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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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2014/2015 report

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May 28-June 4, 2014

Penn State ​Bioinorganic Chemistry Workshop (Bioinformatics section). Hands-on workshop on using the SFLD and sequence similarity networks. 24 hours (12 teaching), 45 attendees.

• Gemma Holliday, Patsy Babbitt

July 24, 2014

Chimera demo for ​COSMOS ​Chemistry of Life summer camp students from UC Davis led by professor ​Mark Mascal. 18 students. Showed plastic 3d models, nano-machine, acetylcholine receptor, hydrophobicity, space navigator, dendritic cell motion, stereo glasses, oculus rift demo. Students got to try all the toys and were an enthusiastic group. 12 hours preparation and delivery.

• Tom Goddard, Scooter Morris

August 11-12, 2014

Wellcome Trust Protein Bioinformatics and Community Resources Retreat, Wellcome Trust Genome Campus, UK. Retreat to network and establish communication between bioinformatics resources such as the SFLD. 24 hours, 20 attendees.

• Gemma Holliday, Patsy Babbitt

September 25, 2014

Chimera visualization for Baylor College of Medicine class "Computational Mathematics for Biomedical Scientists", 12 students, 1 hour, Ebola virus glycoproteins and movie making, hosted by Wah Chiu, 16 hours preparation and delivery (Ebola material was all new).

• Tom Goddard

September 28 - October 3, 2014

EMBO Practical Course: Computational analysis of protein-protein interactions: From sequences to networks. 24 students. Taught a quick introduction to using UCSF Chimera for molecular visualization (1 hour) and a full day tutorial on network biology and Cytoscape. See ​http://events.embo.org/14-comp-ppi/ for details on the course.

• Scooter Morris

October 15, 2014

UCSF BP204,"Macromolecular Interactions" class: 45-minute presentation followed by 45 mins of the students (about 19 of them) doing a Chimera tutorial on their own laptops. The presentation included 5 mins on history of Computer Graphics Lab, 40 mins of Chimera demonstration: basic usage, finding H-bonds, morphing, viewing sequences, showing attribute values, building multimers, measuring buried surface area, stereo. Prep time 12 hours including updating and rehearsing the presentation, updating and preparing handouts.

• Elaine Meng, Eric Pettersen

October 21, 2014

UCSF BP205A,"Physical Underpinnings of Biological Systems" class: 1-hr presentation to 25 students focused on showing sequence conservation on structures using Chimera. Covers obtaining a sequence alignment if you don't already have one, methods available within Chimera for calculating per-column conservation, rendering values with colors and/or worms, importing values that have been calculated outside of Chimera. Prep time 40 hours including creating and rehearsing presentation, making ​web page with images and sample data.

• Elaine Meng, Eric Pettersen

November 21, 2014

Chimera workshop (2 hours) for Professor Danielle Tullman-Ercek's Protein Engineering course (ChmEng C270/BioE C219) at UC Berkeley. Introduction to Chimera demonstration followed by hands-on "structure analysis and comparison" tutorial in the 40-seat computer lab in Tolman Hall. Estimated 35 attendees, 33 students plus TA and professor. Prep time 24 hours. ​photo, Tolman Hall computer lab

• Scooter Morris, Sam Hertig, Elaine Meng

January 29, 2015

​Kilobot T-cell and cancer exhibit for general public attending the UCSF Byer's lecture. Exhibit was presented for one hour before the lecture and one hour after the lecture with about 30 individuals trying and discussing this hands-on demo. Organized by Kara Helmke and Wendell Lim. 40 hours preparation and delivery.

• Thao Do, Megan Riel-Mehan, Tom Goddard, Kara Helmke, Michael Broeker, Wendell Lim

February 6, 2015

​Kilobot demonstration for 6 prospective UCSF graduate students, hands-on programming of swarm robots and discussion of their relation to biological problems. Two 30 minute demos. Organized by Rebecca Brown. 8 hours preparation and delivery.

• Tom Goddard

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Past reports 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007

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