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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)
2014/2015 report
May 16, 2014
UC Davis Biophysics Seminar Series. Studying enzyme sequence-structure-function relationships with the SFLD and sequence similarity networks. 18 hours prep, 40 attendees.
- Patsy Babbitt
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
June 2, 2014
Penn State Bioinorganic Chemistry Workshop (Bioinformatics section). Plenary lecture on enzyme superfamilies and sequence similarity networks, 25 hours prep, 150 attendees.
- Patsy Babbitt
June 5, 2014
Gordon Research Conference on Cyclic Nucleotide Phosphodiesterases, Mt. Holyoke College, MA. Sequence-structure-function relationships and similarity networks of this set of enzymes. 80 hours working with the data, 30 hours preparing presentation, 130 attendees.
- Samuel Thompson, 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
August 25, 2014
Sandia National Labs, Livermore, CA. Presentation on enzyme superfamilies, networks, and the SFLD. 15 hours prep, 20 attendees.
- Patsy Babbitt
September 25, 2014
Chimera visualization by videoconference to 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 9, 2014
Cytoscape developer's workshop offered as part of the Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges conference in San Diego. 20 participants, 10 hours prep time.
- Scooter Morris
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
December 16, 2014
Presentation at UCSF to DeGrado group on enzyme superfamilies, networks, and the SFLD. 20 hours prep, 15 attendees.
- Patsy Babbitt
January 12-16, 2015
Multiple Sequence Alignment workshop hosted by the Institute for Pure & Applied Mathematics in UCLA. Two talks and a poster presentation on the Structure-Function Linkage Database, sequence similarity networks, and Cytoscape. Prep time: 50 hours. Number of attendees: 25-50.
- Eyal Akiva, Patsy Babbitt
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. 20 hours preparation and delivery (RBVI staff only).
- Thao Do, Megan Riel-Mehan, Tom Goddard, Kara Helmke, Michael Broeker, Graham Johnson, 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
February 13, 2015
Kilobot demonstration for 4 prospective UCSF graduate students. Looked at firefly synchronization model with 100 kilobots and the effect of 50% non-cooperating kilobots. Two 30 minute demos. Organized by Rebecca Brown. 4 hours preparation and delivery.
- Tom Goddard
March 10, 2015
European Bioinformatics Institute Annotation Workshop, Georgetown University, Washington DC. Sequence similarity networks for annotation. 5 hours prep, 14 attendees.
- Patsy Babbitt
March 11, 2015
Discussion of careers in science and demonstration of 3-D visualization and kilobot swarm robots for 11 high school students for SF STEM Career Day. Organized by Jennifer Kaelin of UCSF Science and Health Education Partnership (SEP). 60 minutes. 6 hours preparation.
- Tom Goddard
March 24, 2015
Introduction to Chimera tutorial at VIZBI 2015 Visualizing Biological Data Conference in Cambridge, MA. Estimated 8 hours preparation, 5 attendees.
- Sam Hertig
March 25-27, 2015
VIZBI 2015 Visualizing Biological Data Conference at the Broad Institute of MIT and Harvard, Cambridge, MA. Poster on the MultiDomain Assembler in Chimera and creating a model of immature HIV. 20 hours prep, anticipate about 50 visitors to the poster.
- Sam Hertig
Past reports 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007
