--------------------------------------------------------------------------- "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) --------------------------------------------------------------------------- 2013/2014 report --------------------------------------------------------------------------- May 30, 2013 EFI Meeting, Albert Einstein College of Medicine, New York. SFLD representative node networks and Cytoscape. 12 hrs prep. 60 attendees. - Shoshana Brown, Eyal Akiva June 25, 2013 Chimera tutorial at the University of Dundee. 25 attendees. 12 hours prep time. - Scooter Morris June 27, 2013 Seminar on RBVI Cytoscape apps: chemViz, structureViz, and the MPI app RINAlyzer at the University of Dundee. 40 attendees, 14 hours prep time. - Scooter Morris July 22, 2013 27th Symposium of the Protein Society, Boston. Poster presentation on the GST superfamily in the SFLD. 7 hours prep, ~30 visitors. - Eyal Akiva July 25, 2013 [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html Multiscale brain visualization] for COSMOS science program high school students. Used 3-d LCD glasses, and leap motion and space navigator navigation devices in the RBVI Visualization Vault to show 20 students from Davis, California light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, acetylcholine receptor synapse ion channel, and snake neurotoxin. 45 minutes. 30 hours preparation. Organized by Toby Allen and Sarah Driver from UC Davis and Scooter Morris from UCSF. - Tom Goddard, Scooter Morris July 25, 2013 Half day of presentations at UCSF for COSMOS science program high school students. RBVI presented brain visualization (listed above). Presentations on computational docking by Matt Jacobson, drug development for third-world diseases by the Jim McKerrow lab, and tour of the UCSF Center for Advanced Technology by Joe DeRisi. Organized by Scooter Morris from RBVI and Toby Allen and Sarah Driver from UC Davis. 8 hours preparation. - Scooter Morris, Tom Ferrin August 27-28, 2013 Chimera workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley. Seven sessions over two days, including introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis, publication images and movies, and master class. About 35-45 attendees (varied from session to session, 45 was maximum capacity). 40 hours preparation. - Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng, Greg Couch August 29, 2013 Full-day Cytoscape workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley. Three sessions including introduction to Cytoscape, use cases, and master class. About 25 attendees. 15 hours preparation. - Scooter Morris September 19, 2013 Visualization and analysis talk for a dozen first year graduate students at Baylor College of Medicine showing [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html brain imaging], and [http://www.cgl.ucsf.edu/chimera/data/baylor-sep2013/krait.html krait snake venom] effects on acetylcholine receptor. 90 minute presentation via WebEx. Organized by Wah Chiu. 16 hours preparation. - Tom Goddard October 5, 2013 Isoprenoid Synthase Superfamily (ISS) Workshop at UCSF. Outreach to IS Superfamily community; demo of sequence similarity networks and SFLD. Prep time: several weeks; lectures: 8 hours. 30 attendees. - Shoshana Brown, Patsy Babbitt, Gemma Holliday October 9, 2013 UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students (about 15 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 10 hours including updating and rehearsing the presentation, updating and preparing handouts. - Elaine Meng, Eric Pettersen October 10-11, 2013 Training at UCSF on Pythoscape and sequence similarity networks for two members of the Fetrow group (from Wake Forest University). Prep time 16 hours. - Patsy Babbitt, Gemma Holliday, Jeff Yunes, Susan Mashiyama, Rebecca Davidson, Jack Yu October 22-25, 2013 EMBL-Australia Masterclass on Protein Sequence Analysis, Garvan Institute, Sydney, Australia. 24 attendees. 2 sessions on Cytoscape, 40 hours prep time. 2 sessions on Chimera, 12 hours prep time. Plenary talk on networks and structures, 14 hours prep time. Identifying and understanding protein-protein interactions and residues involved in intermolecular contacts using Cytoscape and structureViz/Chimera. Using Chimera for sequence-structure analysis and creating animations. - Scooter Morris October 28, 2013 Cytoscape workshop sponsored by the Systems Biology Institute in Melbourne, Australia. 14 attendees, 10 hours prep time. (1) Introductory tutorial on the analysis and visualization of biological networks; (2) Hands-on tutorial introduction to Cytoscape; (3) Demonstration and hands-on use cases of Cytoscape, with numerous example use cases showing what is possible. (4) Master class: Bring your own data, cancer pathway data, proteomics data, mass spectrometry pull downs, etc. The Master Class will also include demos of Cytoscape features in development, and Cytoscape scripting. - Scooter Morris November 21, 2013 Chimera demo for Biochemistry students from the University of San Francisco. Arranged by instructor Willie Melaugh. 12 attendees, prep time 3 hours. 30-minute demo using stereo graphics, space navigator input device to show a Drexel nanomachine and [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html brain imaging] at multiple levels of resolution ranging from whole brain to atomic detail of the nicotinic acetylcholine receptor. - Tom Goddard January 6-11, 2014 Presentations and training on SFLD and sequence similarity networks to staff at the European Bioinformatics Institute (EMBL-EBI Hinxton Outstation, Cambridge, UK). 12 hours prep time, ~60 hours of meetings. 25-50 attendees. - Gemma Holliday, Patsy Babbitt February 7, 2014 Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. Two half hour demonstrations each with 4 students. 6 hours preparation and delivery. - Tom Goddard February 14, 2014 Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. 30 minute demonstration 3 students. Discussion with another group of 5 students about virus structure and cell motion. 3 hours preparation and delivery. - Tom Goddard February 16-18, 2014 Showed human brain planetarium dome video at the Biophysical Society Annual meeting in San Francisco attended by 7000 researchers. Video was shown to a few hundred visitors per day. The [http://www.youtube.com/watch?v=RE2XMzInX_o video] showed imaging data and molecular structures from the human brain, was made with RBVI Chimera software, and took about 50 hours to produce. - Tom Goddard, Matt Dougherty February 20, 2014 Showed virus, brain, cell and rna videos in a portable 6 meter planetarium dome that we setup at UCSF in Genentech Hall. The RBVI hosted this event and created two of the dome videos on HIV RNA and human brain imaging and molecules. About 150 researchers viewed the videos presented many times over 3 hours in the afternoon. 30 hours preparation. - Matt Dougherty, Tom Goddard, Al Conde, Tom Ferrin May 28-June 7, 2014 Penn State Bioinorganic Chemistry Workshop (Bioinformatics section). Hands-on workshop on using the SFLD and sequence similarity networks. Anticipated 25-50 attendees. - Gemma Holliday, Patsy Babbitt --------------------------------------------------------------------------- Past reports [wiki:COT13 2013], [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007] ---------------------------------------------------------------------------