Changes between Version 71 and Version 72 of COT

Timestamp:

Dec 7, 2011, 2:10:40 PM (14 years ago)

Author:

goddard

Comment:

--

COT

@@ -120 +120 @@
 
 
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-2010/2011 report
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-
-June 2010 - March 2011
-  Created 23 [http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html video tutorials]
-  demonstrating different analysis techniques of electron microscopy density maps and
-  molecular models using UCSF Chimera.  Most videos are 5 to 10 minute long computer
-  screen captures with audio narration showing step-by-step analysis.  Each was made to
-  address specific questions posed by users.  Streaming videos are distributed via the
-  RBVI web site using an in-browser Flash movie player.  Total preparation time 50 hours.
-  - Tom Goddard
-
-June 9, 2010 and July 7, 2010 and July 21, 2010
-  Demonstration showing DNA for total of 38 students ages 8-12 from
-  [http://www.celsiusandbeyond.com/ Celsius and Beyond]
-  summer science camp on 3 separate days.
-  Organized with Auritte Cohen-Ross.  Showed light
-  microscopy volume time series of chromosomes in dividing cells, electron
-  microscopy of chromosomes, DNA molecular structure, nucleosomes and chromatin
-  (http://www.cgl.ucsf.edu/chimera/dna-jun2010/dnademo.html).
-  8 hours preparation.  1 hour demonstration in RBVI visualization room.
-  Many questions from kids "What happens if you eat a bubble?".
-  - Tom Goddard
-
-June 16-17, 2010
-  Summer School '10 : Python Applied to Computational Chemistry and Molecular Modelling,
-  Universitat Autònoma de Barcelona, Spain. ~50 attendees.
-  http://hpc.xrqtc.com/index.php?option=com_content&view=article&id=118:sm10-module-c&catid=54:recent-conference&Itemid=75
-   - Conrad Huang
-
-July 11, 2010
-  Presentation on Cytoscape at ISMB 2010 to an audience of approximately 60.
-  http://www.iscb.org/cms_addon/conferences/ismb2010/technologytrack.php
-  Boston, MA.
-  The presentation provided an introduction to Cytoscape's capabilities and
-  some of the new features in Cytoscape 2.7 along with some new and recently
-  enhanced plugins.
-  - Scooter Morris
-
-July 13, 2010
-  "Network visualization and analysis using Cytoscape" Birds of a Feather
-  session at ISMB 2010.  Scooter Morris facilitated this session to solicit
-  input from Cytoscape users and developers.  About 30 participants.
-
-July 18, 2010
-  "Cytoscape User Tutorial".  2 hour introductory user tutorial given to about
-  50 users as part of the annual Cytoscape Retreat.
-  - Scooter Morris
-
-July 18, 2010
-  Plugin demonstration on CyCommandHandlers as part of the Cytoscape Retreat to
-  about 100 participants. University of Michigan, Ann Arbor, MI.
-  - Scooter Morris
-
-July 22, 2010
-  Gave two 20 minute demonstrations to 24 students, part of [http://www.ucop.edu/cosmos/ COSMOS] science
-  program.  Organized by Ken Dill. Showed DNA atomic models, small duplex, nucleosomes,
-  chromatin filament model, chromosomes seen in electron microscopy.  Used RBVI visualization room.
-  8 hours preparation.
-  - Tom Goddard
-
-August 16, 2010
-   Tutorial given at CSB 2010, Stanford: "Analysis and Visualization of Biological Networks".
-   This was a 1/2 day tutorial given to 15 participants that covered visualization
-   and analytical approaches to understanding biological networks.  Second half of
-   tutorial introduced Cytoscape as a tool and provided a hands-on exercise. 
-   - Scooter Morris
-
-August 16, 2010
-  10 minute SFLD demo, followed by 2 hour SFLD/cytoscape tutorial.  Attendees worked through
-  exercises designed to give them basic familiarity with manipulating a cytoscape sequence
-  and/or structure similarity network of their superfamily of choice, of the sort downloaded
-  from the SFLD, to investigate questions of biological interest.
-  Audience: ~25 grad students, postdocs, staff from the EFI. 15 hours preparation.
-  - Shoshana Brown
-
-September 29, 2010
-  40-minute presentation to ~14 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 12 hours including updating the previous
-  year's presentation, testing with the current version of Chimera, rehearsing.
-  - Elaine Meng, Eric Pettersen
-
-September 29, 2010
-  30-minute presentation to ~50 attendees, then followed by 90-minute tutorial to ~20 students at 
-  Department of Computational and System Biology, School of Medicine and Clinical Translational 
-  Science Institute, University of Pittsburgh. The presentation part, titled "Introduction to UCSF 
-  Chimera, an Extensible Molecular Modeling System", covered the brief history of molecular
-  visualization, RBVI history and Chimera highlighted features. The tutorial part went over
-  several basic examples in the "getting started" document. Prep time 40 hours. 
-  - YZ (Zheng Yang)
-
-October 12-13, 2010
-  Poster presentation on segmentation and measurement of bacteria in termite gut at NIH workshop
-  "Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and 
-  Cellular Structures". 170 participants. 12 hours preparation.  
-  Discussions of research projects with about 10 attendees
-  https://conferences.niaid.nih.gov/vbbethesda/
-  - Tom Goddard
-
-October 25, 2010
-  Invited talk, "Annotation Error in Public Databases," at the 2010 Pathway Tools Workshop,
-  Menlo Park, CA.  http://bioinformatics.ai.sri.com/ptools10/agenda.html
