Changes between Version 223 and Version 224 of COT


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Timestamp:
Jun 15, 2016, 10:50:00 AM (10 years ago)
Author:
meng
Comment:

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  • COT

    v223 v224  
    1818
    1919----
    20 2015/2016 report
     202016/2017 report
    2121
    2222----
    23 
    24 March 24, 2015
    25  
    26   Introduction to Chimera tutorial at [http://www.vizbi.org/2015/ VIZBI 2015] Visualizing Biological Data Conference in Cambridge, MA. Included visual effects, morphing, making movies, and !MultiDomain Assembler. Estimated 8 hours preparation, 8 attendees.
    27 
    28  * Sam Hertig
    29 
    30 March 26, 2015
    31  
    32   Oculus Rift and kilobot demonstrations for Cal Academy of Sciences [http://www.calacademy.org/nightlife/robot-nightlife Robotics Nightlife] event in San Francisco.  Showed migrating neutrophil cell and Tuscany demo using two oculus rift VR headsets, and showed kilobot cancer cell, synchronization and move to light demos.  3500 attended this sold-out event and about 600 people visited our 3 tables, non-stop several people deep for 4 hours.  Prep, setup and presentation time 8 hours (48 person hours for 6 presenters).  Organized by Kara Helmke.
    33 
    34  * Tom Goddard, Thao Do, Megan Riel-Mehan, Kara Helmke, Michael Broeker, Graham Johnson
    35 
    36 April 7, 2015
    37 
    38   Introduction to Cytoscape course given at UCSF (2 hours).  30 participants, 4 hours prep time.
    39 
    40  * Scooter Morris
    41 
    42 April 21, 2015
    43 
    44   1-hour Chimera tutorial by Skype to Georgetown University structural biology course including BLAST searching, morphing, showing MD trajectories, virtual mutation, rendering, and customizing the interface.  Arranged by course instructor Sona Vasudevan. Estimated 8 hours prep, 20 students attending.
    45 
    46   * Eric Pettersen
    47 
    48 April 21-May 7, 2015
    49 
    50     Protein function prediction from a big data perspective using similarity networks Mini course (a formal curricular element for UCSF Graduate Programs) UCSF, Mission Bay Library Computer Workshop Lab.  40 hours preparation 12 attendees.
    51 
    52   * Patricia Babbitt, Eyal Akiva, Gemma Holliday, Shoshana Brown
    53 
    54 June 2, 2015
    55 
    56   American Microbiology Society meeting, New Orleans. Superfamily analysis and protein similarity networks. 10 hours prep. 60 attendees.
    57 
    58   * Patsy Babbitt
    59 
    60 July 6-17, 2015
    61 
    62   Project with 4 high-school students to program kilobot swarm robots to forage.  Students developed and tested code over 8 days to make kilobots disperse from a cluster to find a target, establish a minimum path to that target, and then move to reinforce that path.  They made movies and gave two presentations on their results.  RBVI provided 10 hours of assistance programming and debugging.  Students Emilia, Katrina, Judith and Maya-Claire.  Organized by UCSF professor Wendell Lim.
    63 
    64   * Tom Goddard
    65 
    66 July 11, 2015
    67   ''Cytoscape 3 App Development: Variations on a theme -- "Hello World"'' workshop offered at the 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2015) in Dublin, Ireland.  All day session worked with 12 students to allow them to develop their own Cytoscape "Apps".  During the course of the workshop, students developed 7 apps, each one building on the previous app and utilizing more of the Cytoscape API.  Prep time was about 10 hours.
    68 
    69   * Scooter Morris
    70 
    71 July 13, 2015
    72 
    73   Demonstration of molecular graphics-related hardware for visitors from the Universidad Andrés Bello, Santiago, Chile: Dr. Fernando González-Nilo (https://www.researchgate.net/profile/Fernando_Gonzalez-Nilo), Director of the Center for Bioinformatics & Integrative Biology, and Dr. Luis Velázquez (https://www.researchgate.net/profile/Luis_Velasquez4), Director of the Center for Integrative Medicine and Innovative Science. Showed and/or discussed using the stereo projector, Oculus Rift virtual reality goggles, Space Navigator input device, Leap Motion Controller, and Phantom force feedback device.
    74 
    75   * Tom Goddard, Elaine Meng
    76 
    77 July 14, 2015
    78 
    79   Gordon Conference on Enzymes, Co-enzymes, and Metabolic Pathways, Waterville, NH. Superfamily analysis with the SFLD and protein similarity networks. 15 hours prep time, 135 attendees.
    80 
    81   * Patsy Babbitt
    82 
    83 July 16, 2015
    84    Invited talk at Swansea University covering the visualization of biological structures and processes.  Talk was attended by about 50-60 researchers.  Prep time: 10 hours.
    85 
    86   * Scooter Morris
    87 
    88 July 20, 2015
