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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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2013/2014 report

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May 30, 2013

EFI Meeting, Albert Einstein College of Medicine, New York. SFLD representative node networks and Cytoscape. 12 hrs prep. 60 attendees.

• Shoshana Brown, Eyal Akiva

June 25, 2013

Chimera tutorial at the University of Dundee. 25 attendees. 12 hours prep time.

• Scooter Morris

June 27, 2013

Seminar on RBVI Cytoscape apps: chemViz, structureViz, and the MPI app RINAlyzer at the University of Dundee. 40 attendees, 14 hours prep time.

• Scooter Morris

July 22, 2013

27th Symposium of the Protein Society, Boston. Poster presentation on the glutathione S-transferase (GST) superfamily in the SFLD. 7 hours prep, ~20 visitors.

• Eyal Akiva

July 25, 2013

​Multiscale brain visualization for COSMOS science program high school students. Used 3-d LCD glasses, and leap motion and space navigator navigation devices in the RBVI Visualization Vault to show 20 students from Davis, California light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, acetylcholine receptor synapse ion channel, and snake neurotoxin. 45 minutes. 30 hours preparation. Organized by Toby Allen and Sarah Driver from UC Davis and Scooter Morris from UCSF.

• Tom Goddard, Scooter Morris

July 25, 2013

Half day of presentations at UCSF for COSMOS science program high school students. RBVI presented brain visualization (listed above). Presentations on computational docking by Matt Jacobson, drug development for third-world diseases by the Jim McKerrow lab, and tour of the UCSF Center for Advanced Technology by Joe DeRisi . Organized by Scooter Morris from RBVI and Toby Allen and Sarah Driver from UC Davis. 8 hours preparation.

• Scooter Morris, Tom Ferrin

August 27-28, 2013

Chimera workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley. Seven sessions over two days, including introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis, publication images and movies, and master class. About 35-45 attendees (varied from session to session, 45 was maximum capacity). 40 hours preparation.

• Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng, Greg Couch

August 29, 2013

Full-day Cytoscape workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley. Three sessions including introduction to Cytoscape, use cases, and master class. About 25 attendees. 15 hours preparation.

• Scooter Morris

September 19, 2013

Visualization and analysis talk for a dozen first year graduate students at Baylor College of Medicine showing ​brain imaging , and ​krait snake venom effects on acetylcholine receptor. 90 minute presentation via WebEx . Organized by Wah Chiu. 16 hours preparation.

• Tom Goddard

October 5, 2013

Isoprenoid Synthase Superfamily (ISS) Workshop at UCSF. Outreach to IS Superfamily community; demo of sequence similarity networks and SFLD. Prep time: several weeks; lectures: 8 hours. 30 attendees.

• Shoshana Brown, Patsy Babbitt, Gemma Holliday

October 9, 2013

UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students (about 15 of them) doing a Chimera tutorial on their own laptops. The presentation included 5 mins on history of Computer Graphics Lab, 30 mins of Chimera demonstration: basic usage, finding H-bonds, morphing, viewing sequences, showing attribute values, building multimers, stereo. Prep time 10 hours including updating and rehearsing the presentation, updating and preparing handouts.

• Elaine Meng, Eric Pettersen

October 10-11, 2013

Training at UCSF on Pythoscape and sequence similarity networks for two members of the Fetrow group (from Wake Forest University). Prep time 16 hours.

• Patsy Babbitt, Gemma Holliday, Jeff Yunes, Susan Mashiyama, Rebecca Davidson, Jack Yu

October 22-25, 2013

EMBL-Australia Masterclass on Protein Sequence Analysis, Garvan Institute, Sydney, Australia. 24 attendees. 2 sessions on Cytoscape, 40 hours prep time. 2 sessions on Chimera, 12 hours prep time. Plenary talk on networks and structures, 14 hours prep time. Identifying and understanding protein-protein interactions and residues involved in intermolecular contacts using Cytoscape and structureViz/Chimera. Using Chimera for sequence-structure analysis and creating animations.

• Scooter Morris

October 28, 2013

Cytoscape workshop sponsored by the Systems Biology Institute in Melbourne, Australia. 14 attendees, 10 hours prep time. (1) Introductory tutorial on the analysis and visualization of biological networks; (2) Hands-on tutorial introduction to Cytoscape; (3) Demonstration and hands-on use cases of Cytoscape, with numerous example use cases showing what is possible. (4) Master class: Bring your own data, cancer pathway data, proteomics data, mass spectrometry pull downs, etc. The Master Class will also include demos of Cytoscape features in development, and Cytoscape scripting.

• Scooter Morris

November 21, 2013

Chimera demo for Biochemistry students from the University of San Francisco. Arranged by instructor Willie Melaugh. 12 attendees, prep time 3 hours. 30-minute demo using stereo graphics, space navigator input device to show a Drexel nanomachine and ​brain imaging at multiple levels of resolution ranging from whole brain to atomic detail of the nicotinic acetylcholine receptor.

• Tom Goddard

January 6-11, 2014

Meetings with staff at the European Bioinformatics Institute (EMBL-EBI Hinxton Outstation, Cambridge, UK) including demonstrations of the SFLD; sequence similarity networks and Pythoscape; troubleshooting issues and discussing future collaborations. 12 hours prep time, ~60 hours of meetings. 25-50 attendees.

• Gemma Holliday, Patsy Babbitt

February 7, 2014

Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. Two half hour demonstrations each with 4 students. 6 hours preparation and delivery.

• Tom Goddard

February 14, 2014

Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown. 30 minute demonstration 3 students. Discussion with another group of 5 students about virus structure and cell motion. 3 hours preparation and delivery.

• Tom Goddard

February 16-18, 2014

Showed human brain planetarium dome video at the Biophysical Society Annual meeting in San Francisco attended by 7000 researchers. Video was shown to a few hundred visitors per day. The ​video showed imaging data and molecular structures from the human brain, was made with RBVI Chimera software, and took about 50 hours to produce.

• Tom Goddard, Matt Dougherty

February 20, 2014

Showed virus, brain, cell and rna videos in a portable 6 meter planetarium dome that we setup at UCSF in Genentech Hall. The RBVI hosted this event and created two of the dome videos on HIV RNA and human brain imaging and molecules. About 150 researchers viewed the videos presented many times over 3 hours in the afternoon. 30 hours preparation.

• Matt Dougherty, Tom Goddard, Al Conde, Tom Ferrin

March 5, 2014

Introduction to Chimera 90 minute hands-on tutorial for a workshop at the International Institute of Macromolecular Analysis and Nanomedicine Innovation in Taiwan. Presented via video conference (GoToMeeting .com). 20 students, 8 hours preparation. Organized by Shang-Rung Wu of Natial Cheng Kung University, Tainan, Taiwan.

• Tom Goddard

March 10-11 2014

Taught a two-day course at EMBL in Heidelberg to teach participants to develop Apps for the Cytoscape 3.x series. As part of the course, covered the app development process as well as the key aspects of the Cytoscape API necessary to manipulate Cytoscape tables, networks, and user interface. Also worked through how to set up development environments on multiple platforms, and develop an initial Cytoscape App. The second day of this course provided time for each participant to interact with the instructor and other participants to plan and develop their own Cytoscape app. 20 students 30 hours preparation.

• Scooter Morris

May 28-June 7, 2014 (push to 2014/2015 report)

Penn State Bioinorganic Chemistry Workshop (Bioinformatics section). Hands-on workshop on using the SFLD and sequence similarity networks. Anticipated 25-50 attendees.

• Gemma Holliday, Patsy Babbitt

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

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