Changes between Initial Version and Version 1 of COT10

Timestamp:

Mar 18, 2011, 4:04:59 PM (15 years ago)

Author:

goddard

Comment:

--

COT10

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+2009/2010 report
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+
+May 21, 2009
+  Talk to ten San Francisco high school teachers, part of the Current Science Seminar
+  Series organized by the UCSF Science and Health Education Partnership.
+  (http://biochemistry.ucsf.edu/programs/sep/) Showed stereo visualization and
+  manipulation of man-made molecular machines and viruses. Made paper virus models.
+  Held in RBVI visualization room.  12 hours preparation time.
+  - Tom Goddard
+
+June 11, 2009
+  Second talk to high school teachers in the Current Science Seminar Series given by the
+  UCSF Science and Health Education Partnership.  Showed stereo visualization and
+  manipulation of man-made molecular machines and viruses.  Made paper virus models.
+  Held in RBVI visualization room.  3 hours preparation time.
+  - Tom Goddard
+
+June 24, 2009
+  Virus visualization demonstration for a dozen science summer school students 
+  ages 9 to 12 (http://www.celsiusandbeyond.com/).  Showed stereo visualization,
+  space navigator, phantom force feedback, protein and rna structure and virus
+  paper models.  Held in RBVI visualization room.  12 hours preparation time.
+  - Tom Goddard
+
+July 14, 2009
+  Molecular visualization demonstration for ~30 kids from the COSMOS summer school
+  program at U.C. Davis (http://www.ucop.edu/cosmos/).  Showed stereo visualization,
+  virus structures, protein, dna, and protein docked with dna.
+  - Scooter Morris
+
+July 15, 2009
+  Virus visualization demonstration for 5 science summer school students 
+  ages 9 to 12 (http://www.celsiusandbeyond.com/).  Showed stereo visualization,
+  space navigator, phantom force feedback, protein and rna structure and virus
+  paper models.  Held in RBVI visualization room.  4 hours preparation time.
+  - Tom Goddard
+
+August 19, 2009
+  Chimera talk and demonstration, Molecular Visualization symposium
+  (COMP division, see http://oasys2.confex.com/acs/238nm/techprogram/S32080.HTM )
+  at the 238th American Chemical Society National Meeting (Washington, DC).
+  Prep time by Elaine 60 hours including deciding what features to show and finding an
+  appropriate biological system with which to show them, reading papers about the biological
+  system, generating or finding associated data files, testing the features thoroughly, 
+  and iteratively adjusting presentation order and scope.
+  - Tom Ferrin, Elaine Meng
+
+September 1, 2009
+  Demonstration for NIH visitors from Clinical and Translation Science Awards (CTSA).
+  Showed HIV spike tomography, T-cell tomography, clathrin cage animation, cytoscape.
+  Held in RBVI visualization room.  6 hours preparation time.
+  - Tom Goddard, Scooter Morris, Tom Ferrin
+
+September 22, 2009
+  Gave a talk and training session at the EMBO European School of Genetic Medicine course
+  entitled "Embo Practical course on Networks in Biology analysis, modeling and reverse
+  engineering."  My talk was an introduction to the "Analysis & Visualisation of biological networks"
+  and the practical covered uses of Cytoscape.  There were 60 students from throughout Europe, and 6 
+  faculty in attendance.  Prep time for talk: 16 hours, for lab: 8 hours.
+  - Scooter Morris 
+
+September 28, 2009
+  Gave an informal seminar at Institute Pasteur for 10 members of the Systems Biology Group
+  on uses of Cytoscape for phylogenetic analysis and cheminformatics.
+  - Scooter Morris
+
+September 30, 2009
+  45-minute Chimera demonstration to ~20 students in UCSF BP204A, "Macromolecular
+  Interactions" class.  Included basic usage, morphing, viewing sequences, showing
+  attribute values, building multimers.  Prep time 60 hours including looking up information
+  on the history of molecular graphics, working through exercises from the previous year, 
+  deciding what structures and features to show and in what order, generating or finding 
+  associated data files, testing the features thoroughly, and practicing the presentation.
+  - Elaine Meng, Eric Pettersen
+
+October 20, 2009
+  EMBO practical course: "The combination of electron microscopy and x-ray crystallography
+  for the structure determination of large biological complexes" (http://cwp.embo.org/pc09-18/).