    89     1/2 day workshop at the University of Copenhagen on the use of Cytoscape, including interactions with UCSF Chimera.  25 Participants.  Prep time: 4 hours.
    90 
    91   * Scooter Morris
    92 
    93 July 23, 2015
    94 
    95   29th Annual Symposium of the Protein Society, Barcelona, Spain. Superfamily analysis with the SFLD and protein similarity networks. 15 hours prep time, 150 attendees.
    96 
    97   * Patsy Babbitt
    98 
    99 August 4, 2015
    100 
    101   One hour talk and demonstration of 3d image visualization for Baylor College of Medicine computational methods course, presented via video conference to 5 graduate students. Organized by professor Wah Chiu.  8 hours preparation and delivery.
    102 
    103   * Tom Goddard
    104 
    105 August 24, 2015
    106 
    107   Demonstration of neutrophil migration visualization with Oculus Rift virtual reality headset for Herb Sandler, members of the Sandler Foundation, and a half dozen kids ages 8-14. Estimated 12 attendees total. Organized by Kara Helmke and UCSF professor Wendell Lim. 4 hours preparation and delivery.
    108 
    109   * Tom Goddard, Graham Johnson, Kara Helmke, Dyche Mullins, Lillian Fritz-Laylin, Wendell Lim
    110 
    111 September 16, 2015
    112 
    113   cellPACK talk and 3d visualization of crawling neutrophils for the board of directors of the Long Foundation. Estimated 7 visitors. Organized by Michael Faber and Jessica Jencek. 4 hours preparation and delivery.
    114 
    115   * Graham Johnson, Tom Goddard, Megan Riel-Mehan
    116 
    117 September 28 - October 3, 2015
    118   EMBO Practical Course: Computational analysis of protein-protein interactions, Norwich, UK. 30 students. 3-hr introduction to Chimera and a full-day tutorial on network biology and Cytoscape.  See http://events.embo.org/15-protein-protein/ for details on the course.
    119 
    120  * Scooter Morris
    121 
    122 October 2, 2015
    123 
    124   San Francisco State University, San Francisco, CA.  Presentation on superfamily analysis with protein similarity networks. 12 hours prep, 30 attendees.
    125 
    126   * Patsy Babbitt
    127 
    128 November 2, 2015
    129 
    130   San Francisco State University, San Francisco, CA.  Diversity Outreach Talk on superfamily analysis with protein similarity networks. 20 hours prep, 35 attendees.
    131 
    132   * Patsy Babbitt
    133 
    134 November 20, 2015
    135 
    136     Chimera workshop (2 hours) for Professor Danielle Tullman-Ercek's Protein Engineering course (ChmEng C270/BioE C219) at UC Berkeley. Introduction to Chimera demonstration followed by hands-on "structure analysis and comparison" tutorial in the Tolman Hall computer lab. About 30 students participated. Prep and workshop time about 16 person-hours. [http://www.rbvi.ucsf.edu/Outreach/Workshops/UCB-Nov2015.jpg photo, Tolman Hall computer lab]
    137 
    138   * Scooter Morris, Eric Pettersen, Elaine Meng
    139 
    140 January 2016
    141 
    142   Presentation on SFLD data including multiple sequence alignments. InterPro Consortium Meeting, EMBL-EBI, Hinxton, UK. 20 attendees. 5 hours preparation.
    143 
    144   * Gemma Holliday
    145 
    146 February 3, 2016
    147 
    148   Presentation on SFLD and similarity networks for Sakanari lab meeting at UCSF. 10 hours prep, 15 attendees.
    149 
    150   * Patsy Babbitt
    151 
    152 February 12 and 19, 2016
    153 
    154   Demonstration for 4 groups of student applicants to UCSF iPQB program.  Showed differential gear nano-machine, HIV reverse transcriptase with tenovofir drug, crawling neutrophil light sheet microscopy, using stereo and Oculus Rift. Organized by Rebecca Brown.  Total 14 students.  6 hours preparation and delivery.
    155 
    156   * Tom Goddard
    157 
    158 March 25, 2016
    159 
    160   University of Maryland, College Park, MD. Presentation on superfamily analysis with protein similarity networks. 18 hours prep time, 60 attendees.
    161 
    162   * Patsy Babbitt
    163 
    164 April 14, 2016
    165 
    166   Presentation at [https://www.isb-sib.ch/events/biocuration2016/ Biocuration 2016], Swiss Institute of Bioinformatics, Geneva, on defining functional boundaries within protein similarity networks.  Estimated 200 attendees.  5 hours preparation.
    167 
    168   * Gemma Holliday
    169 
    170 May 2, 2016
    171 
    172   Hands-on Chimera tutorial presented at the [http://qcbnet.ucsf.edu/workshops QCBnet workshop Visualization & Modeling for Cell Biology] hosted by Janet Iwasa at the University of Utah in Salt Lake City.  40 participants, 60 minutes, marking protrusions in 3d optical microscopy of crawling neutrophil cells.  8 hours preparation.
    173 
    174   * Tom Goddard, Megan Riel-Mehan
    17523
    17624June 14, 2016