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2010/2011 report
June 2010 - March 2011
Created 23 video tutorials demonstrating different analysis techniques of electron microscopy density maps and molecular models using UCSF Chimera. Most videos are 5 to 10 minute long computer screen captures with audio narration showing step-by-step analysis. Each was made to address specific questions posed by users. Streaming videos are distributed via the RBVI web site using an in-browser Flash movie player. Total preparation time 50 hours.
- Tom Goddard
June 9, 2010 and July 7, 2010 and July 21, 2010
Demonstration showing DNA for total of 38 students ages 8-12 from Celsius and Beyond summer science camp on 3 separate days. 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
June 16-17, 2010
Summer School '10 : Python Applied to Computational Chemistry and Molecular Modelling, Universitat Autònoma de Barcelona, Spain. ~50 attendees. http://hpc.xrqtc.com/index.php?option=com_content&view=article&id=118:sm10-module-c&catid=54:recent-conference&Itemid=75
- Conrad Huang
July 11, 2010
Presentation on Cytoscape at ISMB 2010 to an audience of approximately 60. http://www.iscb.org/cms_addon/conferences/ismb2010/technologytrack.php Boston, MA. 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. University of Michigan, Ann Arbor, MI.
- Scooter Morris
July 22, 2010
Gave two 20 minute demonstrations to 24 students, part of COSMOS science program. Organized by Ken Dill. Showed DNA atomic models, small duplex, nucleosomes, chromatin filament model, chromosomes seen in electron microscopy. Used RBVI visualization room. 8 hours preparation.
- Tom Goddard
August 16, 2010
Tutorial given at CSB 2010, Stanford: "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
August 16, 2010
10 minute SFLD demo, followed by 2 hour SFLD/cytoscape tutorial. Attendees worked through exercises designed to give them basic familiarity with manipulating a cytoscape sequence and/or structure similarity network of their superfamily of choice, of the sort downloaded from the SFLD, to investigate questions of biological interest. Audience: ~25 grad students, postdocs, staff from the EFI. 15 hours preparation.
- Shoshana Brown
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 25, 2010
Invited talk, "Annotation Error in Public Databases," at the 2010 Pathway Tools Workshop, Menlo Park, CA. http://bioinformatics.ai.sri.com/ptools10/agenda.html Discussed SFLD and using sequence similarity networks in Cytoscape. ~100 attendees.
- Alexandra Schnoes
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 2010
Chimera used to create image for RBVI holiday card: glutamine synthetase 12-mer styled as an "architectural plan" (black outlines around transparent ribbons on aged parchment background). Estimated 36 person-hours of work (including preparing candidate images, voting, format converting).
- YZ (Zheng Yang)
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
December 13, 2010
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 50 attendees, 3 hours for the event, 24 person-hours preparation, publicity, and cleanup.
- Chimera team
January 12, 2010
Created 3 videos showing how to explore virus models for HHMI Viral Outbreak CDROM distribution to US high schools. Videos totaled 15 minutes and explained Chimera virus display, finding viruses structures on the web, and antibodies bound to West Nile virus. Expected distribution is several thousand CDs. Preparation time 15 hours.
- Tom Goddard
January 13, 2011
20 minute SFLD demo, followed by 10 minute Q & A, showing how the SFLD can be used to get information about the biological context of an uncharacterized target of interest. Audience: ~20 EFI investigators and other staff. 15 hours preparation.
- Shoshana Brown
February 11, 2011
Demonstration showing immune system structures to 7 visiting candidate UCSF graduate students. West Nile virus with bound antibodies, cytotoxic T-cell EM data. Also showed 3d printer and plastic molecular models. Two 35 minute demonstrations. 4 hours preparation.
- Tom Goddard
February 11, 2011
Seminar at University of Toronto covering base cytoscape and RBVI plugins to group of about 50. The seminar was 2 hours and included introductory topics as well as some advanced discussion. 10 hours preparation
- Scooter Morris
February 18, 2011
Demonstration showing clathrin cages to 4 visiting candidate UCSF graduate students. Clathrin cage triskelions, molecular assembly model, animation. Also showed 3d printer and plastic molecular models. Two 35 minute demonstrations. 4 hours preparation.
- Tom Goddard
March 14-17, 2011
Chimera tutorial at EMAN single particle reconstruction workshop, showing fitting atomic models in electron microscopy maps, symmetry, presentation images using Rous sarcoma virus data. Produced video version of the workshop tutorial. Tutorial was 1 hour with ~100 participants at University of Houston. Answered approximately 30 Chimera usage questions during 4-day workshop and demonstrated features to individual workshop participants, about 10 hours total time. 20 hours preparation.
- Tom Goddard
March 19, 2011
Half day Cytoscape tutorial at VizBI 2011 to 20 participants, showing basic Cytoscape plus clusterMaker, structureViz, chemViz, and nodeCharts. This was followed by a half day workshop where participants brought their own data sets and collaborated on analyses and visualizations.
16 hours preparation
- Scooter Morris
