Changes between Version 153 and Version 154 of COT


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Timestamp:
Jul 23, 2014, 11:54:00 AM (12 years ago)
Author:
goddard
Comment:

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  • COT

    v153 v154  
    1818
    1919----
    20 2013/2014 report
     202014/2015 report
    2121
    2222----
    23 April 21, 2013
    24 
    25   American Society for Biochemistry and Molecular Biology (ASBMB) Annual Meeting, Boston, MA. Computational Tools for Assigning
    26   Enzymatic Functions Workshop. 8 hours prep, 40 attendees.
    27 
    28   * Patsy Babbitt
    29 
    30 May 30, 2013
    31 
    32   EFI Meeting, Albert Einstein College of Medicine, New York. SFLD representative node networks and Cytoscape. 12 hrs prep. 60 attendees.
    33 
    34  * Shoshana Brown, Eyal Akiva
    35 
    36 June 25, 2013
    37 
    38   Chimera tutorial at the University of Dundee.  25 attendees.  12 hours prep time.
    39 
    40  * Scooter Morris
    41 
    42 June 27, 2013
    43 
    44   Seminar on RBVI Cytoscape apps: chemViz, structureViz, and the MPI app RINAlyzer at the University of Dundee.  40 attendees, 14 hours prep time.
    45 
    46  * Scooter Morris
    47 
    48 July 20, 2013
    49  
    50   International Society for Computational Biology, 3DSig: Structural Bioinformatics and Computational Biophysics,
    51   Berlin, Germany. Keynote speech on the SFLD, similarity networks, and functionally diverse enzyme superfamilies.
    52   15 hours prep, 55 attendees.
    53 
    54   * Patsy Babbitt
    55 
    56 July 21, 2013
    57 
    58   International Society for Computational Biology, Automated Function Prediction SIG. The SFLD, similarity networks, and
    59   functionally diverse enzyme superfamilies. 10 hours prep, 35 attendees.
    60 
    61   * Patsy Babbitt
    62 
    63 July 22, 2013
    64 
    65   27th Symposium of the Protein Society, Boston. Poster presentation on the glutathione S-transferase (GST) superfamily in the SFLD. 7 hours prep, ~20 visitors.
    66 
    67  * Eyal Akiva
    68 
    69 July 25, 2013
    70 
    71   [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html Multiscale brain visualization]  for COSMOS science program high school students. Used 3-d LCD glasses, and leap motion and space navigator navigation devices in the RBVI Visualization Vault to show 20 students from Davis, California light microscopy of whole human brain, traced neurons, rat cortex electron microscopy, neural synapse tomography, acetylcholine receptor synapse ion channel, and snake neurotoxin.  45 minutes.  30 hours preparation.  Organized by Toby Allen and Sarah Driver from UC Davis and Scooter Morris from UCSF.
    72 
    73  * Tom Goddard, Scooter Morris
    74 
    75 July 25, 2013
    76 
    77   Half day of presentations at UCSF for COSMOS science program high school students.  RBVI presented brain visualization (listed above).  Presentations on computational docking by Matt Jacobson, drug development for third-world diseases by the Jim McKerrow  lab, and tour of the UCSF Center for Advanced Technology by Joe DeRisi .  Organized by Scooter Morris from RBVI and Toby Allen and Sarah Driver from UC Davis.  8 hours preparation.
    78 
    79  * Scooter Morris, Tom Ferrin
    80 
    81 August 2, 2013
    82 
    83   GlaxoSmithKline, Philadelphia, PA. The SFLD, similarity networks, and functionally diverse enzyme superfamilies.
    84   12 hours prep, 30 attendees.
    85 
    86   * Patsy Babbitt
    87 
    88 August 27-28, 2013
    89 
    90   Chimera workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley. Seven sessions over two days, including introduction to Chimera, structure analysis, sequence-structure tools, EM density analysis, publication images and movies, and master class. About 35-45 attendees (varied from session to session, 45 was maximum capacity). 40 hours preparation.
    91 
    92  * Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng, Greg Couch
    93 
    94 August 29, 2013
    95 
    96   Full-day Cytoscape workshop hosted by California Institute for Quantitative Biosciences (QB3) at UC Berkeley. Three sessions including introduction to Cytoscape, use cases, and master class. About 25 attendees. 15 hours preparation.
