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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)
2010/2011 report
June 9, 2010
Demonstration showing DNA for 13 students age 8 from Celsius and Beyond summer science camp. Organized with Auritte Cohen-Ross. Showed light microscopy volume time series of chromosomes in dividing cells, electron microscopy of chromosomes, DNA molecular structure, nucleosomes and chromatin (http://www.cgl.ucsf.edu/chimera/dna-jun2010/dnademo.html). 8 hours preparation. 1 hour demonstration in RBVI visualization room. Many questions from kids "What happens if you eat a bubble?".
- Tom Goddard
July 11, 2010
Presentation on Cytoscape at ISMB 2010 to an audience of approximately 60. The presentation provided an introduction to Cytoscape's capabilities and some of the new features in Cytoscape 2.7 along with some new and recently enhanced plugins.
- Scooter Morris
July 13, 2010
"Network visualization and analysis using Cytoscape" Birds of a Feather session at ISMB 2010. Scooter Morris facilitated this session to solicit input from Cytoscape users and developers. About 30 participants.
July 18, 2010
"Cytoscape User Tutorial". 2 hour introductory user tutorial given to about 50 users as part of the annual Cytoscape Retreat.
- Scooter Morris
July 18, 2010
Plugin demonstration on CyCommandHandlers as part of the Cytoscape Retreat to about 100 participants.
- Scooter Morris
August 16, 2010
Tutorial given at CSB 2010: "Analysis and Visualization of Biological Networks". This was a 1/2 day tutorial given to 15 participants that covered visualization and analytical approaches to understanding biological networks. Second half of tutorial introduced Cytoscape as a tool and provided a hands-on exercise.
- Scooter Morris
September 29, 2010
40-minute presentation to ~14 students in UCSF BP204, "Macromolecular Interactions and Assemblies" class. Included 5 min on history of Computer Graphics Lab, the remainder a Chimera demonstration: basic usage, morphing, viewing sequences, showing attribute values, building multimers, stereo. Prep time 12 hours including updating the previous year's presentation, testing with the current version of Chimera, rehearsing.
- Elaine Meng, Eric Pettersen
September 29, 2010
30-minute presentation to ~50 attendees, then followed by 90-minute tutorial to ~20 students at Department of Computational and System Biology, School of Medicine and Clinical Translational Science Institute, University of Pittsburgh. The presentation part, titled "Introduction to UCSF Chimera, an Extensible Molecular Modeling System", covered the brief history of molecular visualization, RBVI history and Chimera highlighted features. The tutorial part went over several basic examples in the "getting started" document. Prep time 40 hours.
- YZ (Zheng Yang)
October 12-13, 2010
Poster presentation on segmentation and measurement of bacteria in termite gut at NIH workshop "Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and Cellular Structures". 170 participants. 12 hours preparation. Discussions of research projects with about 10 attendees https://conferences.niaid.nih.gov/vbbethesda/
- Tom Goddard
October 27, 2010
45-minute Chimera teaching demonstration to ~30 students for a graduate course in protein engineering at UC Berkeley (taught by Danielle Tullman-Ercek, Asst. Professor, Dept. of Chemical and Biomolecular Engineering, UC Berkeley). Covered basic usage, finding H-bonds, morphing, saving trajectories as movies, viewing sequences, showing attribute values, evaluating rotamers, performing virtual mutations, building multimers, and using stereo. Prep time 20 hours including adding more material to the previously developed demo, testing with the current version of Chimera, and rehearsing.
- Elaine Meng, Eric Pettersen
November 18, 2010
Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to SMART team Lincoln high school students. This is a UCSF Science and Health Education Partnership (SEP) program. Showed FIBSEM data, spirochetes, flagella, handedness, endo-flagella, protein morphing, hydrophobic and electrostatic surface coloring to identify transmembrane and binding regions. 16 students. 6 hours preparation.
- Tom Goddard
December 2, 2010
Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to SMART team Galileo high school students. This is a UCSF Science and Health Education Partnership (SEP) program. Showed FIBSEM data, spirochetes, flagella, handedness, endo-flagella, protein morphing, hydrophobic and electrostatic surface coloring to identify transmembrane and binding regions. 20 students. 4 hours preparation.
