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2011/2012 report

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May 2, 2011

Lunch Talk to Faculty, SFLD and enzyme function annotation, Dept. of Bioengineering & Therapeutic Sciences, UCSF, 8 hours prep time, 8 attendees.

• Patsy Babbitt

May 19, 2011

Cytoscape User Tutorial given at the Cytoscape Retreat in San Diego. Had about 60 participants. Total prep time was about 10 hours.

• Scooter Morris

May 24, 2011

Interview and HIV capsid demonstration for an ​NPR Future Lab podcast sponsored by Intel Research on molecular visualization. Showed NPR reporter Deirdre Kennedy 3d stereo visualization and answered questions. Prep and delivery 5 hours.

• Tom Ferrin, Elaine Meng, Tom Goddard

May 24, 2011

SFLD new feature presentation at EFI May Meeting in San Francisco. ~6 hours prep time and ~60 participants.

• Florian Lauck

May 24, 2011

SFLD new progress and future plans at EFI May Meeting in San Francisco. ~6 hours prep time and 15 participants.

• Patsy Babbitt

June 8, 2011

Cytoscape and Proteomics. Training class given at UCSF to 8-10 UCSF campus researchers doing proteomics, specifically using MassSpec-based approaches. Total prep time was 5 hours.

• Scooter Morris

June 23, 2011

​HIV capsid demonstration given to 10 high school students from ​Mo' MAGIC program organized by UCSF Science and Health Education Partnership (SEP). Showed 3-d stereo visualization, space navigator, plastic models in visualization vault. Prep and delivery 5 hours.

• Tom Goddard

June 26 - July 1, 2011

Chimera ​fitting talk demonstrating global, sequential and symmetric fitting at ​3D EM Gordon conference, 200 participants, New Hampshire. Also 2 hour Chimera question and answer session with 20 participants. Prep and delivery 20 hours.

• Tom Goddard

July 11-12, 2011

​Cytoscape User Tutorial and Developer's Workshop at the Swiss Institute of Bioinformatics (SIB). 50 participants. Total prep time was 20 hours.

• Scooter Morris

July 15, 2011

Helped organize the ​Network Biology SIG at ISMB 2011 in Austria, Vienna. Total participants: 160.

• Scooter Morris

July 16, 2011

Gave a ​Tutorial on Network Biology and Cytoscape at ISMB 2011 in Austria, Vienna. Total participants: 35. Total prep time was 40 hours.

• Scooter Morris

July 18, 2011

Gave an invited talk on user interface development in the ​Data Visualization and User Interfaces workshop at ISMB. Total participants: 140. Total prep time was 40 hours.

• Scooter Morris

July 26, 2011

Society for Industrial Microbiology, New Orleans, SFLD intro and discussion, 8 hours prep time, 45 attendees.

• Patsy Babbitt

July 28, 2011

Hosted the ​COSMOS kids from UC Davis' Summer School for Math and Science. Viewed virus capsids in Chimera, influenza hemagglutinin conformational change. Total participants: 21. Total prep/organizational time: 20 hours.

• Scooter Morris

August 16, 2011

​Bay Area Science Festival publicity event demonstrations for House of Representatives Minority Leader Nancy Pelosi and San Francisco Mayor Ed Lee. Showed HIV capsid visualization. Visualization Vault room. 10 guests and press. 4 hours preparation.

• Tom Goddard

September 20, 2011

Two hiv capsid visualization demonstrations, 30 minutes each, for ​22 Swiss high school students who won the Swiss ​Science on the Move national science competition sponsored by Roche and Genentech. Arranged by Susan Jacobson at UCSF. Prep time 4 hours.

• Tom Goddard

September 21, 2011

Introduced SFLD in lecture for BMI206 core graduate course in bioinformatics, Biological and Medical Informatics Graduate Program, 15 hours prep time and 20 students.

• Patsy Babbitt

September 23, 2011

Cytoscape Lab on the annotation of new enzyme functions using SFLD examples and data, BMI206 core graduate course in bioinformatics, Biological and Medical Informatics Graduate Program. 2 hours prep time and 20 students.

• Patsy Babbitt

September 30, 2011

35-minute presentation to >25 students in UCSF BP204, "Macromolecular Interactions and Assemblies" class. Included 5 min on history of Computer Graphics Lab, the remainder a Chimera demonstration: basic usage, morphing, viewing sequences, showing attribute values, building multimers, stereo. Prep time 16 hours including updating the previous year's presentation, testing with the current version of Chimera, rehearsing the demo, preparing handouts, working through the homework assignment with current version of Chimera and making a "cheat sheet" for the TAs of commands that could be used for that homework.

