--------------------------------------------------------------------------- "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 [http://igem.ucsf.edu 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 [http://www.gladstone.ucsf.edu/gladstone/site/cso/section/2461 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 [http://momagic.org 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 [http://ncmi.bcm.edu/ncmi/events/workshops/workshops_125 cryoEM workshop]. [http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/nus.html 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 [http://cosmos.ucdavis.edu 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 [http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html 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. [http://www.cgl.ucsf.edu/Outreach/Workshops/NIH-Oct-2012/ 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. [http://www.cgl.ucsf.edu/Outreach/Workshops/NIH-Oct-2012/ 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. [http://www.cgl.ucsf.edu/chimera/data/ncsm-nov2012/microscopy.html 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 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 December 13, 2012 Gave 3 hour hands-on tutorial for Cytoscape at the annual Cytoscape retreat. 60 participants, 8 hours preparation. - Scooter Morris January 31, 2013 Gave a plenary presentation on Visualization Challenges in Network Biology at the HCI Korea annual conference. 2,000 participants, 20 hours preparation. - Scooter Morris February 7, 2013 [http://www.sbgrid.org/news/article/id=363 Webinar] for [http://www.sbgrid.org/Structural 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 19, 2013 1/2 day Chimera tutorial at VizBI 2013. 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 --------------------------------------------------------------------------- Past reports [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007] ---------------------------------------------------------------------------