Changes between Version 79 and Version 80 of COT


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Timestamp:
Apr 20, 2012, 12:20:10 PM (14 years ago)
Author:
tef
Comment:

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  • COT

    v79 v80  
    2020
    2121---------------------------------------------------------------------------
    22 2011/2012 report
     222012/2013 report
    2323---------------------------------------------------------------------------
    2424
    25 May 2, 2011
    26   Lunch Talk to Faculty, SFLD and enzyme function annotation, Dept. of Bioengineering & Therapeutic Sciences, UCSF, 8 hours prep time, 8 attendees.
    27   - Patsy Babbitt
     25April 21, 2012
     26  UCSF Alumni Homecoming Demonstrations. A series of 30 minute demonstrations were given
     27  to several groups (about 100 individuals overall) of UCSF alumni from the Schools of
     28  Medicine and Pharmacy, and the PhD programs.
    2829
    29 May 19, 2011
    30   Cytoscape User Tutorial given at the Cytoscape Retreat in San Diego.  Had about 60 participants. Total
    31   prep time was about 10 hours.
    32   - Scooter Morris
     30April 23, 2012
     31  Molecular visualization demonstration for 10 high school science teachers from the
     32  San Francisco Unified School District.
    3333
    34 May 24, 2011
    35   Interview and HIV capsid demonstration for an [http://connectedsocialmedia.com/6518/future-lab-3d-molecular-visualization/ NPR Future Lab podcast] sponsored by Intel Research on molecular visualization.  Showed NPR reporter Deirdre Kennedy 3d stereo visualization and answered questions.  Prep and delivery 5 hours.
    36   - Tom Ferrin, Elaine Meng, Tom Goddard
    37 
    38 May 24, 2011
    39   SFLD new feature presentation at EFI May Meeting in San Francisco. ~6 hours prep time and ~60 participants.
    40   - Florian Lauck
    41 
    42 May 24, 2011
    43   SFLD new progress and future plans at EFI May Meeting in San Francisco. ~6 hours prep time and 15 participants.
    44   - Patsy Babbitt
    45 
    46 June 8, 2011
    47   Cytoscape and Proteomics.  Training class given at UCSF to 8-10 UCSF campus researchers doing proteomics, specifically using MassSpec-based approaches.  Total prep time was 5 hours.
    48   - Scooter Morris
    49 
    50 June 23, 2011
    51   [http://www.cgl.ucsf.edu/chimera/hiv-core-june2011/hivcore.html HIV capsid demonstration] given to 10 high school students from [http://momagic.org Mo' MAGIC] program organized by UCSF Science and Health Education Partnership (SEP).  Showed 3-d stereo visualization, space navigator, plastic models in visualization vault.  Prep and delivery 5 hours.
    52   - Tom Goddard
    53 
    54 June 26 - July 1, 2011
    55   Chimera [http://www.cgl.ucsf.edu/chimera/3dem-june2011/fitdemo.html fitting talk] demonstrating global, sequential and symmetric fitting at [http://www.grc.org/programs.aspx?year=2011&program=threedim 3D EM Gordon conference], 200 participants, New Hampshire.  Also 2 hour Chimera question and answer session with 20 participants.  Prep and delivery 20 hours.
    56   - Tom Goddard
    57 
    58 July 11-12, 2011
    59   [http://edu.isb-sib.ch/course/view.php?id=97 Cytoscape User Tutorial and Developer's Workshop] at the Swiss Institute of Bioinformatics (SIB).  50 participants.  Total prep time was 20 hours.
    60   - Scooter Morris
    61 
    62 July 15, 2011
    63   Helped organize the [http://www.iscb.org/ismbeccb2011-program/satellite-meetings#network Network Biology SIG] at ISMB 2011 in Austria, Vienna.  Total participants: 160.
    64   - Scooter Morris
    65 
    66 July 16, 2011
    67   Gave a [http://www.iscb.org/ismbeccb2011-program/tutorials#pm5 Tutorial on Network Biology and Cytoscape] at ISMB 2011 in Austria, Vienna.  Total participants: 35.  Total prep time was 40 hours.
    68   - Scooter Morris
    69 
    70 July 18, 2011
    71    Gave an invited talk on user interface development in the [https://www.iscb.org/ismbeccb2011-program/workshops#w3 Data Visualization and User Interfaces] workshop at ISMB.  Total participants: 140.  Total prep time was 40 hours.