- Tom Goddard
December 8, 2010
Two hour discussion and Chimera demonstration of myosin thick filament regulation for UCSF Tetrad graduate program macromolecules discussion group. Looked at thick filament architecture and myosin 2 heavy and light chain atomic models using stereo 3d visualization. 5 graduate students, led by professor Zev Gartner. 8 hours preparation.
- Tom Goddard
2009/2010 report
May 21, 2009
Talk to ten San Francisco high school teachers, part of the Current Science Seminar Series organized by the UCSF Science and Health Education Partnership. (http://biochemistry.ucsf.edu/programs/sep/) Showed stereo visualization and manipulation of man-made molecular machines and viruses. Made paper virus models. Held in RBVI visualization room. 12 hours preparation time.
- Tom Goddard
June 11, 2009
Second talk to high school teachers in the Current Science Seminar Series given by the UCSF Science and Health Education Partnership. Showed stereo visualization and manipulation of man-made molecular machines and viruses. Made paper virus models. Held in RBVI visualization room. 3 hours preparation time.
- Tom Goddard
June 24, 2009
Virus visualization demonstration for a dozen science summer school students ages 9 to 12 (http://www.celsiusandbeyond.com/). Showed stereo visualization, space navigator, phantom force feedback, protein and rna structure and virus paper models. Held in RBVI visualization room. 12 hours preparation time.
- Tom Goddard
July 14, 2009
Molecular visualization demonstration for ~30 kids from the COSMOS summer school program at U.C. Davis (http://www.ucop.edu/cosmos/). Showed stereo visualization, virus structures, protein, dna, and protein docked with dna.
- Scooter Morris
July 15, 2009
Virus visualization demonstration for 5 science summer school students ages 9 to 12 (http://www.celsiusandbeyond.com/). Showed stereo visualization, space navigator, phantom force feedback, protein and rna structure and virus paper models. Held in RBVI visualization room. 4 hours preparation time.
- Tom Goddard
August 19, 2009
Chimera talk and demonstration, Molecular Visualization symposium (COMP division, see http://oasys2.confex.com/acs/238nm/techprogram/S32080.HTM ) at the 238th American Chemical Society National Meeting (Washington, DC). Prep time by Elaine 60 hours including deciding what features to show and finding an appropriate biological system with which to show them, reading papers about the biological system, generating or finding associated data files, testing the features thoroughly, and iteratively adjusting presentation order and scope.
- Tom Ferrin, Elaine Meng
September 1, 2009
Demonstration for NIH visitors from Clinical and Translation Science Awards (CTSA). Showed HIV spike tomography, T-cell tomography, clathrin cage animation, cytoscape. Held in RBVI visualization room. 6 hours preparation time.
- Tom Goddard, Scooter Morris, Tom Ferrin
September 22, 2009
Gave a talk and training session at the EMBO European School of Genetic Medicine course entitled "Embo Practical course on Networks in Biology analysis, modeling and reverse engineering." My talk was an introduction to the "Analysis & Visualisation of biological networks" and the practical covered uses of Cytoscape. There were 60 students from throughout Europe, and 6 faculty in attendance. Prep time for talk: 16 hours, for lab: 8 hours.
- Scooter Morris
September 28, 2009
Gave an informal seminar at Institute Pasteur for 10 members of the Systems Biology Group on uses of Cytoscape for phylogenetic analysis and cheminformatics.
- Scooter Morris
September 30, 2009
45-minute Chimera demonstration to ~20 students in UCSF BP204A, "Macromolecular Interactions" class. Included basic usage, morphing, viewing sequences, showing attribute values, building multimers. Prep time 60 hours including looking up information on the history of molecular graphics, working through exercises from the previous year, deciding what structures and features to show and in what order, generating or finding associated data files, testing the features thoroughly, and practicing the presentation.
- Elaine Meng, Eric Pettersen
October 20, 2009
EMBO practical course: "The combination of electron microscopy and x-ray crystallography for the structure determination of large biological complexes" (http://cwp.embo.org/pc09-18/). One day (7 hours) of hands-on Chimera training during 5 day workshop. 20 students. Grenoble, France. 60 hours preparing materials (http://www.cgl.ucsf.edu/chimera/tutorials/emfit09/emfit.html).
