Changes between Initial Version and Version 1 of COT15

Timestamp:

Mar 18, 2015, 10:51:15 AM (11 years ago)

Author:

meng

Comment:

--

COT15

@@ +1 @@
+----
+2014/2015 report
+
+----
+
+May 16, 2014
+
+  UC Davis Biophysics Seminar Series. Studying enzyme sequence-structure-function relationships with the SFLD and sequence similarity networks. 18 hours prep, 40 attendees.
+
+ * Patsy Babbitt
+
+May 28-June 4, 2014
+
+  Penn State [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. 
+
+ * Gemma Holliday, Patsy Babbitt
+
+June 2, 2014
+
+  Penn State [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.
+
+ * Patsy Babbitt
+
+June 5, 2014
+
+  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.
+
+ * Samuel Thompson, Patsy Babbitt
+
+July 24, 2014
+
+  Chimera demo for [http://cosmos.ucdavis.edu COSMOS] [http://cosmos.ucdavis.edu/cluster8.htm Chemistry of Life] summer camp students from UC Davis
+  led by professor [http://chemgroups.ucdavis.edu/~mascal/pages/mascalhtm.htm Mark Mascal].
+  18 students.  Showed plastic 3d models, nano-machine, acetylcholine receptor, hydrophobicity, space navigator, dendritic cell motion, stereo glasses, oculus rift demo.
+  Students got to try all the toys and were an enthusiastic group.
+  12 hours preparation and delivery.
+
+ * Tom Goddard, Scooter Morris
+
+August 11-12, 2014
+
+  Wellcome Trust Protein Bioinformatics and Community Resources Retreat, Wellcome Trust Genome Campus, UK. Retreat to network and establish communication between bioinformatics resources such as the SFLD. 24 hours, 20 attendees.
+
+ * Gemma Holliday, Patsy Babbitt
+
+August 25, 2014
+
+  Sandia National Labs, Livermore, CA. Presentation on enzyme superfamilies, networks, and the SFLD. 15 hours prep, 20 attendees.
+
+ * Patsy Babbitt
+
+September 25, 2014
+
+  Chimera visualization by videoconference to Baylor College of Medicine class "Computational Mathematics for Biomedical Scientists", 12 students, 1 hour, Ebola virus glycoproteins and movie making,
+  hosted by Wah Chiu, 16 hours preparation and delivery ([http://www.rbvi.ucsf.edu/chimera/data/baylor-sep2014/ebola.html Ebola material] was all new).
+
+ * Tom Goddard
+
+September 28 - October 3, 2014
+  EMBO Practical Course: Computational analysis of protein-protein interactions: From sequences to networks.  24 students.  Taught a quick introduction to using UCSF Chimera for
+  molecular visualization (1 hour) and a full day tutorial on network biology and Cytoscape.  See http://events.embo.org/14-comp-ppi/ for details on the course.
+
+ * Scooter Morris
+
+October 15, 2014
+
+  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.
+
+ * Elaine Meng, Eric Pettersen 
+
+October 21, 2014
+
+  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.
+
+ * Elaine Meng, Eric Pettersen 
+
+November 9, 2014
+
+  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.
+
+ * Scooter Morris
+
+November 21, 2014
+
+  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]
+
+ * Scooter Morris, Sam Hertig, Elaine Meng
+
+December 16, 2014
+
+  Presentation at UCSF to !DeGrado group on enzyme superfamilies, networks, and the SFLD. 20 hours prep, 15 attendees.
+
+ * Patsy Babbitt
+
+January 12-16, 2015
+
+  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.
+
+ * Eyal Akiva, Patsy Babbitt
+
+January 29, 2015
+
+  [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).
+
+ * Thao Do, Megan Riel-Mehan, Tom Goddard, Kara Helmke, Michael Broeker, Graham Johnson, Wendell Lim
+
+February 6, 2015
+
+  [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.
+
+ * Tom Goddard
+
+February 13, 2015
+
+  [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.
+
+ * Tom Goddard
+
+March 10, 2015
+
+  European Bioinformatics Institute Annotation Workshop, Georgetown University, Washington DC. Sequence similarity networks for annotation. 5 hours prep, 14 attendees.
+
+ * Patsy Babbitt
+
+March 11, 2015
+
+  Discussion of careers in science and demonstration of 3-D visualization and kilobot swarm robots for 11 high school students for SF STEM Career Day.  Organized by Jennifer Kaelin of UCSF Science and Health Education Partnership (SEP).  60 minutes.  6 hours preparation.
+
+ * Tom Goddard
+
+March 25-27, 2015
+
+  [http://www.vizbi.org/2015/ VIZBI 2015] Visualizing Biological Data Conference at the Broad Institute of MIT and Harvard, Cambridge, MA. Poster on the !MultiDomain Assembler in Chimera and creating a model of immature HIV. 20 hours prep, anticipate about 50 visitors to the poster.
+
+ * Sam Hertig
+
+----
+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]
+
+----