    72   - Scooter Morris
    73 
    74 July 26, 2011
    75   Society for Industrial Microbiology, New Orleans, SFLD intro and discussion, 8 hours prep time, 45 attendees.
    76   - Patsy Babbitt
    77 
    78 July 28, 2011
    79   Hosted the [http://cosmos.ucdavis.edu/ COSMOS kids] from UC Davis' Summer School for Math and Science. Viewed virus capsids in Chimera, influenza hemagglutinin conformational change. Total participants: 21.  Total prep/organizational time: 20 hours.
    80   - Scooter Morris
    81 
    82 August 16, 2011
    83   [http://www.ucsf.edu/news/2011/07/10230/ucsf-lead-first-annual-bay-area-science-festival Bay Area Science Festival]
    84   publicity event demonstrations for House of Representatives Minority Leader
    85   Nancy Pelosi and San Francisco Mayor Ed Lee.  Showed HIV capsid visualization.  Visualization Vault room.
    86   10 guests and press.  4 hours preparation.
    87   - Tom Goddard
    88 
    89 September 20, 2011
    90   Two hiv capsid visualization demonstrations, 30 minutes each, for
    91   [http://scienceonthemove.wordpress.com/2011/08/12/hello-world/ 22 Swiss high school students]
    92   who won the Swiss
    93   [http://www.simplyscience.ch/desktopdefault.aspx/tabid-335/admin-1/ "Science on the Move"]
    94   national science competition sponsored by Roche and Genentech.  Arranged by Susan Jacobson at UCSF.
    95   Prep time 4 hours.
    96   - Tom Goddard
    97 
    98 September 21, 2011
    99   Introduced SFLD in lecture for BMI206 core graduate course in bioinformatics, Biological and Medical Informatics Graduate Program, 15 hours prep time and 20 students.
    100   - Patsy Babbitt
    101 
    102 September 23, 2011
    103   Cytoscape Lab on the annotation of new enzyme functions using SFLD examples and data, BMI206 core graduate course in bioinformatics, Biological and Medical Informatics Graduate Program. 2 hours prep time and 20 students.
    104   - Patsy Babbitt
    105 
    106 September 30, 2011
    107   35-minute presentation to >25 students in UCSF BP204, "Macromolecular Interactions
    108   and Assemblies" class.  Included 5 min on history of Computer Graphics Lab, the remainder
    109   a Chimera demonstration: basic usage, morphing, viewing sequences, showing attribute
    110   values, building multimers, stereo.  Prep time 16 hours including updating the previous
    111   year's presentation, testing with the current version of Chimera, rehearsing the demo,
    112   preparing handouts, working through the homework assignment with current version of Chimera
    113   and making a "cheat sheet" for the TAs of commands that could be used for that homework.
    114   - Elaine Meng, Eric Pettersen, Tom Goddard
    115 
    116 October 18, 2011
    117   Talk to new iPQB (Integrative Program in Quantitative Biology) graduate students, UCSF, SFLD intro and discussion, 8 hours prep time, 45 attendees.
    118   - Patsy Babbitt
    119 
    120 October 19, 2011
    121   Talk to new PSPG (Pharmaceutical Sciences and Pharmacogenomics) graduate students, UCSF, SFLD intro and discussion, 4 hours prep time, 12 attendees.
    122   - Patsy Babbitt
    123 
    124 October 22, 2011
    125   Talk at joint UCB/UCSF graduate student retreat, Lake Tahoe, SFLD intro and discussion, 8 hours prep time, 100 attendees.
    126   - Patsy Babbitt
    127 
    128 November 2, 2011
    129   Bay Area Science Festival 20 minute demonstration of HIV capsid visualization for 10 Balboa High School
    130   students. Presented in visualization vault room.
    131   - Scooter Morris
    132 
    133 November 13, 2011
    134   Lecture for BioE 280: joint UCB/UCSF graduate seminar series, SFLD intro and discussion, 5 hours prep time, 30
    135 attendees.
    136   - Patsy Babbitt
    137 
    138 November 30, 2011
    139   Hands-on Chimera tutorial at Purdue University.  90 minutes, 25 participants, 8 hours preparation.
    140   Organized by Michael Rossmann.  Covered building a ParM filament using an EM map and Xray stucture.
    141   - Tom Goddard
    142 
    143 November 30, 2011
    144   Structural Biology Seminar talk at Purdue University, by invitation of Michael Rossmann.
    145   1 hour, 45 in audience, 16 hours preparation.  Demonstrated hypothetical modeling of alpha
    146   crystallin and HIV capsid and RNA.
