Changes between Version 116 and Version 117 of COT


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Timestamp:
Jul 8, 2013, 11:54:31 AM (13 years ago)
Author:
Scooter Morris
Comment:

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  • COT

    v116 v117  
    2020
    2121---------------------------------------------------------------------------
    22 2012/2013 report
     222013/2014 report
    2323---------------------------------------------------------------------------
    2424
    25 April 18, 2012
    26   NASA AbSciCon meeting, Atlanta, GA. Presentation on enzyme evolution, networks,
    27   and the SFLD. 9 hours prep, 35 attendees.
    28   - Patsy Babbitt
    29 
    30 April 21, 2012
    31   UCSF Alumni Homecoming Demonstrations. A series of 30 minute demonstrations were given
    32   to several groups (about 100 individuals overall) of UCSF alumni from the Schools of
    33   Medicine and Pharmacy, and the PhD programs.
    34   - Tom Ferrin
    35 
    36 April 23, 2012
    37   Molecular visualization demonstration for 10 high school science teachers from the
    38   San Francisco Unified School District.
    39   - Tom Ferrin
    40 
    41 April 27, 2012
    42   Full day Cytoscape workshop for 30 participants at the University of Missouri.
     25June 25, 2013
     26  Chimera tutorial at the University of Dundee.  25 attendees.  12 hours prep time.
    4327  - Scooter Morris
    4428
    45 April 28, 2012
    46   2 1/2 hour Chimera workshop for 25 participants at the University of Missouri.
    47   - Scooter Morris
    48 
    49 May 23, 2012
    50   EFI Meeting, San Francisco. SFLD new progress and future plans. ~6 hours prep,
    51   15 attendees.
    52   - Patsy Babbitt
    53 
    54 June 21, 2012
    55   Lecture for UC systemwide Bioengineering Symposium, Berkeley, CA.
    56   Computational guidance for protein design, including superfamilies, networks, and
    57   use of the SFLD. 8 hours prep time, 35 attendees.
    58   - Patsy Babbitt
    59 
    60 June 22, 2012
    61   Nanomachine and virus visualization demo for 11 [http://igem.ucsf.edu iGem] students ages 17-19.
    62   30 minutes, stereo visualization in viz vault, discussion of differences between human
    63   designed and biological molecular machines. 1 hour preparation.  Organized by Shannon
    64   Noonan, Community Outreach Specialist, Gladstone Institutes.
    65   - Tom Goddard
    66 
    67 June 22, 2012
    68   HIV virus visualization demonstration for 7 high school students in the
    69   [http://www.gladstone.ucsf.edu/gladstone/site/cso/section/2461 Gladstone Summer Scholars (GSS) Internship Program]. 
    70   Looked at electron microscopy and
    71   atomic models of virus core and drug binding.  30 minute demo in viz vault.
    72   1 hour preparation.  Organized by Shannon Noonan, Community Outreach Specialist,
    73   Gladstone Institutes.
    74   - Tom Goddard
    75 
    76 June 22, 2012
    77   Nanomachine and virus visualization demo for 6 [http://momagic.org Mo Magic] high school
    78   students.
    79   30 minutes, stereo visualization in viz vault, discussion of differences between human
    80   designed and biological molecular machines. 1 hour preparation.  Sponsored by Patricia
    81   Caldera, UCSF, Science & Health Education Partnership.
    82   - Tom Goddard
    83 
    84 July 3, 2012
    85   Chimera training (3-hr session) for 4 members of the DeGrado group at UCSF, covering
    86   fetching data, structural analysis and comparison, H-bonds, superposition, morphing,
    87   attributes, working with sequences, density display, making movies; Q & A. 20 hours prep.
    88   - Elaine Meng, Eric Pettersen, Tom Ferrin
    89 
    90 July 11, 2012
    91   Hands-on Chimera tutorials for 50 participants at the National University of Singapore
    92   [http://ncmi.bcm.edu/ncmi/events/workshops/workshops_125 cryoEM workshop].
    93   [http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/nus.html Tutorials] covering
    94   electron tomography segmentation, molecule display, and fitting as well as an open
    95   question and answer session totaling 3 hours were
    96   presented via teleconference using WebEx with participants trying what they were shown
    97   on lab computers.  Hosted by Cynthia He and Wah Chiu.  15 hours preparation.
    98   - Tom Goddard
    99 
    100 July 16, 2012
    101   5th International Conference on Paraoxonases, Columbus, OH. Presented research on the
    102   "nucleophilic attack 6-bladed beta-propeller" (N6P) superfamily, including network
    103   analysis and data dissemination using the SFLD.  12 hours prep time, 120 attendees.
