Outreach
One of the key missions of the TCB Group is community outreach, as envisioned through the categories of Service, Training, and Dissemination. The following projects exemplify this outreach.
Service
"Service", as defined by the NIH, primarily regards the sharing of an actual physical resource with other groups institutions. The canonical example is an electron microscope - one institute owns and runs the equipment, but many groups get to use the microscope using the web.
The TCB Group regularly invites speakers to Urbana to give seminars on a variety of scientific topics related to our studies. These seminars are announced through email and over the web. Records are maintained in our extensive Seminar Database, going back to Fall 1996; the source code for this database is available here.
The TCB Group is dedicated to helping both the biomedical community, and the computational world as a whole, by sharing the knowledge developed while administering the group internally. This knowledge is shared in the user and sysadmin documentation libraries. Addititionally, source code can be found as part of the MDTools library.
Training
"Training" refers to classes, workshops, lectures, and other situations where the Group's knowledge is explicitly shared with those outside the group in a formal or semi-formal setting.
For those looking for an introduction to VMD and NAMD, or to hone their skills with either program, self-guided tutorials on each program are available. In the VMD Molecular Graphics Tutorial, participants build an image of ubiquitin as a means of learning basic VMD commands. In the NAMD Tutorial participants learn how to set up basic molecular dynamics simulation, to understand input and output files, and to accomplish other tasks using NAMD. Tutorial text is available in web and pdf format, and files needed for the tutorials are provided for download.
The TCB Group's case studies exploit the molecular graphics program VMD for teaching molecular cell biology. The case studies start out like a conventional textbook chapter, but utilize VMD molecular graphics to offer a much more detailed view of the subjects than commonly possible in textbooks.
A set of tutorials that introduce participants to the scientific pursuits of the TCB group, as well as methods and tools for scientific research. Topics include parameterization, evolution of protein structure, topology files, interactive and steered molecular dynamics, and water permeation through nanotubes. Tutorial text is available in web and pdf format, and files needed for the tutorials are provided for download.
The TCB Group has hosted a number of workshops on Molecular Dynamics and Cluster Building in locations across the country (and beyond!). Our web site not only offers reports on these workshops, but offers the same materials used by the participants, allowing users to reproduce much of the material from home.
TCBG faculty members teach a variety of classes, from the traditional classroom format on the University of Illinois Urbana-Champaign campus to short-term mini-courses for external organizations. The focus of these courses has included amongst others biomolecular physics, theoretical biophysics, non-equilibrium statistical mechanics, and quantum field theory.
Dissemination
"Dissemination" is the transfer of information developed or gathered by the Group into the community. Our primary Dissemination tool is, of course, the World Wide Web and this web site; the following pages are specifically helpful towards this information transfer.
The TCB Group maintains a gallery of images and brochures that visually represent the Group and its science - photos taken of various group events, posters used for presentations at conferences, scientific images prepared for demos, publications, journal covers, and more. These images are regularly used by scientists and others from all over the world in a variety of presentations and publications.
All of the research papers published in the TCB Group are available over the web through our Publications Database. Over 385 papers are currently managed through the searchable system, most of which can be immediately downloaded from our site or the publishing journal. The source code for this database is available here.
