picture of Timothy Lenoir

Tools for enabling collaboration in research and teaching

In order to enable the web-based research collaborations such as the STIM and Bioinformatics, and videogames projects, I have assembled a lab for developing collaborative research tools. Among the tools we have developed are:

Interactive Collaborative Timelines
This tool allows a community to construct multiple parallel timeline categories representing various structural dimensions significant to the development of a research field (or just about any subject of interest). Events can be added to the timeline by any member of the designated community together with any documentation related to the event, including original documentation to be stored in our database, or links to already existing documentation on the web. Links with commentary and accompanying documentation can be drawn between events deemed to be closely connected. Events can be "flagged" by members of the community for importance. The entire structure can be filtered to reflect the views of individual contributors or groups of contributors. All levels of the timelines, including events, commentary, and links are supported by a forum-type threaded discussion that is fully searchable.

Interactive Web-based Genealogy
This tool allows a community to document its lineage. Authorized community members can enter their own profiles, general information, and contact data. Publication information can be uploaded. Publication data in generally supported formats, such as PubMed, will be automatically linked to the corresponding abstract and full-text version of a document if it is made available for us to database. The "offspring" of the individual is generated in a scalable window to enable easy viewing of that individual–s location in the family tree. Links to other members of the tree are generated for rapid navigation. The user can edit his/her entry and add ancestors and descendants. If the contact information for these individuals is included, they are contacted automatically by email and asked to contribute to the genealogy. Multiple options are provided for initiating threaded discussions, either about individuals themselves, or commentary on their positioning in the tree. The program also supports the capability to add "outsiders" (individuals who are not descendants of a member of the tree), and hence, it can support the representation of multiple genealogies. The genealogy tool has several reconfigurable features for personalized use, and it can be used to trace lineages of groups of individuals, organizations, products, concepts, and many other uses.

Forum and Video Chat Rooms
Forum discussion spaces are among the standard toolkit for online communities. We have traditionally linked to third-party clients in order to incorporate this feature into our collaborative web spaces. However, this option has not been particularly helpful for archiving the conversations in the forum for future scholarly use; nor has it been advantageous for building a seamlessly integrated collaboratory. Building on the commentary and annotation functions in the timelines and genealogy programs above, we have recently built forum software to support our own research groups.
Another useful tool we have incorporated into our collaborative workspaces is video chat with whiteboard capability. We use this feature to facilitate preparation of projects and class presentations.

Integrated Collaboratory Environment for Teaching and Research
The various component elements described above (timeline, genealogy, forum, video chat) have been deployed singly or in combination in several of the projects described above. All of these tools have been brought together recently in an integrated environment for supporting both research and teaching. The best example is my course, Science and Technology in the Silicon Valley, offered at Stanford (winter quarter 2003). This course uses all of these features in a seamless, integrated framework linking ongoing research and data collection to teaching. In addition this course takes advantage of high bandwidth internet video conferencing capabilities of the Wallenberg Learning Center to provide a face-to-face small group seminar setting in which students from the Georgia Institute of Technology led by Professor Steven Usselman convene for a three-hour weekly seminar with a group of Stanford students.

Transgenic Light
Transgenic Light was a collaborative experiment among Tim Lenoir, Nancy Anderson, Ben Dean (Stanford University Digital Art Center—SUDAC), Casey Alt, and Zach Pogue exploring the aesthetics of images produced using Green Fluorescent Protein (GFP). GFP is a bioluminescent molecule naturally produced by the glowing Pacific Northwest jellyfish Aequorea victoria. In the early 1990s scientists began using the protein produced by the GFP gene as a fluorescent reporter molecule for the visualization of intracellular processes in nearly every laboratory organism, including yeast, bacteria, fruit flies, frogs, zebrafish and more. In order to view GFP-tagged protein molecules in organisms, researchers employ a diverse range of technologies, including confocal microscopes coupled with sophisticated digital imaging and modeling systems. In doing so, scientists have engineered these new transgenic organisms as digital media objects right down to the molecular level. Transgenic Light sought to map this rapidly advancing zone of mediation opened up by GFP—a realm that connects several converging strata, including the discursive and the phenomenal, the semiotic and the material, the digital and the organismal, the natural and the artificial, and the scientific and the aesthetic. The installation was on display from 12 June-25 August 2002 at Stanford University’s Cantor Center for the Visual Arts.

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