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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 particpants, 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

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 kilobits 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 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

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. 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

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

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