    104   - Patsy Babbitt
    105 
    106 July 26, 2012
    107   Chimera visualization of HIV virus core and drug binding for 20 high school students from the UC Davis
    108   [http://cosmos.ucdavis.edu COSMOS program].  Organized by Sarah Driver from UC Davis. 20 minute demo.
    109   1 hour preparation.
    110   - Tom Goddard, Tom Ferrin, Scooter Morris
    111 
    112 August 14, 2012
    113   Chimera visualization demonstration covering protein structures and sequences (dipeptide epimerase)
    114   and multiple length scales, atoms through cells (T-cell tomography and termite gut EM).  90 minutes.
    115   12 first year graduate students in structural and computational biology, Baylor College of Medicine.
    116   Presented via WebEx screen sharing.  Hosted by Wah Chiu.  6 hours preparation.
    117   - Tom Goddard
    118 
    119 August 27, 2012
    120   [http://www.cgl.ucsf.edu/chimera/data/santa-cruz-aug2012/animate.html Movie making demonstration]
    121   showing how to morph electron microscopy maps and molecular structures fit into maps using Chimera.
    122   Used actin-like ParM filament data.  Presented to 60 people at the Bay Area cryoEM meeting at Santa Cruz.
    123   Hosted by Melissa Jurica.  8 hours preparation.
    124   - Tom Goddard
    125 
    126 September 29, 2012
    127   Workshop on the Radical SAM Superfamily (data in SFLD) at UCSF, full-day meeting with experts. Estimated 8 hours talk preparation, 30 attendees.
    128   - Gemma Holliday
    129 
    130 October 2-3, 2012
    131   Chimera workshop at NIH, Bethesda MD. Eight sessions over two days, including
    132   introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis,
    133   publication images and movies. About 30 attendees, the room capacity.  About 20 more participants
    134   off-site with video and audio using Adobe Connect.  150 hours preparation.
    135   [http://www.cgl.ucsf.edu/Outreach/Workshops/NIH-Oct-2012/ workshop materials]
    136   - Tom Ferrin, Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng
    137 
    138 October 4, 2012
    139   Full-day Cytoscape workshop at NIH, Bethesda MD. Network visualization and analysis with Cytoscape.
    140   About 30 attendees, the room capacity.  About 10 more participants
    141   off-site with video and audio using Adobe Connect.
    142   [http://www.cgl.ucsf.edu/Outreach/Workshops/NIH-Oct-2012/ workshop materials]
    143   - Scooter Morris, Elaine Meng
    144 
    145 October 4-5, 2012
    146   Visits to NIH labs (Sriram Subramaniam, John Patton, Bernard Heymann, BK Lee, and others) for Chimera
    147   training using their data sets.  Two days with RBVI staff divided into groups to help different labs.
    148   Topics included Chimera Python programming, HIV virus spikes, annotating FIBSEM imaging data, rotavirus
    149   RNA structures, hybrid model representations, and many others.
    150   - Tom Ferrin, Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng
    151 
    152 October 14-30, 2012
    153   4 hours lecture in BMI206, Introduction to Bioinformatics (UCSF), featuring superfamily analysis,
    154   protein similarity networks, and the SFLD. The SFLD was also used as a primary data resource for
    155   a course lab assignment. 25 hours prep, ~9 attendees.
    156   - Patsy Babbitt
    157 
    158 October 17, 2012
    159   UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the
    160   students (about 25 of them) doing a Chimera tutorial on their own laptops.  The presentation included
    161   5 mins on history of Computer Graphics Lab, 30 mins of Chimera demonstration: basic usage, finding
    162   H-bonds, morphing, viewing sequences, showing attribute values, building multimers, stereo. Prep time
    163   16 hours including updating and rehearsing the presentation, updating and preparing handouts.
    164   - Elaine Meng, Eric Pettersen
    165 
    166 November 8, 2012
    167   EFI meeting, San Francisco.  SFLD new features. ~6 hours prep, ~15 participants including
    168   EFI Advisory Committee and NIH representatives.
    169   - Patsy Babbitt
    170 
    171 November 15, 2012
    172   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.
    173   - Tom Goddard
    174 
    175 December 2, 2012
    176   Lunch talk to faculty, Department of Bioengineering and Therapeutic Sciences, UCSF.  The SFLD and
    177   enzyme functional annotation.  8 hours prep, 8 attendees.
    178   - Patsy Babbitt
    179 
    180 December 5, 2012
    181   Gave 3 hour hands-on Chimera tutorial on map display and analysis at UC Berkeley.  Covered basic molecular display,
    182   segmenting and fitting single particle maps, and extracting regions from termite gut FIBSEM data.
    183   12 participants (Auer, Downing, Nogales, Berger labs). 8 hours preparation.  Organized by Danielle Jorgens.
