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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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2015/2016 report

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March 24, 2015

Introduction to Chimera tutorial at ​VIZBI 2015 Visualizing Biological Data Conference in Cambridge, MA. Included visual effects, morphing, making movies, and MultiDomain Assembler. Estimated 8 hours preparation, 8 attendees.

• Sam Hertig

March 26, 2015

Oculus Rift and kilobot demonstrations for Cal Academy of Sciences ​Robotics Nightlife event in San Francisco. Showed migrating neutrophil cell and Tuscany demo using two oculus rift VR headsets, and showed kilobot cancer cell, synchronization and move to light demos. 3500 attended this sold-out event and about 600 people visited our 3 tables, non-stop several people deep for 4 hours. Prep, setup and presentation time 8 hours (48 person hours for 6 presenters). Organized by Kara Helmke.

• Tom Goddard, Thao Do, Megan Riel-Mehan, Kara Helmke, Michael Broeker, Graham Johnson

April 7, 2015

Introduction to Cytoscape course given at UCSF (2 hours). 30 participants, 4 hours prep time.

• Scooter Morris

April 21, 2015

1-hour Chimera tutorial by Skype to Georgetown University structural biology course including BLAST searching, morphing, showing MD trajectories, virtual mutation, rendering, and customizing the interface. Arranged by course instructor Sona Vasudevan. Estimated 8 hours prep, 20 students attending.

• Eric Pettersen

April 21-May 7, 2015

Protein function prediction from a big data perspective using similarity networks Mini course (a formal curricular element for UCSF Graduate Programs) UCSF, Mission Bay Library Computer Workshop Lab. 40 hours preparation 12 attendees.

• Patricia Babbitt, Eyal Akiva, Gemma Holliday, Shoshana Brown

June 2, 2015

American Microbiology Society meeting, New Orleans. Superfamily analysis and protein similarity networks. 10 hours prep. 60 attendees.

• Patsy Babbitt

July 6-17, 2015

Project with 4 high-school students to program kilobot swarm robots to forage. Students developed and tested code over 8 days to make kilobots disperse from a cluster to find a target, establish a minimum path to that target, and then move to reinforce that path. They made movies and gave two presentations on their results. RBVI provided 10 hours of assistance programming and debugging. Students Emilia, Katrina, Judith and Maya-Claire. Organized by UCSF professor Wendell Lim.

• Tom Goddard

July 11, 2015

Cytoscape 3 App Development: Variations on a theme -- "Hello World" workshop offered at the 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2015) in Dublin, Ireland. All day session worked with 12 students to allow them to develop their own Cytoscape "Apps". During the course of the workshop, students developed 7 apps, each one building on the previous app and utilizing more of the Cytoscape API. Prep time was about 10 hours.

• Scooter Morris

July 13, 2015

Demonstration of molecular graphics-related hardware for visitors from the Universidad Andrés Bello, Santiago, Chile: Dr. Fernando González-Nilo (​https://www.researchgate.net/profile/Fernando_Gonzalez-Nilo), Director of the Center for Bioinformatics & Integrative Biology, and Dr. Luis Velázquez (​https://www.researchgate.net/profile/Luis_Velasquez4), Director of the Center for Integrative Medicine and Innovative Science. Showed and/or discussed using the stereo projector, Oculus Rift virtual reality goggles, Space Navigator input device, Leap Motion Controller, and Phantom force feedback device.

• Tom Goddard, Elaine Meng

July 14, 2015

Gordon Conference on Enzymes, Co-enzymes, and Metabolic Pathways, Waterville, NH. Superfamily analysis with the SFLD and protein similarity networks. 15 hours prep time, 135 attendees.

• Patsy Babbitt

July 16, 2015

Invited talk at Swansea University covering the visualization of biological structures and processes. Talk was attended by about 50-60 researchers. Prep time: 10 hours.

• Scooter Morris

July 20, 2015

1/2 day workshop at the University of Copenhagen on the use of Cytoscape, including interactions with UCSF Chimera. 25 Participants. Prep time: 4 hours.

• Scooter Morris

July 23, 2015

29th Annual Symposium of the Protein Society, Barcelona, Spain. Superfamily analysis with the SFLD and protein similarity networks. 15 hours prep time, 150 attendees.

• Patsy Babbitt

August 4, 2015

One hour talk and demonstration of 3d image visualization for Baylor College of Medicine computational methods course, presented via video conference to 5 graduate students. Organized by professor Wah Chiu. 8 hours preparation and delivery.

• Tom Goddard

August 24, 2015

Demonstration of neutrophil migration visualization with Oculus Rift virtual reality headset for Herb Sandler, members of the Sandler Foundation, and a half dozen kids ages 8-14. Estimated 12 attendees total. Organized by Kara Helmke and UCSF professor Wendell Lim. 4 hours preparation and delivery.

• Tom Goddard, Graham Johnson, Kara Helmke, Dyche Mullins, Lillian Fritz-Laylin, Wendell Lim

September 16, 2015

cellPACK talk and 3d visualization of crawling neutrophils for the board of directors of the Long Foundation. Estimated 7 visitors. Organized by Michael Faber and Jessica Jencek. 4 hours preparation and delivery.

• Graham Johnson, Tom Goddard, Megan Riel-Mehan

September 28 - October 3, 2015

EMBO Practical Course: Computational analysis of protein-protein interactions, Norwich, UK. 30 students. 3-hr introduction to Chimera and a full-day tutorial on network biology and Cytoscape. See ​http://events.embo.org/15-protein-protein/ for details on the course.

• Scooter Morris

October 2, 2015

San Francisco State University, San Francisco, CA. Presentation on superfamily analysis with protein similarity networks. 12 hours prep, 30 attendees.

• Patsy Babbitt

November 2, 2015

San Francisco State University, San Francisco, CA. Diversity Outreach Talk on superfamily analysis with protein similarity networks. 20 hours prep, 35 attendees.

• Patsy Babbitt

November 20, 2015

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 Tolman Hall computer lab. About 30 students participated. Prep and workshop time about 16 person-hours. ​photo, Tolman Hall computer lab

• Scooter Morris, Eric Pettersen, Elaine Meng

January 2016

Presentation on SFLD data including multiple sequence alignments. InterPro Consortium Meeting, EMBL-EBI, Hinxton, UK. 20 attendees. 5 hours preparation.

• Gemma Holliday

February 3, 2016

Presentation on SFLD and similarity networks for Sakanari lab meeting at UCSF. 10 hours prep, 15 attendees.

• Patsy Babbitt

February 12 and 19, 2016

Demonstration for 4 groups of student applicants to UCSF iPQB program. Showed differential gear nano-machine, HIV reverse transcriptase with tenovofir drug, crawling neutrophil light sheet microscopy, using stereo and Oculus Rift. Organized by Rebecca Brown. Total 14 students. 6 hours preparation and delivery.

• Tom Goddard

March 25, 2016

University of Maryland, College Park, MD. Presentation on superfamily analysis with protein similarity networks. 18 hours prep time, 60 attendees.

• Patsy Babbitt

April 14, 2016

Presentation at ​Biocuration 2016, Swiss Institute of Bioinformatics, Geneva, on defining functional boundaries within protein similarity networks. Estimated 200 attendees. 5 hours preparation.

• Gemma Holliday

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Past reports 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007

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