-on products that met our needs
We also had some in-house knowledge and experience.
Implementation
Initial Plone/Zope instance lived on a PC 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 bibliographic entries
- PloneExFile; type that supports cataloging of MS Word & PDF files
- PloneArticle; structured document with images, links, and files attached
- ZWiki; collaborative writing environment
The main page
The main page features navigation tabs and a content area with a RSS feed of recent changes. The basic folder structure of the whole project can be seen in the left navigation portlet.
Add an article
The add item button has been activated in this image. An article is a Plone type that lets the user author a webpage from scratch.
Create/edit an article
A WYSIWYG editor provides a familiar writing interface.
A bibliographic reference
Catalogued bibliographic entries with notes, links, and an embedded link to the PubMed entry.
A bibliography folder
Results are sorted by year and author. "Smart" bibliographies can self-populate based on user-defined criteria.
An image folder
Wiki change tracking
An example of collaborative editing and change tracking using a wiki.
Text preview of a PDF
An uploaded PDF is catalogued by the system and a text preview is rendered.
Finding content
Start typing in the search field and the contextualized results come up quickly, including document-type icons.
Successes
- Massive, concise bibliography
- User's difficulties with the system were related to back-end performance (speed), rather than front-end functionality
- One
instance of questionable academic integrity was successfully detected
(every change in the site generates an automatic time stamp)
- Ability to search through all site objects, including external PDF and MS Word documents
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
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 users 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."
A view of a finished project
- "HIV-1 Protease: Research at the Edge of Chemical Biology and Enzymology", by Emily Bruce, Adam Goldman-Yassem and Philipose Mulugeta
Why was all this worth the effort?
- Some outstanding papers came as result of student final projects
- Big advantage for time management:
- Students:
ease in collaborative writing (avoid conflict in working with different
versions of a document by having a single instance of it)
- Faculty: simplifies critical evaluation of student papers
- Benefit of having a single web location where all these materials reside, which translates to easier evaluation and grading of student work
Future directions
- Reimplementation will 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 focused 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, CIS)
- Natalie Friedman (Writing Specialist, Learning and Teaching Center)
- Flora Grabowska (Science Librarian, VC Libraries)
- Vassar College