    184   - Tom Goddard
    185 
    186 December 13, 2012
    187   Gave 3 hour hands-on tutorial for Cytoscape at the 2012 Cytoscape retreat (Gladstone Institutes, UCSF).  60 participants, 8 hours preparation.
    188   - Scooter Morris
    189 
    190 December 13, 2012
    191   Cytoscape retreat (Gladstone Institutes, UCSF). Presentation on protein similarity networks and dissemination using the SFLD.
    192   8 hours prep time, 60 attendees.
    193   - Patsy Babbitt
    194 
    195 December 19, 2012
    196   Gave 3 hour hands-on advanced Chimera tutorial on map segmentation at UC Berkeley.
    197   Covered surface masking, watershed segmentation, and zones around markers and atoms
    198   using HIV virus, microtubule and T-cell maps.  10 participants.  8 hours preparation.
    199   Organized by Danielle Jorgens.
    200   - Tom Goddard
    201 
    202 January 7, 2013
    203   Enzyme Mechanisms Meeting Workshop, San Diego, CA. Introduction to similarity networks and the SFLD.
    204   12 hours prep time, 50 attendees.
    205   - Patsy Babbitt
    206 
    207 January 21, 2013
    208   iPQB graduate program (UCSF) pizza talk including an introduction to the SFLD.
    209   3 hours prep, ~30 attendees.
    210   - Patsy Babbitt
    211 
    212 January 29, 2013
    213   Biophysics seminar at UT Southwestern Medical School, Dallas, TX. Similarity networks and the SFLD.
    214   9 hours prep, 45 attendees.
    215   - Patsy Babbitt
    216 
    217 January 31, 2013
    218   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.
    219   - Scooter Morris
    220 
    221 February 7, 2013
    222   [http://www.sbgrid.org/news/article/id=363 Webinar] for [http://www.sbgrid.org/Structural Biology Grid] demonstrating Chimera molecular assembly
    223   and electron microscopy tools.  Built alpha crystallin model. 30 minute demo. 6 hours preparation.
    224   35 participants.  Organized by Michelle Ottaviano, Jason Key, and Piotr Sliz.
    225   - Tom Goddard
    226 
    227 February 8, 2013
    228   Demonstrated Chimera visualization, satellite tobacco mosaic virus, differential gear nano-machine, x-ray density maps,
    229   to two groups of candidate graduate students for the UCSF iPQB program (biophysics and bioinformatics).
    230   8 participants. 30 minutes each demo. 2 hours preparation. Organized by Rebecca Brown.
    231   - Tom Goddard
    232 
    233 February 15, 2013
    234   Demonstrated Chimera visualization, white blood cell 3d motion and HIV reverse transcriptase inhibitor binding,
    235   to two groups of candidate graduate students for the UCSF iPQB program (biophysics and bioinformatics).
    236   14 participants. 30 minutes each demo. 4 hours preparation. Organized by Rebecca Brown.
    237   - Tom Goddard
    238 
    239 March 4, 2013
    240   Short introduction to the SFLD database, Conference on Predicting Cell Metabolism and Phenotypes, SRI international, Menlo Park, CA.
    241   3 hours prep time and ~100 participants.
    242   - Eyal Akiva
    243 
    244 March 8, 2013
    245   Demonstration showing molecules of life, water, protein, dna, drugs (THC and nevirapine), to 8 students from
    246   Dewey High School in Oakland using 3-d projection in the visualization vault. 30 minute demo.  6 hours
    247   preparation.  Organized by Veronica Zepeda, UCSF iGEM and Education Coordinator.
    248   - Tom Goddard
    249 
    250 March 19, 2013
    251   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.
    252   - Scooter Morris
    253 
    254 March 20, 2013
    255   Invited talk on Network Visualization at [http://vizbi.org/2013/ VizBI 2013].  Anticipate an audience of about 200.
    256   - Scooter Morris
    257 
    258 April 5, 2013
    259   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.
    260   - Gemma Holliday
    261 
    262 April 21, 2013
    263   ASBMB (American Society for Biochemistry and Molecular Biology) annual meeting, Boston, MA.
    264   Introduction to networks and downloadable information available from the SFLD, as part of the
    265   EFI workshop "New strategies for function assignment." Anticipate 8 hours prep time, 75 attendees.
    266   - Patsy Babbitt
    267 
    268 May 29, 2013
    269   EFI 3-year review. SFLD vision for the next 5 years. Anticipate 8 hours prep time, 15 participants.
    270   - Patsy Babbitt
    27129
    27230---------------------------------------------------------------------------
    273 Past reports [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
     31Past reports [wiki:COT13 2013], [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
    27432---------------------------------------------------------------------------