--------------------------------------------------------------------------- 2012/2013 report --------------------------------------------------------------------------- April 18, 2012 NASA AbSciCon meeting, Atlanta, GA. Presentation on enzyme evolution, networks, and the SFLD. 9 hours prep, 35 attendees. - Patsy Babbitt April 21, 2012 UCSF Alumni Homecoming Demonstrations. A series of 30 minute demonstrations were given to several groups (about 100 individuals overall) of UCSF alumni from the Schools of Medicine and Pharmacy, and the PhD programs. - Tom Ferrin April 23, 2012 Molecular visualization demonstration for 10 high school science teachers from the San Francisco Unified School District. - Tom Ferrin April 27, 2012 Full day Cytoscape workshop for 30 participants at the University of Missouri. - Scooter Morris April 28, 2012 2 1/2 hour Chimera workshop for 25 participants at the University of Missouri. - Scooter Morris May 23, 2012 EFI Meeting, San Francisco. SFLD new progress and future plans. ~6 hours prep, 15 attendees. - Patsy Babbitt June 21, 2012 Lecture for UC systemwide Bioengineering Symposium, Berkeley, CA. Computational guidance for protein design, including superfamilies, networks, and use of the SFLD. 8 hours prep time, 35 attendees. - Patsy Babbitt June 22, 2012 Nanomachine and virus visualization demo for 11 [http://igem.ucsf.edu iGem] students ages 17-19. 30 minutes, stereo visualization in viz vault, discussion of differences between human designed and biological molecular machines. 1 hour preparation. Organized by Shannon Noonan, Community Outreach Specialist, Gladstone Institutes. - Tom Goddard June 22, 2012 HIV virus visualization demonstration for 7 high school students in the [http://www.gladstone.ucsf.edu/gladstone/site/cso/section/2461 Gladstone Summer Scholars (GSS) Internship Program]. Looked at electron microscopy and atomic models of virus core and drug binding. 30 minute demo in viz vault. 1 hour preparation. Organized by Shannon Noonan, Community Outreach Specialist, Gladstone Institutes. - Tom Goddard June 22, 2012 Nanomachine and virus visualization demo for 6 [http://momagic.org Mo Magic] high school students. 30 minutes, stereo visualization in viz vault, discussion of differences between human designed and biological molecular machines. 1 hour preparation. Sponsored by Patricia Caldera, UCSF, Science & Health Education Partnership. - Tom Goddard July 3, 2012 Chimera training (3-hr session) for 4 members of the DeGrado group at UCSF, covering fetching data, structural analysis and comparison, H-bonds, superposition, morphing, attributes, working with sequences, density display, making movies; Q & A. 20 hours prep. - Elaine Meng, Eric Pettersen, Tom Ferrin July 11, 2012 Hands-on Chimera tutorials for 50 participants at the National University of Singapore [http://ncmi.bcm.edu/ncmi/events/workshops/workshops_125 cryoEM workshop]. [http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/nus.html Tutorials] covering electron tomography segmentation, molecule display, and fitting as well as an open question and answer session totaling 3 hours were presented via teleconference using WebEx with participants trying what they were shown on lab computers. Hosted by Cynthia He and Wah Chiu. 15 hours preparation. - Tom Goddard July 16, 2012 5th International Conference on Paraoxonases, Columbus, OH. Presented research on the "nucleophilic attack 6-bladed beta-propeller" (N6P) superfamily, including network analysis and data dissemination using the SFLD. 12 hours prep time, 120 attendees. - Patsy Babbitt July 26, 2012 Chimera visualization of HIV virus core and drug binding for 20 high school students from the UC Davis [http://cosmos.ucdavis.edu COSMOS program]. Organized by Sarah Driver from UC Davis. 20 minute demo. 1 hour preparation. - Tom Goddard, Tom Ferrin, Scooter Morris August 14, 2012 Chimera visualization demonstration covering protein structures and sequences (dipeptide epimerase) and multiple length scales, atoms through cells (T-cell tomography and termite gut EM). 