Contact Information:

Resource for Biocomputing, Visualization, and Informatics (RBVI)
University of California, Box 2240
600 16th Street, Rm N472E
San Francisco, CA 94143
Email: tef [at] cgl.ucsf.edu

Assistant: Cheryl Cain
Cheryl.Cain [at] ucsf.edu

Education/Affiliations:

Research Interests:

My research focuses on developing cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualization and analyses of molecular structures and related non-structural biological information. Our tools are applied daily to diverse types of biomolecular data, including atomic-resolution coordinates, 3D cryo-EM and x-ray density maps, light microscopy data sets, and protein and nucleic acid sequences, annotations, and networks. Our primary research efforts are in the interactive visualization and analysis of structures of molecules and molecular assemblies, protein sequence-structure relationships, and network representations of protein similarity, binding interactions, and biological pathways. These areas are critical for addressing important and highly relevant biomedical problems such as identifying the molecular bases of disease, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. Our lab has a strong track record of creating well-documented robust software tools and disseminating these via our web site (https://www.rbvi.ucsf.edu) so that other scientists can advance their own research programs effectively. Our current efforts in this regard are focused on ChimeraX.

Potential students and postdocs please note: I moved to emertius status in July 2019 and am no longer taking students or postdocs into the lab. Our research efforts are now exclusively built around a team of dedicated full-time professional research scientists. We welcome creative contributions to our research projects, which you can do through the addition of new "plug-in" tools to our ChimeraX visualization application. Please see ChimeraX Toolshed.

Also see my UCSF Profiles page.

Awards:

I've received several awards over the years, but because of the broad and significant impact my work has had on my UCSF colleagues, feel most honored by this 1998 Academic Senate University Service Award that acknowledges the contributions I made to the early development and implementation of the UCSF data network, including implementing a 56 kbps link to the ARPAnet in 1982 and the founding (together with colleagues from other local Bay Area universities) of BARRNet in 1986 that linked UCSF to NSFnet, the precursor to today's Internet.

Selected Publications:

PubMed search of all publications authored by T.E. Ferrin, or view my Google Scholar Profile.

Some Invited Lectures and Seminars:

From Long, Long Ago:

Molecular graphics for visualizing proteins and drugs (1980):
The Computer Revolution in Biomedical Science
Interactive Molecular Graphics (video, 13:39 minutes -- no audio track)
My UNIX kernel-hacking days (late 70's / early 80's) -- Adding interactive graphics to UNIX:
Interactive Computer Graphics and the UNIX Time-Sharing System (1979)
Picture System 2 Graphics Subroutine Package (ps2gsp)
Modifying PDP-11/70 hardware instructions and the Letter reprinted from ;login: that raised a few eyebrows (1978)
Our Unix Version 6 License from Western Electric Co. (1976)
Twenty Years of Berkeley Unix by Marshall Kirk McKusick
The Daemon, the GNU, and the Penguin: A History of Free and Open Source by Dr. Peter H. Salus
BSD and the Computer Systems Research Group (CSRG)
CSRG Members, Supporters, and Contributors
Young and (maybe a little) Reckless -- My drag racing days (late 60's):
Ky Michaelson's AA/GD dragsters [picture (1970)]
The Snow Dragster
Hydrogen Peroxide Rocket Dragsters

Other Fun / Interesting Links: