Changes between Initial Version and Version 1 of COT11


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Timestamp:
Dec 7, 2011, 2:09:48 PM (14 years ago)
Author:
goddard
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  • COT11

    v1 v1  
     1---------------------------------------------------------------------------
     22010/2011 report
     3---------------------------------------------------------------------------
     4
     5June 2010 - March 2011
     6  Created 23 [http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html video tutorials]
     7  demonstrating different analysis techniques of electron microscopy density maps and
     8  molecular models using UCSF Chimera.  Most videos are 5 to 10 minute long computer
     9  screen captures with audio narration showing step-by-step analysis.  Each was made to
     10  address specific questions posed by users.  Streaming videos are distributed via the
     11  RBVI web site using an in-browser Flash movie player.  Total preparation time 50 hours.
     12  - Tom Goddard
     13
     14June 9, 2010 and July 7, 2010 and July 21, 2010
     15  Demonstration showing DNA for total of 38 students ages 8-12 from
     16  [http://www.celsiusandbeyond.com/ Celsius and Beyond]
     17  summer science camp on 3 separate days.
     18  Organized with Auritte Cohen-Ross.  Showed light
     19  microscopy volume time series of chromosomes in dividing cells, electron
     20  microscopy of chromosomes, DNA molecular structure, nucleosomes and chromatin
     21  (http://www.cgl.ucsf.edu/chimera/dna-jun2010/dnademo.html).
     22  8 hours preparation.  1 hour demonstration in RBVI visualization room.
     23  Many questions from kids "What happens if you eat a bubble?".
     24  - Tom Goddard
     25
     26June 16-17, 2010
     27  Summer School '10 : Python Applied to Computational Chemistry and Molecular Modelling,
     28  Universitat Autònoma de Barcelona, Spain. ~50 attendees.
     29  http://hpc.xrqtc.com/index.php?option=com_content&view=article&id=118:sm10-module-c&catid=54:recent-conference&Itemid=75
     30   - Conrad Huang
     31
     32July 11, 2010
     33  Presentation on Cytoscape at ISMB 2010 to an audience of approximately 60.
     34  http://www.iscb.org/cms_addon/conferences/ismb2010/technologytrack.php
     35  Boston, MA.
     36  The presentation provided an introduction to Cytoscape's capabilities and
     37  some of the new features in Cytoscape 2.7 along with some new and recently
     38  enhanced plugins.
     39  - Scooter Morris
     40
     41July 13, 2010
     42  "Network visualization and analysis using Cytoscape" Birds of a Feather
     43  session at ISMB 2010.  Scooter Morris facilitated this session to solicit
     44  input from Cytoscape users and developers.  About 30 participants.
     45
     46July 18, 2010
     47  "Cytoscape User Tutorial".  2 hour introductory user tutorial given to about
     48  50 users as part of the annual Cytoscape Retreat.
     49  - Scooter Morris
     50
     51July 18, 2010
     52  Plugin demonstration on CyCommandHandlers as part of the Cytoscape Retreat to
     53  about 100 participants. University of Michigan, Ann Arbor, MI.
     54  - Scooter Morris
     55
     56July 22, 2010
     57  Gave two 20 minute demonstrations to 24 students, part of [http://www.ucop.edu/cosmos/ COSMOS] science
     58  program.  Organized by Ken Dill. Showed DNA atomic models, small duplex, nucleosomes,
     59  chromatin filament model, chromosomes seen in electron microscopy.  Used RBVI visualization room.
     60  8 hours preparation.
     61  - Tom Goddard
     62
     63August 16, 2010
     64   Tutorial given at CSB 2010, Stanford: "Analysis and Visualization of Biological Networks".
     65   This was a 1/2 day tutorial given to 15 participants that covered visualization
     66   and analytical approaches to understanding biological networks.  Second half of
     67   tutorial introduced Cytoscape as a tool and provided a hands-on exercise.
     68   - Scooter Morris
     69
     70August 16, 2010
     71  10 minute SFLD demo, followed by 2 hour SFLD/cytoscape tutorial.  Attendees worked through
     72  exercises designed to give them basic familiarity with manipulating a cytoscape sequence
     73  and/or structure similarity network of their superfamily of choice, of the sort downloaded
     74  from the SFLD, to investigate questions of biological interest.
     75  Audience: ~25 grad students, postdocs, staff from the EFI. 15 hours preparation.
     76  - Shoshana Brown
     77
     78September 29, 2010
     79  40-minute presentation to ~14 students in UCSF BP204, "Macromolecular Interactions
     80  and Assemblies" class.  Included 5 min on history of Computer Graphics Lab, the remainder
     81  a Chimera demonstration: basic usage, morphing, viewing sequences, showing attribute
     82  values, building multimers, stereo.  Prep time 12 hours including updating the previous
     83  year's presentation, testing with the current version of Chimera, rehearsing.
     84  - Elaine Meng, Eric Pettersen
     85
     86September 29, 2010
     87  30-minute presentation to ~50 attendees, then followed by 90-minute tutorial to ~20 students at
     88  Department of Computational and System Biology, School of Medicine and Clinical Translational
     89  Science Institute, University of Pittsburgh. The presentation part, titled "Introduction to UCSF
     90  Chimera, an Extensible Molecular Modeling System", covered the brief history of molecular
     91  visualization, RBVI history and Chimera highlighted features. The tutorial part went over
     92  several basic examples in the "getting started" document. Prep time 40 hours.
