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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)

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2011/2012 report

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May 19, 2011

Cytoscape User Tutorial given at the Cytoscape Retreat in San Diego. Had about 60 participants. Total prep time was about 10 hours.

• Scooter Morris

May 24, 2011

Interview and HIV capsid demonstration for an ​NPR Future Lab podcast sponsored by Intel Research on molecular visualization. Showed NPR reporter Deirdre Kennedy 3d stereo visualization and answered questions. Prep and delivery 5 hours.

• Tom Ferrin, Elaine Meng, Tom Goddard

June 8, 2011

Cytoscape and Proteomics. Training class given at UCSF to 8-10 UCSF campus researchers doing proteomics, specifically using MassSpec-based approaches. Total prep time was 5 hours.

• Scooter Morris

June 23, 2011

​HIV capsid demonstration given to 10 high school students from ​Mo' MAGIC program organized by UCSF Science and Health Education Partnership (SEP). Showed 3-d stereo visualization, space navigator, plastic models in visualization vault. Prep and delivery 5 hours.

• Tom Goddard

June 26 - July 1, 2011

Chimera ​fitting talk demonstrating global, sequential and symmetric fitting at ​3D EM Gordon conference, 200 participants, New Hampshire. Also 2 hour Chimera question and answer session with 20 participants. Prep and delivery 20 hours.

• Tom Goddard

July 11-12, 2011

​Cytoscape User Tutorial and Developer's Workshop at the Swiss Institute of Bioinformatics (SIB). 50 participants. Total prep time was 20 hours.

• Scooter Morris

July 15, 2011

Helped organize the ​Network Biology SIG at ISMB 2011 in Austria, Vienna. Total participants: 160.

• Scooter Morris

July 16, 2011

Gave a ​Tutorial on Network Biology and Cytoscape at ISMB 2011 in Austria, Vienna. Total participants: 35. Total prep time was 40 hours.

• Scooter Morris

July 18, 2011

Gave an invited talk on user interface development in the ​Data Visualization and User Interfaces workshop at ISMB. Total participants: 140. Total prep time was 40 hours.

• Scooter Morris

July 28, 2011

Hosted the ​COSMOS kids from UC Davis' Summer School for Math and Science. Viewed virus capsids in Chimera, influenza hemagglutinin conformational change. Total participants: 21. Total prep/organizational time: 20 hours.

• Scooter Morris

August 16, 2011

​Bay Area Science Festival publicity event demonstrations for House of Representatives Minority Leader Nancy Pelosi and San Francisco Mayor Ed Lee. Showed HIV capsid visualization. Visualization Vault room. 10 guests and press. 4 hours preparation.

• Tom Goddard

September 20, 2011

Two hiv capsid visualization demonstrations, 30 minutes each, for ​22 Swiss high school students who won the Swiss ​Science on the Move national science competition sponsored by Roche and Genentech. Arranged by Susan Jacobson at UCSF. Prep time 4 hours.

• Tom Goddard

September 30, 2011

35-minute presentation to >25 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 16 hours including updating the previous year's presentation, testing with the current version of Chimera, rehearsing the demo, preparing handouts, working through the homework assignment with current version of Chimera and making a "cheat sheet" for the TAs of commands that could be used for that homework.

• Elaine Meng, Eric Pettersen, Tom Goddard

November 2, 2011

Bay Area Science Festival 20 minute demonstration of HIV capsid visualization for 10 Balboa High School students. Presented in visualization vault room.

• Scooter Morris

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2010/2011 report

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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

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Past reports 2010, 2009, 2008, 2007

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