- Tom Goddard
October 23, 2009
Gave a 3 hour training session to the UCSF BMI206 class (14 Graduate Students) on Cytoscape and structureViz. Prep time: 12 hours. Tutorials are available on-line at http://opentutorials.rbvi.ucsf.edu/
- Scooter Morris
December 1, 2009
Demonstrations for three Galileo High School student groups, part of SEP SMART team program organized by Sabine Jeske (http://biochemistry.ucsf.edu/programs/sep/school-programs-smart-teams.html). Presentations covered their proteins: HIV Rev, capase-3, and strictosidine synthase. Included protein analysis, EM data, stereo viewing, space navigator, plastic and paper models. Three groups of ~10 students each in RBVI viz vault. 15 hours preparation and execution.
- Tom Goddard
December 10, 2009
Demonstrations for two Lincoln High School student groups, part of SEP SMART team program organized by Sabine Jeske (http://biochemistry.ucsf.edu/programs/sep/school-programs-smart-teams.html). Presentations covered their proteins: P-glycoprotein and HIV protease. Also included stereo visualization of nano-gears, ice, water, and lipid bilayers, space navigator and plastic models. Three groups of ~10 students each in RBVI viz vault. 12 hours preparation and execution.
- Tom Goddard
December 2009
Chimera and Cytoscape used to create image for RBVI holiday card: some of the nuclear pore complex proteins arranged into a Christmas tree, RBVI logo as star, phylogenetic tree as white fronds along the "ground." Estimated 24 person-hours of work.
- Zheng Yang, Elaine Meng, Conrad Huang, Scooter Morris
December 11, 2009
Chimera Release Party and RBVI Open House (2-5 pm in Genentech Hall N453, UCSF Mission Bay) for local researchers and students to meet the Chimera developers, see demonstrations and discuss features, tour the RBVI facilities, and share refreshments. Estimated 80 attendees, 3 hours for the event, 24 person-hours preparation, publicity, and cleanup.
- Chimera team
January 26, 2010
Remote training using desktop sharing (vnc/skype) for using the Segger segmentation tool to separate bacteria seen in termite gut by focused-ion-beam scanning-EM. Two hours of training for Bernhard Knierim and Monica at Lawrence Berkeley Lab. Four hours preparation time.
- Tom Goddard
February 1, 2010
All day Cytoscape training for Cell Signaling Technologies in Salem, Mass. 20 Participants including Sr. Scientists, CEO, Marketing personnel, and developers. Preparation time ~20 hours.
- Scooter Morris
February 11, 2010
Talk at Scripps Research Institute Automated Molecular Imaging (AMI) Forum (http://ami.scripps.edu/forum/) Demonstrated Segger segmentation and fitting capabilities (40 min + 20 min questions) to 35 EM (single-particle and tomography) researchers. Preparation time ~20 hours.
- Tom Goddard
February 21-23, 2010
Exhibit booth at Biophysical Society Meeting in San Francisco, organized by Scooter Morris of RBVI. Three days, ~24 demonstrations/talks, ~4 NCRR resource centers.
- Scooter Morris, Elaine Meng, Eric Pettersen, Zheng Yang, Tom Goddard
February 25-26, 2010
Molecular Animation workshop sponsored by RBVI and NCMI. Two days, ~25 participants, 14 talks. Preparation time ~150 person-hours. Hosted by and planned by Tom Ferrin and Scooter Morris from RBVI and Wah Chiu from NCMI. Two talks given by RBVI. http://plato.cgl.ucsf.edu/trac/Workshops/login/wiki/AnimationWorkshop
- Tom Ferrin, Scooter Morris, Tom Goddard, Zheng Yang
March 11-13, 2010
Poster on HIV spike visualization presented at the 5th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods in Lake Tahoe (http://www.hybridmethods2010.com/). About 180 researchers primarily using electron microscopy attended. Discussed EM map fitting using Chimera and EMDB map and segmentation file formats with approximately 20 people. Preparation time ~15 hours.
- Zheng Yang, Tom Goddard
March 17, 2010
1/2 Day Cytoscape training for Al Burlingame's group. 13 participants. Preparation time: ~10 hours.
- Scooter Morris
