Changes between Initial Version and Version 1 of COT13

Timestamp:

Jul 8, 2013, 11:51:21 AM (13 years ago)

Author:

Scooter Morris

Comment:

--

COT13

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+
+---------------------------------------------------------------------------
+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