+  One day (7 hours) of hands-on Chimera training during 5 day workshop.  20 students.  Grenoble, France.
+  60 hours preparing materials (http://www.cgl.ucsf.edu/chimera/tutorials/emfit09/emfit.html).
+  - Tom Goddard
+
+October 23, 2009
+  Gave a 3 hour training session to the UCSF BMI206 class (14 Graduate Students) on 
+  Cytoscape and structureViz.  Prep time: 12 hours.  Tutorials are available on-line
+  at http://opentutorials.rbvi.ucsf.edu/
+  - Scooter Morris
+
+December 1, 2009
+  Demonstrations for three Galileo High School student groups, part of SEP SMART team
+  program organized by Sabine Jeske (http://biochemistry.ucsf.edu/programs/sep/school-programs-smart-teams.html).
+  Presentations covered their proteins: HIV Rev,
+  capase-3, and strictosidine synthase.  Included protein analysis, EM data, stereo viewing,
+  space navigator, plastic and paper models.  Three groups of ~10 students each in RBVI
+  viz vault.  15 hours preparation and execution.
+  - Tom Goddard
+
+December 10, 2009
+  Demonstrations for two Lincoln High School student groups, part of SEP SMART team
+  program organized by Sabine Jeske (http://biochemistry.ucsf.edu/programs/sep/school-programs-smart-teams.html).
+  Presentations covered their proteins: P-glycoprotein and HIV protease.
+  Also included stereo visualization of nano-gears, ice, water, and lipid bilayers,
+  space navigator and plastic models.  Three groups of ~10 students each in RBVI
+  viz vault.  12 hours preparation and execution.
+  - Tom Goddard
+
+December 2009
+  Chimera and Cytoscape used to create image for RBVI holiday card: some of the nuclear pore complex proteins
+  arranged into a Christmas tree, RBVI logo as star, phylogenetic tree as white fronds along the "ground."
+  Estimated 24 person-hours of work.
+ - YZ (Zheng Yang) , Elaine Meng, Conrad Huang, Scooter Morris
+
+December 11, 2009
+  Chimera Release Party and RBVI Open House (2-5 pm in Genentech Hall N453,
+  UCSF Mission Bay) for local researchers and students to meet the Chimera
+  developers, see demonstrations and discuss features, tour the RBVI
+  facilities, and share refreshments. Estimated 80 attendees, 3 hours for the event,
+  24 person-hours preparation, publicity, and cleanup.
+  - Chimera team
+
+January 26, 2010
+  Remote training using desktop sharing (vnc/skype) for using the Segger segmentation tool to separate
+  bacteria seen in termite gut by focused-ion-beam scanning-EM.  Two hours of training for Bernhard
+  Knierim and Monica at Lawrence Berkeley Lab.  Four hours preparation time.
+  - Tom Goddard
+
+February 1, 2010
+  All day Cytoscape training for Cell Signaling Technologies in Salem, Mass.  20 Participants including Sr. Scientists,
+  CEO, Marketing personnel, and developers.  Preparation time ~20 hours. 
+  - Scooter Morris
+
+February 11, 2010
+  Talk at Scripps Research Institute Automated Molecular Imaging (AMI) Forum (http://ami.scripps.edu/forum/)
+  Demonstrated Segger segmentation and fitting capabilities (40 min + 20 min questions)
+  to 35 EM (single-particle and tomography) researchers.  Preparation time ~20 hours.
+  - Tom Goddard
+
+February 21-23, 2010
+  Exhibit booth at Biophysical Society Meeting in San Francisco, organized by Scooter Morris of RBVI.
+  Three days, ~24 demonstrations/talks, ~4 NCRR resource centers.
+  - Scooter Morris, Elaine Meng, Eric Pettersen, Zheng Yang, Tom Goddard
+
+February 25-26, 2010
+  Molecular Animation workshop sponsored by RBVI and NCMI.  Two days, ~25 participants, 14 talks.
+  Preparation time ~150 person-hours.  Hosted by and planned by Tom Ferrin and Scooter Morris from RBVI
+  and Wah Chiu from NCMI.  Two talks given by RBVI. [http://plato.cgl.ucsf.edu/trac/Workshops/login/wiki/AnimationWorkshop]
+  - Tom Ferrin, Scooter Morris, Tom Goddard, Zheng Yang
+
+March 11-13, 2010
+  Poster on HIV spike visualization presented at the 5th International Conference on Structural Analysis of Supramolecular
+  Assemblies by Hybrid Methods in Lake Tahoe (http://www.hybridmethods2010.com/).  About 180 researchers primarily using
+  electron microscopy attended.  Discussed EM map fitting using Chimera
+  and EMDB map and segmentation file formats with approximately 20 people.  Preparation time ~15 hours.
+  - Zheng Yang, Tom Goddard
+
+March 17, 2010
+  1/2 Day Cytoscape training for Al Burlingame's group.  13 participants.  Preparation time: ~10 hours.
+  - Scooter Morris