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Selected Presentations and Dissemination Activities
RBVI researchers, collaborators, and staff members regularly present their
work at workshops, conferences, and other scientific meetings
to share results and techniques, to get input on development directions
for existing and new tools, and to explore needs within the biomedical
research community. The following table lists selected presentations.
See also Engaging Youth in Science (below)
and RBVI Workshops and Training.
| Event |
Date |
Topics |
| Enzyme Function
Initiative three-year review |
May 29 2013 |
Vision for the Structure-Function Linkage Database
for the next five years |
| Biocuration 2013
(International Society for Biocuration conference), Cambridge, England |
Apr 5 2013 |
Protein function curation: linking sequence & chemical reaction spaces
in the Structure-Function Linkage Database |
| VIZBI 2013
(Visualizing Biological Data), Broad Institute, Cambridge, MA |
Mar 20 2013 |
Network visualization |
| Conference on Predicting Cell Metabolism and Phenotypes,
SRI International, Menlo Park, CA |
Mar 4 2013 |
Short introduction to the Structure-Function Linkage Database |
| Demos at UCSF for candidate graduate students,
Integrative Program in
Quantitative Biology |
Feb 8, 15 2013 |
Chimera visualization of a variety of systems, including satellite
tobacco mosaic virus, differential gear nanomachine, X-ray density maps,
white blood cell 3D motion, HIV reverse transcriptase inhibitor binding |
| HCI (Human-Computer Interaction) Korea annual conference |
Jan 31 2013 |
Visualization challenges in network biology |
| Biophysics seminar at the
University of Texas Southwestern Medical School, Dallas, TX |
Jan 29 2013 |
Protein similarity networks and
the Structure-Function Linkage Database |
| Integrative Program in
Quantitative Biology pizza talk, UCSF |
Jan 21 2013 |
Introduction to the Structure-Function Linkage Database |
| Cytoscape retreat (Gladstone Institutes, UCSF) |
Dec 13 2012 |
Protein similarity networks and dissemination using
the Structure-Function Linkage Database |
| Lunch talk to faculty, Department of Bioengineering and Therapeutic
Sciences, UCSF |
Dec 2 2012 |
The Structure-Function Linkage Database and enzyme
functional annotation |
| Enzyme Function
Initiative meeting, San Francisco, CA |
Nov 8 2012 |
New features in the Structure-Function Linkage Database |
| 5th International Conference on Paraoxonases, Columbus, OH |
Jul 16 2012 |
Research on the “nucleophilic attack 6-bladed beta-propeller”
(N6P) superfamily, including network analysis and data dissemination using
the Structure-Function Linkage Database |
| Lecture for UC systemwide Bioengineering Symposium, Berkeley, CA |
Jun 21 2012 |
Computational guidance for protein design, including superfamilies,
networks, and use of the Structure-Function Linkage Database |
| Enzyme Function
Initiative meeting, San Francisco, CA |
May 23 2012 |
Structure-Function Linkage Database progress and future plans |
| Demos for UCSF Alumni Homecoming |
Apr 21 2012 |
Molecular visualization with Chimera, stereo graphics |
| NASA AbSciCon meeting, Atlanta, GA |
Apr 18 2012 |
Enzyme evolution, networks, and the Structure-Function Linkage Database |
| Planetarium dome animation shown multiple times in the
Biomolecular
Discovery Dome at the Biophysical Society
56th Annual Meeting, San Diego |
Feb 26-27 2012 |
Molecular machines that replicate HIV RNA, 6-min. animation with music
and narration
[HTML storyboard]
|
| Demos at UCSF for VIP guests attending the Byer's Lecture |
Feb 23 2012 |
Chimera visualization of HIV, stereo graphics |
| Demos at UCSF for candidate graduate students,
Integrative Program in
Quantitative Biology |
Feb 10, 17 2012 |
Chimera visualization of HIV |
| Seminar at Institut Pasteur, Paris, France |
Feb 2 2012 |
Network biology and Cytoscape |
| Stereo graphics demonstration for
Li Ka Shing
Foundation |
Jan 9 2012 |
HIV core particle |
The RBVI is involved in several educational activities targeting students
of high-school age and younger. The visual, interactive nature of molecular
graphics combined with increasing awareness and interest of the general
public in topics such as viruses and DNA make Chimera well suited for
reaching out and engaging students of a wide range of ages and backgrounds.
Along these lines,
Chimera has been included with educational materials produced by
the Howard Hughes Medical Institute (HHMI). Our collaborator
Dr. Joseph DeRisi (Hughes Investigator, Biochemistry and Biophysics, UCSF)
was one of two scientists featured in the HHMI 2010 holiday lectures,
Viral Outbreak: The Science of Emerging Disease.
The lectures and associated materials are distributed
to high schools throughout the country, and can be
ordered online free of charge.
With the advocacy of Dr. DeRisi, we were invited by HHMI to include a
simple tool for viewing viruses in 3D with Chimera.
Selected presentations to student and educator groups:
| Elementary/High School Group |
Date |
Topics |
| Students from Dewey High School (Oakland)
as part of the iGem program,
a partnership between UCSF and the San Francisco Unified School District |
Mar 8 2013 |
Molecules of life, water, protein, DNA, drugs (THC and nevirapine) |
| California State Summer School for Mathematics and Science (COSMOS)
students, UC Davis program |
Jul 26 2012 |
Chimera visualization of HIV core and drug binding |
| Students from the iGem program,
a partnership between UCSF and the San Francisco Unified School District |
Jun 22 2012 |
Nanomachine and virus visualization, discussion of differences
between human-designed and biological molecular machines |
| High school students in the
Gladstone Summer Scholars (GSS) internship program |
Jun 22 2012 |
HIV virus visualization; electron microscopy, atomic models of
virus core and drug binding |
| High school students from the
Mo' MAGIC program
organized by the UCSF Science & Health Education Partnership (SEP) |
Jun 22 2012 |
Nanomachine and virus visualization, discussion of differences
between human-designed and biological molecular machines |
| Demo at UCSF for high school science teachers
from the San Francisco Unified School District |
Apr 23 2012 |
Molecular visualization with Chimera |
| Students from Balboa High School, Bay Area Science Festival event |
Nov 2 2011 |
HIV capsid structure |
| Swiss high school students, winners of the
Science on the Move science competition
sponsored by Roche and Genentech |
Sep 20 2011 |
HIV capsid structure |
| California State Summer School for Mathematics and Science (COSMOS)
students, UC Davis program |
Jul 28 2011 |
Virus capsid structures, influenza hemagglutinin |
| High school students from the
Mo' MAGIC program
organized by the UCSF Science & Health Education Partnership (SEP) |
Jun 23 2011 |
Structure of HIV capsid and RNA
[HTML] |
| SEP SMART team students from Lincoln and Galileo High Schools |
Nov 18 2010 Dec 2 2010 |
Spirochetes, flagella, handedness, morphing, hydrophobic and electrostatic coloring to identify transmembrane and binding regions |
| California State Summer School for Mathematics and Science (COSMOS)
students, UC Davis program |
Jul 22 2010 |
DNA and chromosome structure |
| Celsius and Beyond summer camp students, ages 8-12 |
Jul 7,21 2010 Jun 9 2010 |
DNA and chromosome structure, light microscopy time series of dividing cells |
|