90 minutes. 12 first year graduate students in structural and computational biology, Baylor College of Medicine. Presented via WebEx screen sharing. Hosted by Wah Chiu. 6 hours preparation. - Tom Goddard August 27, 2012 [http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html Movie making demonstration] showing how to morph electron microscopy maps and molecular structures fit into maps using Chimera. Used actin-like ParM filament data. Presented to 60 people at the Bay Area cryoEM meeting at Santa Cruz. Hosted by Melissa Jurica. 8 hours preparation. - Tom Goddard September 29, 2012 Workshop on the Radical SAM Superfamily (data in SFLD) at UCSF, full-day meeting with experts. Estimated 8 hours talk preparation, 30 attendees. - Gemma Holliday October 2-3, 2012 Chimera workshop at NIH, Bethesda MD. Eight sessions over two days, including introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis, publication images and movies. About 30 attendees, the room capacity. About 20 more participants off-site with video and audio using Adobe Connect. 150 hours preparation. [http://www.cgl.ucsf.edu/Outreach/Workshops/NIH-Oct-2012/ workshop materials] - Tom Ferrin, Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng October 4, 2012 Full-day Cytoscape workshop at NIH, Bethesda MD. Network visualization and analysis with Cytoscape. About 30 attendees, the room capacity. About 10 more participants off-site with video and audio using Adobe Connect. [http://www.cgl.ucsf.edu/Outreach/Workshops/NIH-Oct-2012/ workshop materials] - Scooter Morris, Elaine Meng October 4-5, 2012 Visits to NIH labs (Sriram Subramaniam, John Patton, Bernard Heymann, BK Lee, and others) for Chimera training using their data sets. Two days with RBVI staff divided into groups to help different labs. Topics included Chimera Python programming, HIV virus spikes, annotating FIBSEM imaging data, rotavirus RNA structures, hybrid model representations, and many others. - Tom Ferrin, Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng October 14-30, 2012 4 hours lecture in BMI206, Introduction to Bioinformatics (UCSF), featuring superfamily analysis, protein similarity networks, and the SFLD. The SFLD was also used as a primary data resource for a course lab assignment. 25 hours prep, ~9 attendees. - Patsy Babbitt October 17, 2012 UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students (about 25 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 16 hours including updating and rehearsing the presentation, updating and preparing handouts. - Elaine Meng, Eric Pettersen November 8, 2012 EFI meeting, San Francisco. SFLD new features. ~6 hours prep, ~15 participants including EFI Advisory Committee and NIH representatives. - Patsy Babbitt November 15, 2012 Demonstration of Chimera for viewing, segmenting and measuring microscopy data given at the Northern California Society for Microscopy meeting at UCSF. [http://www.cgl.ucsf.edu/chimera/data/ncsm-nov2012/microscopy.html Slides]. Walk through of segmenting and measuring termite gut bacteria. Audience of 50. Preparation time 20 hours. Hosted by Larry Ackerman and Steven Samuelsson. - Tom Goddard December 2, 2012 Lunch talk to faculty, Department of Bioengineering and Therapeutic Sciences, UCSF. The SFLD and enzyme functional annotation. 8 hours prep, 8 attendees. - Patsy Babbitt December 5, 2012 Gave 3 hour hands-on Chimera tutorial on map display and analysis at UC Berkeley. Covered basic molecular display, segmenting and fitting single particle maps, and extracting regions from termite gut FIBSEM data. 12 participants (Auer, Downing, Nogales, Berger labs). 8 hours preparation. Organized by Danielle Jorgens. - Tom Goddard December 13, 2012 Gave 3 hour hands-on tutorial for Cytoscape at the 2012 Cytoscape retreat (Gladstone Institutes, UCSF). 