• Elaine Meng, Eric Pettersen, Tom Goddard

October 18, 2011

Talk to new iPQB (Integrative Program in Quantitative Biology) graduate students, UCSF, SFLD intro and discussion, 8 hours prep time, 45 attendees.

• Patsy Babbitt

October 19, 2011

Talk to new PSPG (Pharmaceutical Sciences and Pharmacogenomics) graduate students, UCSF, SFLD intro and discussion, 4 hours prep time, 12 attendees.

• Patsy Babbitt

October 22, 2011

Talk at joint UCB/UCSF graduate student retreat, Lake Tahoe, SFLD intro and discussion, 8 hours prep time, 100 attendees.

• Patsy Babbitt

November 2, 2011

Bay Area Science Festival 20 minute demonstration of HIV capsid visualization for 10 Balboa High School students. Presented in visualization vault room.

• Scooter Morris

November 13, 2011

Lecture for BioE 280: joint UCB/UCSF graduate seminar series, SFLD intro and discussion, 5 hours prep time, 30

attendees.

• Patsy Babbitt

November 30, 2011

Hands-on Chimera tutorial at Purdue University. 90 minutes, 25 participants, 8 hours preparation. Organized by Michael Rossmann. Covered building a ParM filament using an EM map and Xray stucture.

• Tom Goddard

November 30, 2011

Structural Biology Seminar talk at Purdue University, by invitation of Michael Rossmann. 1 hour, 45 in audience, 16 hours preparation. Demonstrated hypothetical modeling of alpha crystallin and HIV capsid and RNA.

• Tom Goddard

November 30, 2011

SFLD new feature presentation at EFI November-December Meeting in San Francisco. ~3 hours prep time

and ~40 participants.

• Florian Lauck

November 30, 2011

SFLD new progress and future plans at EFI Advisory Committee Meeting in San Francisco. ~6 hours prep time and 25 participants.

• Patsy Babbitt

December 1, 2011

Chimera hands-on training at Indiana University. 2.5 hours, 30 participants primarily undergraduates, 8 hours preparation. Organized by David Morgan. Covered alpha crystallin model building using Xray structures and an EM map. 90 minute follow-along tutorial, 60 minute question and answer session on all Chimera topics.

• Tom Goddard

December 6, 2011

Chimera demonstration for University of San Francisco biochemistry class. 30 minutes, 8 participants, 4 hours preparation. USF teacher Willie Melaugh. Showed pombe cell x-ray tomography and dipeptide epimerase enzyme structure which performs a step in recycling bacterial peptidoglycan cell wall.

• Tom Goddard, Elaine Meng

January 9, 2012

Stereo visualization demonstration for Li Ka Shing Foundation, Solina Chau and 5 others. HIV core particle. 20 minute demo, 2 hours preparation and delivery. Organized by Michael Faber.

• Tom Goddard, Tom Ferrin

February 2, 2012

Talk on Network Biology at the Institute Pasteur. Hosted by Benno Schwikowski. Talk was 45 minutes with 15 minutes of Q&A. Had 30-35 participants. About 2 hours of preparation.

• Scooter Morris

February 10, 2012

HIV visualization demonstration for UCSF iPQB candidate students. 5 students, 30 minutes demo, 2 hours preparation and delivery. Organized by Rebecca Brown.

• Tom Goddard

February 17, 2012

HIV visualization demonstration for UCSF iPQB candidate students. 5 students, two 30 minute demonstrations, 2 hours preparation and delivery. Organized by Rebecca Brown.

• Tom Goddard

February 23, 2012

HIV visualization and stereo demonstrations for VIP guests attending the Byer's Lecture Celebration. 30 guests split in 3 groups, 10 minute demonstrations for each group, 3 hours preparation. Organized by Michael Faber of the UCSF donor development office.

• Tom Goddard, Tom Ferrin

February 26-27, 2012

Planetarium dome animation at the 2012 Biophysical Society meeting in San Diego. Created 6 minute ​animation shown several times over two days in the ​biomolecular discovery dome. Molecular machines that replicate HIV RNA. 20 days production effort. Organized by Wah Chiu, Matt Daugherty and Ed Egelman.

• Tom Goddard, Tom Ferrin

March 5, 2012

Chimera tutorial at the VizBI conference in Heidelberg, Germany. Tutorial covered basics of molecular visualization and molecular animation. Total duration, 3 hours. 10 participants. 8 hours preparation time.

• Scooter Morris, Graham Johnson

March 5, 2012

Cytoscape plugin development tutorial at the VizBI conference in Heidelberg, Germany. Total duration, 3 hours. 20 participants. 8 hours preparation time.

• Scooter Morris

March 12-13, 2012

Cytoscape tutorial at the Swiss Institute of Bioinformatics in Lausanne. Total duration: 2 days. 40 participants.

• Scooter Morris