    97 
    98  * Scooter Morris
    99 
    100 September 18, 2013
    101 
    102   6th Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations (ESCEC), Rüdesheim, Germany.
    103   The SFLD, similarity networks, and functionally diverse enzyme superfamilies. 20 hours prep, 30 attendees.
    104  
    105  * Patsy Babbitt
    106 
    107 September 19, 2013
    108 
    109   Visualization and analysis talk for a dozen first year graduate students at Baylor College of Medicine showing [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html brain imaging] , and [http://www.cgl.ucsf.edu/chimera/data/baylor-sep2013/krait.html krait snake venom]  effects on acetylcholine receptor. 90 minute presentation via WebEx .  Organized by Wah Chiu.  16 hours preparation.
    110 
    111  * Tom Goddard
    112 
    113 October 5, 2013
    114 
    115   Isoprenoid Synthase Superfamily (ISS) Workshop at UCSF. Outreach to IS Superfamily community; demo of  sequence similarity networks and SFLD. Prep time: several weeks; lectures: 8 hours. 30 attendees.
    116 
    117  * Shoshana Brown, Patsy Babbitt, Gemma Holliday
    118 
    119 October 9, 2013
    120 
    121   UCSF BP204,"Macromolecular Interactions" class: 35-minute presentation followed by 45 mins of the students (about 15 of them) doing a Chimera tutorial on their own laptops. The presentation included 5 mins on history of Computer Graphics Lab, 30 mins of Chimera demonstration: basic usage, finding H-bonds, morphing, viewing  sequences, showing attribute values, building multimers, stereo. Prep time 10 hours including updating and rehearsing the presentation, updating and preparing handouts.
    122 
    123  * Elaine Meng, Eric Pettersen
    124 
    125 October 10-11, 2013
    126 
    127   Training at UCSF on Pythoscape and sequence similarity networks for two members of the Fetrow group (from Wake Forest University). Prep time 16 hours.
    128 
    129  * Patsy Babbitt, Gemma Holliday, Jeff Yunes, Susan Mashiyama, Rebecca Davidson, Jack Yu
    130 
    131 October 22-25, 2013
    132 
    133   EMBL-Australia Masterclass on Protein Sequence Analysis, Garvan Institute, Sydney, Australia.  24 attendees. 2 sessions on Cytoscape, 40 hours prep time. 2 sessions on Chimera, 12 hours prep time. Plenary talk on networks and structures, 14 hours prep time. Identifying and understanding protein-protein interactions and residues involved in intermolecular contacts using Cytoscape and structureViz/Chimera. Using Chimera for sequence-structure analysis and creating animations.
    134 
    135  * Scooter Morris
    136 
    137 October 28, 2013
    138 
    139   Cytoscape workshop sponsored by the Systems Biology Institute in Melbourne, Australia. 14 attendees, 10 hours prep time. (1) Introductory tutorial on the analysis and visualization of biological networks; (2) Hands-on tutorial introduction to Cytoscape; (3) Demonstration and hands-on use cases of Cytoscape, with numerous example use cases showing what is possible. (4) Master class: Bring your own data, cancer pathway data, proteomics data, mass spectrometry pull downs, etc. The Master Class will also include demos of Cytoscape features in development, and Cytoscape scripting.
    140 
    141  * Scooter Morris
    142 
    143 November 21, 2013
    144 
    145   Chimera demo for Biochemistry students from the University of San Francisco.  Arranged by instructor Willie Melaugh. 12 attendees, prep time 3 hours.  30-minute demo using stereo graphics, space navigator input device to show a Drexel nanomachine and [http://www.cgl.ucsf.edu/chimera/data/cosmos-jul2013/brain.html brain imaging]  at multiple levels of resolution ranging from whole brain to atomic detail of the nicotinic acetylcholine receptor.
    146 
    147  * Tom Goddard
    148 
    149 January 6-11, 2014
    150 
    151   Meetings with staff at the European Bioinformatics Institute (EMBL-EBI Hinxton Outstation, Cambridge, UK) including demonstrations of the SFLD; sequence similarity networks and Pythoscape; troubleshooting issues and discussing future collaborations.  12 hours prep time, ~60 hours of meetings. 25-50 attendees.
    152 
    153  * Gemma Holliday, Patsy Babbitt
    154 
    155 February 7, 2014
    156 
    157   Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown.  Two half hour demonstrations each with 4 students.  6 hours preparation and delivery.