60 participants, 8 hours preparation. - Scooter Morris December 13, 2012 Cytoscape retreat (Gladstone Institutes, UCSF). Presentation on protein similarity networks and dissemination using the SFLD. 8 hours prep time, 60 attendees. - Patsy Babbitt December 19, 2012 Gave 3 hour hands-on advanced Chimera tutorial on map segmentation at UC Berkeley. Covered surface masking, watershed segmentation, and zones around markers and atoms using HIV virus, microtubule and T-cell maps. 10 participants. 8 hours preparation. Organized by Danielle Jorgens. - Tom Goddard January 7, 2013 Enzyme Mechanisms Meeting Workshop, San Diego, CA. Introduction to similarity networks and the SFLD. 12 hours prep time, 50 attendees. - Patsy Babbitt January 21, 2013 iPQB graduate program (UCSF) pizza talk including an introduction to the SFLD. 3 hours prep, ~30 attendees. - Patsy Babbitt January 29, 2013 Biophysics seminar at UT Southwestern Medical School, Dallas, TX. Similarity networks and the SFLD. 9 hours prep, 45 attendees. - Patsy Babbitt January 31, 2013 Gave a plenary presentation on Visualization Challenges in Network Biology at the HCI (Human-Computer Interaction) Korea annual conference. 2,000 participants, 20 hours preparation. - Scooter Morris February 7, 2013 [http://www.sbgrid.org/news/article/id=363 Webinar] for [http://www.sbgrid.org/Structural Biology Grid] demonstrating Chimera molecular assembly and electron microscopy tools. Built alpha crystallin model. 30 minute demo. 6 hours preparation. 35 participants. Organized by Michelle Ottaviano, Jason Key, and Piotr Sliz. - Tom Goddard February 8, 2013 Demonstrated Chimera visualization, satellite tobacco mosaic virus, differential gear nano-machine, x-ray density maps, to two groups of candidate graduate students for the UCSF iPQB program (biophysics and bioinformatics). 8 participants. 30 minutes each demo. 2 hours preparation. Organized by Rebecca Brown. - Tom Goddard February 15, 2013 Demonstrated Chimera visualization, white blood cell 3d motion and HIV reverse transcriptase inhibitor binding, to two groups of candidate graduate students for the UCSF iPQB program (biophysics and bioinformatics). 14 participants. 30 minutes each demo. 4 hours preparation. Organized by Rebecca Brown. - Tom Goddard March 4, 2013 Short introduction to the SFLD database, Conference on Predicting Cell Metabolism and Phenotypes, SRI international, Menlo Park, CA. 3 hours prep time and ~100 participants. - Eyal Akiva March 8, 2013 Demonstration showing molecules of life, water, protein, dna, drugs (THC and nevirapine), to 8 students from Dewey High School in Oakland using 3-d projection in the visualization vault. 30 minute demo. 6 hours preparation. Organized by Veronica Zepeda, UCSF iGEM and Education Coordinator. - Tom Goddard March 19, 2013 1/2 day Chimera tutorial at [http://vizbi.org/2013/ VizBI 2013], the 4th international meeting on Visualizing Biological Data (Broad Institute, Cambridge, MA). Anticipate about 15 participants. - Scooter Morris March 20, 2013 Invited talk on Network Visualization at [http://vizbi.org/2013/ VizBI 2013]. Anticipate an audience of about 200. - Scooter Morris April 5, 2013 Presentation on "Protein function curation: linking sequence & chemical reaction spaces in the SFLD" at [http://www.ebi.ac.uk/biocuration2013/content/meeting-schedule Biocuration 2013], the conference of the International Society for Biocuration (Cambridge, England). Anticipate 6 hours preparation, 100 attendees. - Gemma Holliday April 21, 2013 ASBMB (American Society for Biochemistry and Molecular Biology) annual meeting, Boston, MA. Introduction to networks and downloadable information available from the SFLD, as part of the EFI workshop "New strategies for function assignment." Anticipate 8 hours prep time, 75 attendees. - Patsy Babbitt May 29, 2013 EFI 3-year review. SFLD vision for the next 5 years. Anticipate 8 hours prep time, 15 participants. - Patsy Babbitt