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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)
2013/2014 report
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 25, 2013
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 brain imaging, and krait snake venom effects on acetylcholine receptor. 90 minute presentation via WebEx. Organized by Wah Chiu. 16 hours preparation.
- Tom Goddard
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 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 3D structures to gain insight into protein function.
- 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 brain imaging at multiple levels of resolution ranging from whole brain to atomic detail of the nicotinic acetylcholine receptor.
- Tom Goddard
Past reports 2013, 2012, 2011, 2010, 2009, 2008, 2007
