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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)

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2012/2013 report

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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

September 29, 2012

Workshop on the Radical SAM Superfamily (data in SFLD) at UCSF, full-day meeting with experts. Estimated 8 hours talk preparation, 30 attendees.

• Gemma Holliday

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

October 17, 2012

UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students (about 25 of them) doing a Chimera tutorial on their own laptops. The presentation 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

November 15, 2012

Demonstration of Chimera for viewing, segmenting and measuring microscopy data given at the Northern California Society for Microscopy meeting at UCSF. ​Slides. Walk through of segmenting and measuring termite gut bacteria. Audience of 50. Preparation time 20 hours. Hosted by Larry Ackerman and Steven Samuelsson.

• Tom Goddard

December 5, 2012

Gave 3 hour hands-on Chimera tutorial on map display and analysis at UC Berkeley. Covered basic molecular display, segmenting and fitting single particle maps, and extracting regions from termite gut FIBSEM data. 12 participants (Auer, Downing, Nogales, Berger labs). 8 hours preparation. Organized by Danielle Jorgens.

• Tom Goddard

December 13, 2012

Gave 3 hour hands-on tutorial for Cytoscape at the 2012 Cytoscape retreat (Gladstone Institutes, UCSF). 60 participants, 8 hours preparation.

• Scooter Morris

December 19, 2012

Gave 3 hour hands-on advanced Chimera tutorial on map segmentation at UC Berkeley. Covered surface masking, watershed segmentation, and zones around markers and atoms using HIV virus, microtubule and T-cell maps. 10 participants. 8 hours preparation. Organized by Danielle Jorgens.

• Tom Goddard

January 31, 2013

Gave a plenary presentation on Visualization Challenges in Network Biology at the HCI (Human-Computer Interaction) Korea annual conference. 2,000 participants, 20 hours preparation.

• Scooter Morris

February 7, 2013

​Webinar for ​Biology Grid demonstrating Chimera molecular assembly and electron microscopy tools. Built alpha crystallin model. 30 minute demo. 6 hours preparation. 35 participants. Organized by Michelle Ottaviano, Jason Key, and Piotr Sliz.

• Tom Goddard

February 8, 2013

Demonstrated Chimera visualization, satellite tobacco mosaic virus, differential gear nano-machine, x-ray density maps, to two groups of candidate graduate students for the UCSF iPQB program (biophysics and bioinformatics). 8 participants. 30 minutes each demo. 2 hours preparation. Organized by Rebecca Brown.

• Tom Goddard

February 15, 2013

Demonstrated Chimera visualization, white blood cell 3d motion and HIV reverse transcriptase inhibitor binding, to two groups of candidate graduate students for the UCSF iPQB program (biophysics and bioinformatics). 14 participants. 30 minutes each demo. 4 hours preparation. Organized by Rebecca Brown.

• Tom Goddard

March 8, 2013

Demonstration showing molecules of life, water, protein, dna, drugs (THC and nevirapine), to 8 students from Dewey High School in Oakland using 3-d projection in the visualization vault. 30 minute demo. 6 hours preparation. Organized by Veronica Zepeda, UCSF iGEM and Education Coordinator.

• Tom Goddard

March 19, 2013

1/2 day Chimera tutorial at ​VizBI 2013, the 4th international meeting on Visualizing Biological Data (Broad Institute, Cambridge, MA). Anticipate about 15 participants.

• Scooter Morris

March 20, 2013

Invited talk on Network Visualization at ​VizBI 2013. Anticipate an audience of about 200.

• Scooter Morris

April 5, 2013

Presentation on "Protein function curation: linking sequence & chemical reaction spaces in the SFLD" at ​Biocuration 2013, the conference of the International Society for Biocuration (Cambridge, England). Anticipate 6 hours preparation, 100 attendees.

• Gemma Holliday

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Past reports 2012, 2011, 2010, 2009, 2008, 2007

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