-  Discussed SFLD and using sequence similarity networks in Cytoscape. ~100 attendees.
-  - Alexandra Schnoes
-
-October 27, 2010
-  45-minute Chimera teaching demonstration to ~30 students for a graduate course in protein 
-  engineering at UC Berkeley (taught by Danielle Tullman-Ercek, Asst. Professor, Dept. of
-  Chemical and Biomolecular Engineering, UC Berkeley). Covered basic usage, finding H-bonds,
-  morphing, saving trajectories as movies, viewing sequences, showing attribute values, 
-  evaluating rotamers, performing virtual mutations, building multimers, and using stereo.  
-  Prep time 20 hours including adding more material to the previously developed demo, 
-  testing with the current version of Chimera, and rehearsing.
-  - Elaine Meng, Eric Pettersen
-
-November 18, 2010
-  Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to
-  SMART team Lincoln high school students.  This is a UCSF Science and Health Education
-  Partnership (SEP) program.  Showed FIBSEM data, spirochetes, flagella, handedness,
-  endo-flagella, protein morphing, hydrophobic and electrostatic surface coloring to identify
-  transmembrane and binding regions. 16 students.  6 hours preparation.
-  - Tom Goddard
-
-December 2010
-  Chimera used to create image for RBVI holiday card: glutamine synthetase 12-mer styled as an 
-  "architectural plan" (black outlines around transparent ribbons on aged parchment background). Estimated 36 person-hours of work (including preparing candidate images, voting, format converting).
- - YZ (Zheng Yang) 
-
-December 2, 2010
-  Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to
-  SMART team Galileo high school students.  This is a UCSF Science and Health Education Partnership (SEP)
-  program.  Showed FIBSEM data, spirochetes, flagella, handedness, endo-flagella, protein morphing,
-  hydrophobic and electrostatic surface coloring to identify transmembrane and binding regions.
-  20 students.  4 hours preparation.
-  - Tom Goddard
-
-December 8, 2010
-  Two hour discussion and Chimera demonstration of myosin thick filament regulation for
-  UCSF Tetrad graduate program macromolecules discussion group. Looked at thick filament architecture and
-  myosin 2 heavy and light chain atomic models using stereo 3d visualization.  5 graduate
-  students, led by professor Zev Gartner.  8 hours preparation.
-  - Tom Goddard
-
-December 13, 2010
-  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 50 attendees, 3 hours for the event,
-  24 person-hours preparation, publicity, and cleanup.
-  - Chimera team
-
-January 12, 2010
-  Created 3 videos showing how to explore virus models for HHMI Viral Outbreak
-  CDROM distribution to US high schools.  Videos totaled 15 minutes and explained
-  Chimera virus display, finding viruses structures on the web, and antibodies
-  bound to West Nile virus.  Expected distribution is several thousand CDs.
-  Preparation time 15 hours.
-  - Tom Goddard
-
-January 13, 2011
-  20 minute SFLD demo, followed by 10 minute Q & A, showing how the SFLD can be used to get
-  information about the biological context of an uncharacterized target of interest.  
-  Audience: ~20 EFI investigators and other staff. 15 hours preparation.
-  - Shoshana Brown
-
-February 11, 2011
-  Demonstration showing immune system structures to 7 visiting candidate UCSF graduate
-  students.  West Nile virus with bound antibodies, cytotoxic T-cell EM data.  Also
-  showed 3d printer and plastic molecular models.  Two 35 minute demonstrations.
-  4 hours preparation.
-  - Tom Goddard
-
-February 11, 2011
-  Seminar at University of Toronto covering base cytoscape and RBVI plugins to group
-  of about 50.  The seminar was 2 hours and included introductory topics as well as
-  some advanced discussion.
-  10 hours preparation
-  - Scooter Morris
-
-February 18, 2011
-  Demonstration showing clathrin cages to 4 visiting candidate UCSF graduate
-  students.  Clathrin cage triskelions, molecular assembly model, animation.  Also
-  showed 3d printer and plastic molecular models.  Two 35 minute demonstrations.
-  4 hours preparation.
-  - Tom Goddard
-
-March 14-17, 2011
-  Chimera tutorial at [http://blake.bcm.edu/emanwiki/Ws2011/Agenda EMAN single particle reconstruction workshop],
-  showing fitting atomic models in electron microscopy maps, symmetry, presentation images
-  using Rous sarcoma virus data.  Produced
-  [http://www.cgl.ucsf.edu/chimera/videodoc/RousSarcomaVirus/ video version] of the workshop tutorial.
-  Tutorial was 1 hour with ~100 participants at University of Houston.
-  Answered approximately 30 Chimera usage questions during 4-day workshop
-  and demonstrated features to individual workshop participants, about 10 hours total time.
-  20 hours preparation.
-  - Tom Goddard
-
-March 19, 2011
-  Half day Cytoscape tutorial at [http://vizbi.org/2011/ VizBI 2011] to 20 participants, showing basic Cytoscape plus clusterMaker, structureViz, chemViz, and nodeCharts.  This was followed by a half day workshop where participants brought their own data sets and collaborated on analyses and visualizations.
-
-  16 hours preparation
-  - Scooter Morris
 
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-Past reports [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
+Past reports [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
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