     93  - YZ (Zheng Yang)
     94
     95October 12-13, 2010
     96  Poster presentation on segmentation and measurement of bacteria in termite gut at NIH workshop
     97  "Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and
     98  Cellular Structures". 170 participants. 12 hours preparation. 
     99  Discussions of research projects with about 10 attendees
     100  https://conferences.niaid.nih.gov/vbbethesda/
     101  - Tom Goddard
     102
     103October 25, 2010
     104  Invited talk, "Annotation Error in Public Databases," at the 2010 Pathway Tools Workshop,
     105  Menlo Park, CA.  http://bioinformatics.ai.sri.com/ptools10/agenda.html
     106  Discussed SFLD and using sequence similarity networks in Cytoscape. ~100 attendees.
     107  - Alexandra Schnoes
     108
     109October 27, 2010
     110  45-minute Chimera teaching demonstration to ~30 students for a graduate course in protein
     111  engineering at UC Berkeley (taught by Danielle Tullman-Ercek, Asst. Professor, Dept. of
     112  Chemical and Biomolecular Engineering, UC Berkeley). Covered basic usage, finding H-bonds,
     113  morphing, saving trajectories as movies, viewing sequences, showing attribute values,
     114  evaluating rotamers, performing virtual mutations, building multimers, and using stereo. 
     115  Prep time 20 hours including adding more material to the previously developed demo,
     116  testing with the current version of Chimera, and rehearsing.
     117  - Elaine Meng, Eric Pettersen
     118
     119November 18, 2010
     120  Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to
     121  SMART team Lincoln high school students.  This is a UCSF Science and Health Education
     122  Partnership (SEP) program.  Showed FIBSEM data, spirochetes, flagella, handedness,
     123  endo-flagella, protein morphing, hydrophobic and electrostatic surface coloring to identify
     124  transmembrane and binding regions. 16 students.  6 hours preparation.
     125  - Tom Goddard
     126
     127December 2010
     128  Chimera used to create image for RBVI holiday card: glutamine synthetase 12-mer styled as an
     129  "architectural plan" (black outlines around transparent ribbons on aged parchment background). Estimated 36 person-hours of work (including preparing candidate images, voting, format converting).
     130 - YZ (Zheng Yang)
     131
     132December 2, 2010
     133  Two 45-minute demonstrations showing termite gut and OpcA meningitis bacterium protein to
     134  SMART team Galileo high school students.  This is a UCSF Science and Health Education Partnership (SEP)
     135  program.  Showed FIBSEM data, spirochetes, flagella, handedness, endo-flagella, protein morphing,
     136  hydrophobic and electrostatic surface coloring to identify transmembrane and binding regions.
     137  20 students.  4 hours preparation.
     138  - Tom Goddard
     139
     140December 8, 2010
     141  Two hour discussion and Chimera demonstration of myosin thick filament regulation for
     142  UCSF Tetrad graduate program macromolecules discussion group. Looked at thick filament architecture and
     143  myosin 2 heavy and light chain atomic models using stereo 3d visualization.  5 graduate
     144  students, led by professor Zev Gartner.  8 hours preparation.
     145  - Tom Goddard
     146
     147December 13, 2010
     148  Chimera Release Party and RBVI Open House (2-5 pm in Genentech Hall N453,
     149  UCSF Mission Bay) for local researchers and students to meet the Chimera
     150  developers, see demonstrations and discuss features, tour the RBVI
     151  facilities, and share refreshments. Estimated 50 attendees, 3 hours for the event,
     152  24 person-hours preparation, publicity, and cleanup.
     153  - Chimera team
     154
     155January 12, 2010
     156  Created 3 videos showing how to explore virus models for HHMI Viral Outbreak
     157  CDROM distribution to US high schools.  Videos totaled 15 minutes and explained
     158  Chimera virus display, finding viruses structures on the web, and antibodies
     159  bound to West Nile virus.  Expected distribution is several thousand CDs.
     160  Preparation time 15 hours.
     161  - Tom Goddard
     162
     163January 13, 2011
     164  20 minute SFLD demo, followed by 10 minute Q & A, showing how the SFLD can be used to get
     165  information about the biological context of an uncharacterized target of interest. 
     166  Audience: ~20 EFI investigators and other staff. 15 hours preparation.
     167  - Shoshana Brown
     168
     169February 11, 2011
     170  Demonstration showing immune system structures to 7 visiting candidate UCSF graduate
     171  students.  West Nile virus with bound antibodies, cytotoxic T-cell EM data.  Also
     172  showed 3d printer and plastic molecular models.  Two 35 minute demonstrations.
     173  4 hours preparation.
     174  - Tom Goddard
     175
     176February 11, 2011
     177  Seminar at University of Toronto covering base cytoscape and RBVI plugins to group
     178  of about 50.  The seminar was 2 hours and included introductory topics as well as
     179  some advanced discussion.
     180  10 hours preparation
     181  - Scooter Morris
     182
     183February 18, 2011
     184  Demonstration showing clathrin cages to 4 visiting candidate UCSF graduate
     185  students.  Clathrin cage triskelions, molecular assembly model, animation.  Also
     186  showed 3d printer and plastic molecular models.  Two 35 minute demonstrations.
     187  4 hours preparation.
     188  - Tom Goddard
     189
     190March 14-17, 2011
     191  Chimera tutorial at [http://blake.bcm.edu/emanwiki/Ws2011/Agenda EMAN single particle reconstruction workshop],
     192  showing fitting atomic models in electron microscopy maps, symmetry, presentation images
     193  using Rous sarcoma virus data.  Produced
     194  [http://www.cgl.ucsf.edu/chimera/videodoc/RousSarcomaVirus/ video version] of the workshop tutorial.
     195  Tutorial was 1 hour with ~100 participants at University of Houston.
     196  Answered approximately 30 Chimera usage questions during 4-day workshop
     197  and demonstrated features to individual workshop participants, about 10 hours total time.
     198  20 hours preparation.
     199  - Tom Goddard
     200
     201March 19, 2011
     202  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.
     203
     204  16 hours preparation
     205  - Scooter Morris