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Changes between Version 175 and Version 176 of COT
- Timestamp:
- Feb 26, 2015, 9:52:28 AM (11 years ago)
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COT
v175 v176 22 22 ---- 23 23 24 May 16, 2014 25 26 UC Davis Biophysics Seminar Series. Studying enzyme sequence-structure-function relationships with the SFLD and sequence similarity networks. 18 hours prep, 40 attendees. 27 28 * Patsy Babbitt 29 24 30 May 28-June 4, 2014 25 31 26 Penn State [http://http://www.chem.psu.edu/bioinorganic/outreach/bioinorganic-training-workshop-1/bioinorganic-training-workshop Bioinorganic Chemistry Workshop] (Bioinformatics section). Hands-on workshop on using the SFLD and sequence similarity networks. 24 hours (12 teaching), 45 attendees.32 Penn State [http://http://www.chem.psu.edu/bioinorganic/outreach/bioinorganic-training-workshop-1/bioinorganic-training-workshop Bioinorganic Chemistry Workshop] (Bioinformatics section). Plenary lecture on enzyme superfamilies and sequence similarity networks, 25 hours prep, 150 attendees. Hands-on workshop on using the SFLD and sequence similarity networks. 24 hours (12 teaching), 45 attendees. 27 33 28 34 * Gemma Holliday, Patsy Babbitt 35 36 June 5, 2014 37 38 Gordon Research Conference on Cyclic Nucleotide Phosphodiesterases, Mt. Holyoke College, MA. Sequence-structure-function relationships and similarity networks of this set of enzymes. 80 hours working with the data, 30 hours preparing presentation, 130 attendees. 39 40 * Samuel Thompson, Patsy Babbitt 29 41 30 42 July 24, 2014 … … 44 56 * Gemma Holliday, Patsy Babbitt 45 57 58 August 25, 2014 59 60 Sandia National Labs, Livermore, CA. Presentation on enzyme superfamilies, networks, and the SFLD. 15 hours prep, 20 attendees. 61 62 * Patsy Babbitt 63 46 64 September 25, 2014 47 65 … … 59 77 October 15, 2014 60 78 61 79 UCSF BP204,"Macromolecular Interactions" class: 45-minute presentation followed by 45 mins of the students (about 19 of them) doing a Chimera tutorial on their own laptops. The presentation included 5 mins on history of Computer Graphics Lab, 40 mins of Chimera demonstration: basic usage, finding H-bonds, morphing, viewing sequences, showing attribute values, building multimers, measuring buried surface area, stereo. Prep time 12 hours including updating and rehearsing the presentation, updating and preparing handouts. 62 80 63 81 * Elaine Meng, Eric Pettersen 64 82 65 83 October 21, 2014 66 84 67 85 UCSF BP205A,"Physical Underpinnings of Biological Systems" class: 1-hr presentation to 25 students focused on showing sequence conservation on structures using Chimera. Covers obtaining a sequence alignment if you don't already have one, methods available within Chimera for calculating per-column conservation, rendering values with colors and/or worms, importing values that have been calculated outside of Chimera. Prep time 40 hours including creating and rehearsing presentation, making [http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html web page] with images and sample data. 68 86 69 87 * Elaine Meng, Eric Pettersen 70 88 71 89 November 9, 2014 72 Cytoscape developer's workshop offered as part of the [http://www.iscb.org/recomb-regsysgen2014 Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges] conference in San Diego. 20 participants, 10 hours prep time.73 90 74 * Scooter Morris 91 Cytoscape developer's workshop offered as part of the [http://www.iscb.org/recomb-regsysgen2014 Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges] conference in San Diego. 20 participants, 10 hours prep time. 92 93 * Scooter Morris 75 94 76 95 November 21, 2014 77 96 78 97 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 40-seat computer lab in Tolman Hall. Estimated 35 attendees, 33 students plus TA and professor. Prep time 24 hours. [http://www.rbvi.ucsf.edu/Outreach/Workshops/BerkeleyTolman-2014.jpeg photo, Tolman Hall computer lab] 79 98 80 * Scooter Morris, Sam Hertig, Elaine Meng 99 * Scooter Morris, Sam Hertig, Elaine Meng 100 101 December 16, 2014 102 103 Presentation at UCSF to !DeGrado group on enzyme superfamilies, networks, and the SFLD. 20 hours prep, 15 attendees. 104 105 * Patsy Babbitt 81 106 82 107 January 12-16, 2015 83 108 84 Multiple Sequence Alignment workshop hosted by the Institute for Pure & Applied Mathematics in UCLA. Two talks and a poster presentation on the Structure-Function Linkage Database, sequence similarity networks, and Cytoscape. Prep time: 20 hours. Number of attendees: 25-50.109 Multiple Sequence Alignment workshop hosted by the Institute for Pure & Applied Mathematics in UCLA. Two talks and a poster presentation on the Structure-Function Linkage Database, sequence similarity networks, and Cytoscape. Prep time: 50 hours. Number of attendees: 25-50. 85 110 86 111 * Eyal Akiva, Patsy Babbitt 87 112 88 113 January 29, 2015 89 114 90 115 [http://www.cgl.ucsf.edu/chimera/data/kilobots-jan2015/cancerbots.html Kilobot T-cell and cancer exhibit] for general public attending the UCSF Byer's lecture. Exhibit was presented for one hour before the lecture and one hour after the lecture with about 30 individuals trying and discussing this hands-on demo. Organized by Kara Helmke and Wendell Lim. 20 hours preparation and delivery (RBVI staff only). 91 116 92 117 * Thao Do, Megan Riel-Mehan, Tom Goddard, Kara Helmke, Michael Broeker, Graham Johnson, Wendell Lim 93 118 94 119 February 6, 2015 95 120 96 121 [http://www.cgl.ucsf.edu/chimera/data/kilobots-feb2015/kilodemo.html Kilobot demonstration] for 6 prospective UCSF graduate students, hands-on programming of swarm robots and discussion of their relation to biological problems. Two 30 minute demos. Organized by Rebecca Brown. 8 hours preparation and delivery. 97 122 98 123 * Tom Goddard 99 124 100 125 February 13, 2015 101 126 102 127 [http://www.cgl.ucsf.edu/chimera/data/kilobots-feb2015/kilodemo.html Kilobot demonstration] for 4 prospective UCSF graduate students. Looked at firefly synchronization model with 100 kilobots and the effect of 50% non-cooperating kilobots. Two 30 minute demos. Organized by Rebecca Brown. 4 hours preparation and delivery. 103 128 104 129 * Tom Goddard 105 130 131 March 10, 2015 132 133 European Bioinformatics Institute Annotation Workshop, Georgetown University, Washington DC. Sequence similarity networks for annotation. 5 hours prep, 14 attendees. 134 135 * Patsy Babbitt 106 136 ---- 107 137 Past 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]
