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"Outreach and Training" activities for RBVI annual report and competitive grant renewals
This wiki encompasses all RBVI outreach and training activities, not just those related to Chimera.
The overall goal of the training component of the RBVI is twofold: to improve the general understanding of our technologies in the appropriate population and to create a cadre of biomedical researchers trained in the technology so that they can effectively apply it in their own research.
Each entry below should include the following:
- Title of event (e.g., EMBO electron microscopy workshop)
- Nature of training (e.g., hands-on use of Chimera volume visualization tools)
- Date(s)
- Location
- RBVI staff involved
- Hours of instruction (includes lectures, labs, and prep time)
- Number of attendees
- Comments/remarks/related URLs (e.g., students brought their own data sets for analysis)
2012/2013 report
April 21, 2012
UCSF Alumni Homecoming Demonstrations. A series of 30 minute demonstrations were given to several groups (about 100 individuals overall) of UCSF alumni from the Schools of Medicine and Pharmacy, and the PhD programs.
- Tom Ferrin
April 23, 2012
Molecular visualization demonstration for 10 high school science teachers from the San Francisco Unified School District.
- Tom Ferrin
April 27, 2012
Full day Cytoscape workshop for 30 participants at the University of Missouri.
- Scooter Morris
April 28, 2012
2 1/2 hour Chimera workshop for 25 participants at the University of Missouri.
- Scooter Morris
June 22, 2012
Nanomachine and virus visualization demo for 11 iGem students ages 17-19. 30 minutes, stereo visualization in viz vault, discussion of differences between human designed and biological molecular machines. 1 hour preparation. Organized by Shannon Noonan, Community Outreach Specialist, Gladstone Institutes.
- Tom Goddard
June 22, 2012
HIV virus visualization demonstration for 7 high school students in the Gladstone Summer Scholars (GSS) Internship Program. Looked at electron microscopy and atomic models of virus core and drug binding. 30 minute demo in viz vault. 1 hour preparation. Organized by Shannon Noonan, Community Outreach Specialist, Gladstone Institutes.
- Tom Goddard
June 22, 2012
Nanomachine and virus visualization demo for 6 Mo Magic high school students. 30 minutes, stereo visualization in viz vault, discussion of differences between human designed and biological molecular machines. 1 hour preparation. Sponsored by Patricia Caldera, UCSF, Science & Health Education Partnership.
- Tom Goddard
July 3, 2012
Chimera training (3-hr session) for 4 members of the DeGrado group at UCSF, covering fetching data, structural analysis and comparison, H-bonds, superposition, morphing, attributes, working with sequences, density display, making movies; Q & A. 20 hours prep.
- Elaine Meng, Eric Pettersen, Tom Ferrin
July 11, 2012
Hands-on Chimera tutorials for 50 participants at the National University of Singapore cryoEM workshop. Tutorials covering electron tomography segmentation, molecule display, and fitting as well as an open question and answer session totaling 3 hours were presented via teleconference using WebEx with participants trying what they were shown on lab computers. Hosted by Cynthia He and Wah Chiu. 15 hours preparation.
- Tom Goddard
July 26, 2012
Chimera visualization of HIV virus core and drug binding for 20 high school students from the UC Davis COSMOS program. Organized by Sarah Driver from UC Davis. 20 minute demo. 1 hour preparation.
- Tom Goddard, Tom Ferrin, Scooter Morris
August 14, 2012
Chimera visualization demonstration covering protein structures and sequences (dipeptide epimerase) and multiple length scales, atoms through cells (T-cell tomography and termite gut EM). 90 minutes. 12 first year graduate students in structural and computational biology, Baylor College of Medicine. Presented via WebEx screen sharing. Hosted by Wah Chiu. 6 hours preparation.
- Tom Goddard
August 27, 2012
Movie making demonstration showing how to morph electron microscopy maps and molecular structures fit into maps using Chimera. Used actin-like ParM filament data. Presented to 60 people at the Bay Area cryoEM meeting at Santa Cruz. Hosted by Melissa Jurica. 8 hours preparation.
- Tom Goddard
October 2-3, 2012
Chimera workshop at NIH, Bethesda MD. Eight sessions over two days, including introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis, publication images and movies. About 30 attendees, the room capacity. About 20 more participants off-site with video and audio using Adobe Connect. 150 hours preparation. workshop materials
- Tom Ferrin, Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng
October 4, 2012
Full-day Cytoscape workshop at NIH, Bethesda MD. Network visualization and analysis with Cytoscape. About 30 attendees, the room capacity. About 10 more participants off-site with video and audio using Adobe Connect. workshop materials
- Scooter Morris, Elaine Meng
October 4-5, 2012
Visits to NIH labs (Sriram Subramaniam, John Patton, Bernard Heymann, BK Lee, and others) for Chimera training using their data sets. Two days with RBVI staff divided into groups to help different labs. Topics included Chimera Python programming, HIV virus spikes, annotating FIBSEM imaging data, rotavirus RNA structures, hybrid model representations, and many others.
- Tom Ferrin, Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng
Oct 17, 2012
35-minute presentation to ~25 students in UCSF BP204, "Macromolecular Interactions" class followed by 45 mins of students going through a tutorial on their own laptops. The presentation part included 5 mins on history of Computer Graphics Lab, 30 mins of Chimera demonstration: basic usage, finding H-bonds, morphing viewing sequences, showing attribute values, building multimers, stereo. Prep time 16 hours including updating and rehearsing the presentation, updating and preparing handouts.
- Elaine Meng, Eric Pettersen
Past reports 2012, 2011, 2010, 2009, 2008, 2007