    147   - Tom Goddard
    148 
    149 November 30, 2011
    150   SFLD new feature presentation at EFI November-December Meeting in San Francisco. ~3 hours prep time
    151 and ~40 participants.
    152   - Florian Lauck
    153 
    154 November 30, 2011
    155   SFLD new progress and future plans at EFI Advisory Committee Meeting in San Francisco. ~6 hours prep time and 25 participants.
    156   - Patsy Babbitt
    157 
    158 December 1, 2011
    159   Chimera hands-on training at Indiana University.  2.5 hours, 30 participants primarily undergraduates,
    160   8 hours preparation.  Organized by David Morgan.  Covered alpha crystallin model building using Xray
    161   structures and an EM map.  90 minute follow-along tutorial, 60 minute question and answer session on all
    162   Chimera topics.
    163   - Tom Goddard
    164 
    165 December 6, 2011
    166   Chimera demonstration for University of San Francisco biochemistry class.  30 minutes, 8 participants,
    167   4 hours preparation.  USF teacher Willie Melaugh.  Showed pombe cell x-ray tomography and dipeptide epimerase
    168   enzyme structure which performs a step in recycling bacterial peptidoglycan cell wall.
    169   - Tom Goddard, Elaine Meng
    170 
    171 January 9, 2012
    172   Stereo visualization demonstration for Li Ka Shing Foundation, Solina Chau and 5 others. HIV core particle.
    173   20 minute demo, 2 hours preparation and delivery.  Organized by Michael Faber.
    174   - Tom Goddard, Tom Ferrin
    175 
    176 February 2, 2012
    177   Talk on Network Biology at the Institute Pasteur.  Hosted by Benno Schwikowski.  Talk was 45 minutes with
    178   15 minutes of Q&A.  Had 30-35 participants.  About 2 hours of preparation.
    179   - Scooter Morris
    180 
    181 February 10, 2012
    182   HIV visualization demonstration for UCSF iPQB candidate students.  5 students, 30 minutes demo, 2 hours
    183   preparation and delivery.  Organized by Rebecca Brown.
    184   - Tom Goddard
    185 
    186 February 17, 2012
    187   HIV visualization demonstration for UCSF iPQB candidate students.  5 students, two 30 minute demonstrations,
    188   2 hours preparation and delivery.  Organized by Rebecca Brown.
    189   - Tom Goddard
    190 
    191 February 23, 2012
    192   HIV visualization and stereo demonstrations for VIP guests attending the Byer's Lecture Celebration.
    193   30 guests split in 3 groups, 10 minute demonstrations for each group, 3 hours preparation.  Organized
    194   by Michael Faber of the UCSF donor development office.
    195   - Tom Goddard, Tom Ferrin
    196 
    197 February 26-27, 2012
    198   Planetarium dome animation at the 2012 Biophysical Society meeting in San Diego. Created 6 minute
    199   [http://www.cgl.ucsf.edu/chimera/data/hiv-rna-jan2012/story.html animation] shown several times over two days in the
    200   [http://www.biophysics.org/2012meeting/Program/SpecialFunctions/BiomolecularDiscoveryDome/tabid/3857/Default.aspx biomolecular discovery dome].  Molecular machines that replicate HIV RNA. 20 days production effort.
    201   Organized by Wah Chiu, Matt Daugherty and Ed Egelman.
    202   - Tom Goddard, Tom Ferrin
    203 
    204 March 5, 2012
    205   Chimera tutorial at the VizBI conference in Heidelberg, Germany.  Tutorial covered basics of molecular visualization and molecular animation.  Total duration, 3 hours.  10 participants.  8 hours preparation time.
    206   - Scooter Morris, Graham Johnson
    207 
    208 March 5, 2012
    209   Cytoscape plugin development tutorial at the VizBI conference in Heidelberg, Germany.  Total duration, 3 hours.  20 participants.  8 hours preparation time.
    210   - Scooter Morris
    211 
    212 March 12-13, 2012
    213   Cytoscape tutorial at the Swiss Institute of Bioinformatics in Lausanne.  Total duration: 2 days.  40 participants.
    214   - Scooter Morris
    21534
    21635---------------------------------------------------------------------------
    217 Past reports [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
     36Past reports [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
    21837---------------------------------------------------------------------------