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Design Element


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
Demos at UCSF for iPQB program candidate graduate students Feb 10,17 2017 Virtual reality demonstrations of antibiotic bound to E. coli ribosome, crawling neutrophil in collagen filaments
Byer's Award reception, Genentech Hall, UCSF Jan 31 2017 Virtual reality demonstration of antibiotic bound to E. coli ribosome and antibiotic resistance mutations [HTML]
EMBO Conference: Molecular Machines: Integrative Structural and Molecular Biology, Heidelberg Nov 21 2016 Visualization and analysis challenges of large biomolecular complexes, ChimeraX demo [HTML]
Bay Area Science Festival organized by the Science & Health Education Partnership (SEP) at UCSF in partnership with local scientific, cultural, and educational institutions Oct 30 2016 Virtual reality and white blood cells event including crawling neutrophils shown with the Vive VR system and nuclear pore shown with the Oculus VR headset
Virtual reality demo for officers of the University of California Extramural Funding Group Oct 10 2016 Crawling neutrophils shown with the Vive virtual reality system
Invited talk at University of Maryland, College Park, MD Mar 25 2016 Superfamily analysis with protein similarity networks
Demos at UCSF for iPQB program candidate graduate students Feb 12,19 2016 Differential gear nanomachine, HIV reverse transcriptase with the drug tenovofir, light-sheet microscopy of crawling neutrophils, stereo visualization and Oculus Rift virtual reality goggles
Sakanari group meeting, UCSF Feb 3 2016 Superfamilies, the SFLD, and protein similarity networks
InterPro Consortium meeting, EMBL-EBI, Hinxton, UK Jan 2016 Data available from the SFLD including enzyme family annotations and multiple sequence alignments
San Francisco State University Diversity Outreach talk Nov 2 2015 Superfamily analysis with protein similarity networks
San Francisco State University invited talk Oct 2 2015 Superfamily analysis with protein similarity networks
Demonstration for Long Foundation board of directors Sep 16 2015 CellPACK models of large-scale systems such as viruses, 3D visualization of neutrophil migration
Demonstration for Sandler Foundation members and their families Aug 24 2015 Visualization of neutrophil migration with Oculus Rift virtual reality headset
29th Annual Symposium of the Protein Society, Barcelona, Spain Jul 23 2015 Superfamily analysis with the SFLD and protein similarity networks
Invited talk at Swansea University, Wales, United Kingdom Jul 16 2015 Visualization of biological structures and processes
Gordon Research Conference on Enzymes, Co-enzymes, and Metabolic Pathways, Waterville, NH Jul 14 2015 Superfamily analysis with the SFLD and protein similarity networks
Demonstration of molecular graphics-related hardware for visitors from the Universidad Andrés Bello, Santiago, Chile: Dr. Fernando González-Nilo, Director of the Center for Bioinformatics & Integrative Biology, and Dr. Luis Velázquez, Director of the Center for Integrative Medicine and Innovative Science Jul 13 2015 Stereo projector, Oculus Rift virtual reality goggles, Space Navigator input device, Leap Motion Controller, and Phantom force feedback device
American Microbiology Society meeting, New Orleans Jun 2 2015 Superfamily analysis and protein similarity networks
Robot NightLife event at the California Academy of Sciences museum, San Francisco Mar 26 2015 Virtual reality (VR) and kilobot swarm demonstrations: viewing migrating neutrophil cell and Tuscany demos with Oculus Rift VR headsets; kilobot cancer-cell, synchronization, and move-to-light demos
VIZBI 2015 Visualizing Biological Data Conference at the Broad Institute of MIT and Harvard, Cambridge, MA Mar 25-27 2015 Poster on the MultiDomain Assembler in Chimera and creating a model of immature HIV
European Bioinformatics Institute Annotation Workshop, Georgetown University, Washington DC Mar 10 2015 Sequence similarity networks for annotation
Demos at UCSF for candidate graduate students Feb 13 2015 Kilobot demonstration, firefly synchronization model with 100 kilobots, effect of 50% non-cooperating kilobots
Demos at UCSF for candidate graduate students Feb 6 2015 Kilobot demonstration with hands-on programming of swarm robots and discussion of how they can model biological problems
Exhibit for general public attending the UCSF Byers lecture Jan 29 2015 Kilobot T-cell and cancer exhibit with hands-on demo
Multiple Sequence Alignment workshop hosted by the Institute for Pure & Applied Mathematics at UCLA Jan 12-16 2015 Two talks and a poster presentation on the Structure-Function Linkage Database, sequence similarity networks, and Cytoscape

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 our lab well suited for reaching out and engaging students of a wide range of ages and backgrounds.

Along these lines, our software 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
UCSF STEM Career Day for San Francisco high school students Mar 7 2017 Presentations to two groups (90 and 75 minutes) including virtual reality visualization of neutrophil crawling in collagen filaments, antibiotic bound to E. coli ribosome
Science & Health Education Partnership (SEP) San Francisco Health Investigators 4-week program for high-school students Jun 14 2016 Two 45-minute presentations on Zika virus and related topics, including 3D printing, cryoEM and atomic models, protein structure, crawling neutrophils, stereo visualization and Oculus Rift virtual reality
High-school student project to program kilobot swarm robots Jul 6-17 2015 Students developed and tested code over eight days to make kilobots disperse from a cluster to find a target, establish a minimum path to that target, and then move to reinforce that path; they also made movies and gave presentations on their results
San Francisco STEM Career Day for high school students organized by the UCSF Science and Health Education Partnership (SEP) Mar 11 2015 3D visualization, kilobot swarm robots, discussion of careers in science
California State Summer School for Mathematics and Science (COSMOS) students, UC Davis program Jul 24 2014 Chimera molecular graphics showing nanomachine, acetylcholine receptor, hydrophobicity, dendritic cell motion; Space Navigator input device, stereo glasses, Oculus Rift virtual reality goggles; 3D printed plastic models
California State Summer School for Mathematics and Science (COSMOS) students, UC Davis program Jul 25 2013 Multiscale brain visualization with Chimera, including light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, and atomic-level structures of the nicotinic acetylcholine receptor and a neurotoxin from snake venom [HTML]; stereo visualization with LCD glasses, 3D manipulation with Leap Motion Controller and Space Navigator devices
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)

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