    158 
    159  * Tom Goddard
    160 
    161 February 14, 2014
    162 
    163   Visualization demo for UCSF student recruitment tours. Showed differential gear nano machine, stereo glasses, space navigator, dendritic cells in collagen, oculus rift goggles collagen visualization. Arranged by Rebecca Brown.  30 minute demonstration 3 students. Discussion with another group of 5 students about virus structure and cell motion.  3 hours preparation and delivery.
    164 
    165  * Tom Goddard
    166 
    167 February 16-18, 2014
    168 
    169   Showed human brain planetarium dome video at the Biophysical Society Annual meeting in San Francisco attended by 7000 researchers. Video was shown to a few hundred visitors per day.  The [http://www.youtube.com/watch?v=RE2XMzInX_o video]  showed imaging data and molecular structures from the human brain, was made with RBVI Chimera software, and took about 50 hours to produce.
    170 
    171  * Tom Goddard, Matt Dougherty
    172 
    173 February 20, 2014
    174 
    175   Showed virus, brain, cell and rna videos in a portable 6 meter planetarium dome that we setup at UCSF in Genentech Hall. The RBVI hosted this event and created two of the dome videos on HIV RNA and human brain imaging and molecules. About 150 researchers viewed the videos presented many times over 3 hours in the afternoon.  30 hours preparation.
    176 
    177  * Matt Dougherty, Tom Goddard, Al Conde, Tom Ferrin
    178 
    179 February 21, 2014
    180 
    181   New England Biolabs, Ipswich, MA. The SFLD, similarity networks, and functionally diverse enzyme superfamilies.
    182   12 hours prep, 25 attendees.
    183 
    184   * Patsy Babbitt
    185 
    186 March 5, 2014
    187 
    188   Introduction to Chimera 90 minute hands-on tutorial for a workshop at the International Institute of Macromolecular Analysis and Nanomedicine Innovation in Taiwan. Presented via video conference (GoToMeeting .com).  20 students, 8 hours preparation. Organized by Shang-Rung Wu of Natial Cheng Kung University, Tainan, Taiwan.
    189 
    190  * Tom Goddard
    191 
    192 March 10-11, 2014
    193 
    194   Two-day course at EMBL in Heidelberg to teach participants to develop Apps for the Cytoscape 3.x series. As part of the course, covered the app development process as well as the key aspects of the Cytoscape API necessary to manipulate Cytoscape tables, networks, and user interface. Also worked through how to set up development environments on multiple platforms, and develop an initial Cytoscape App.  The second day of this course provided time for each participant to interact with the instructor and other participants to  plan and develop their own Cytoscape app. 20 students 30 hours preparation.
    195 
    196  * Scooter Morris
    197 
    198 April 8, 2014
    199 
    200   International Society for Biocuration, Toronto, Canada. Plenary lecture on the SFLD, similarity networks, and functionally diverse
    201   enzyme superfamilies. 20 hours prep, 80 attendees (anticipated).
    202 
    203  * Patsy Babbitt
    204 
    205 April 10, 2014
    206 
    207   Texas A&M University, Dept. of Biochemistry & Biophysics, College Station, TX. Seminar on the SFLD, similarity networks, and
    208   functionally diverse enzyme superfamilies. 15 hours prep, 40 attendees (anticipated).
    209 
    210  * Patsy Babbitt
    211 
    212 April 11, 2014
    213 
    214   ADVANCE Center Speaker Series, Texas A&M University. The SFLD, similarity networks, and functionally diverse enzyme superfamilies.
    215   8 hours prep, 25 attendees (anticipated).
    216 
    217  * Patsy Babbitt
    218 
    219 April 12, 2014
    220 
    221   2014 Texas Protein Folders & Function Meeting, Cleveland, TX. Keynote speech on the SFLD, similarity networks, and
    222   functionally diverse enzyme superfamilies. 18 hours prep, 60 attendees (anticipated).
    223 
    224  * Patsy Babbitt
    22523
    22624May 28-June 7, 2014 (push to 2014/2015 report)
    … …  
    23129
    23230----
    233 Past reports [wiki:COT13 2013], [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
     31Past reports [wiki:COT14 2014], [wiki:COT13 2013], [wiki:COT12 2012], [wiki:COT11 2011], [wiki:COT10 2010], [wiki:COT09 2009], [wiki:COT08 2008], [wiki:COT07 2007]
    23432
    23533----