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
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
Chimera demo at UCSF for biochemistry students from the University of San Francisco	Dec 6 2011	X-ray tomography of Saccharomyces pombe, structure of dipeptide epimerase
Structural biology seminar at Purdue University	Nov 30 2011	Hypothetical modeling of α-crystallin and HIV capsid and RNA
Enzyme Function Initiative Advisory Committee Meeting	Nov 30 2011	Structure-Function Linkage Database progress and future plans
Lecture for BioE, a joint UCB/UCSF graduate seminar series	Nov 13 2011	Structure-Function Linkage Database introduction and discussion
Talk at joint UCB/UCSF graduate student retreat, Lake Tahoe	Oct 22 2011	Structure-Function Linkage Database introduction and discussion
Talk to new PSPG (Pharmaceutical Sciences and Pharmacogenomics) graduate students, UCSF	Oct 19 2011	Structure-Function Linkage Database introduction and discussion
Talk to new iPQB (Integrative Program in Quantitative Biology) graduate students, UCSF	Oct 18 2011	Structure-Function Linkage Database introduction and discussion
Demos at UCSF for House Democratic Leader Pelosi and San Francisco Mayor Lee	Aug 16 2011	Chimera stereo graphics, HIV capsid [UCSF News]
Society for Industrial Microbiology Meeting, New Orleans	Jul 26 2011	Structure-Function Linkage Database introduction and discussion
Interview and demo for National Public Radio podcast	May 24 2011	Chimera stereo graphics, HIV capsid [Future Lab: 3D Molecular Visualization]
Enzyme Function Initiative May Meeting	May 24 2011	Structure-Function Linkage Database progress and future plans
Lunch Talk to Faculty, Dept. of Bioengineering & Therapeutic Sciences, UCSF	May 2 2011	Functionally diverse enzyme superfamilies, Structure-Function Linkage Database
Demos at UCSF for candidate graduate students	Feb 11,18 2011	Chimera showing virus and T cell EM data, clathrin cages, 3D “printed” plastic models
Seminar at the University of Toronto, Canada	Feb 11 2011	Cytoscape and RBVI plugins
Enzyme Function Initiative (EFI) meeting, UCSF	Jan 13 2011	SFLD functionality, Cytoscape protein similarity networks
UCSF Tetrad graduate program macromolecules discussion group	Dec 8 2010	Discussion and visualization of myosin thick filament regulation
2010 Pathway Tools Workshop, Menlo Park, CA	Oct 25 2010	Invited talk “Annotation Error in Public Databases” discussing SFLD and Cytoscape similarity networks
Intelligent Systems for Molecular Biology (ISMB) 2010 Birds of a Feather session	Jul 13 2010	Network analysis in Cytoscape
ISMB 2010, Boston, MA	Jul 11 2010	Technology track presentation on Cytoscape 2.7 and new plugins
Enzyme Function Initiative (EFI) meeting, UCSF	Mar 16 2010	SFLD, Cytoscape protein similarity networks
Molecular Animation Workshop at UCSF sponsored by the RBVI and the National Center for Macromolecular Imaging (NCMI)	Feb 25-26 2010	Discussions of approaches and technology needs for molecular animation
Biophysical Society Meeting, San Francisco, CA	Feb 21-23 2010	National Center for Research Resources (NCRR) booth: intro to Chimera, animation, Cytoscape
Seminar for Systems Biology group at Institut Pasteur, Paris, France	Sep 28 2009	Uses of Cytoscape for phylogenetic analysis and cheminformatics
Demo at UCSF for NIH visitors from Clinical and Translational Science Awards (CTSA)	Sep 1 2009	HIV spike tomography, T cell tomography, clathrin cage animation, Cytoscape
Biophysical Society Meeting, Boston, MA	Mar 1-3 2009	National Center for Research Resources (NCRR) booth: intro to Chimera, visualizing EM data, animation, Cytoscape structureViz
AMBER Developers Meeting, St. Simons Island, GA	Feb 28 2009	AMBER-related Chimera features and development plans
Demonstration for supporters of the UCSF School of Pharmacy	Dec 11 2008	Visualization of the RNA genome of influenza virus in EM tomography data using LCD stereo glasses, Space Navigator input device, and Phantom force feedback input device
National Center for Research Resources (NCRR) PI meeting, Bethesda, MD	Nov 13 2008	Chimera multiscale modeling capabilities with animations of rat brain data and Space Navigator use
Demonstration for University of San Francisco organic chemistry students	Jul 31 2008	Chimera and Cytoscape
Intelligent Systems for Molecular Biology (ISMB) 2008, Toronto, Canada	Jul 22 2008	Technology track presentation on structureViz: Cytoscape and Chimera
National Center for X-Ray Tomography software discussion, Lawrence Berkeley National Laboratory, CA	Feb 6 2008	Working with tomographic data in Chimera
Biophysical Society Meeting, Long Beach, CA	Feb 3-5 2008	National Center for Research Resources (NCRR) booth: intro to Chimera, new features, visualizing EM data, using the SFLD

Engaging Youth in Science

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 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	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
COSMOS students	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
SEP SMART team students from Lincoln High School	Dec 10 2009	Presentations on focus proteins: P-glycoprotein, HIV protease
SEP SMART team students from Galileo High School	Dec 1 2009	Presentations on focus proteins: HIV rev, caspase-3, strictosidine synthase
COSMOS students	Jul 14 2009	Stereo visualization, virus structures, protein and DNA
Celsius and Beyond summer camp students, ages 9-12	Jul 15 2009 Jun 24 2009	Virus visualization with Chimera, special-purpose input devices, paper virus models
SEP high school teachers, Current Science Seminar Series	Jun 11 2009 May 21 2009	Stereo visualization of man-made molecular machines and viruses, paper virus models
SEP students from Lincoln High School	Jan 14 2009	Viewing a nanomachine and the enzyme mevalonate kinase in stereo
Elementary- and middle-school-age students (Kids at UCSF Day)	Apr 24 2008	Presentations on “What causes colds and flu?” with interactive computer graphics and paper virus models
Students from Lincoln High School	Apr 17 2008	Chimera demonstration
High school students	Apr 4 2008	Chimera display of EM data and crowded cellular environments