Changes between Initial Version and Version 1 of COT14

Timestamp:

Jul 23, 2014, 11:53:06 AM (12 years ago)

Author:

goddard

Comment:

--

COT14

@@ +1 @@
+2013/2014 Outreach and Training
+
+----
+April 21, 2013
+
+  American Society for Biochemistry and Molecular Biology (ASBMB) Annual Meeting, Boston, MA. Computational Tools for Assigning
+  Enzymatic Functions Workshop. 8 hours prep, 40 attendees.
+
+  * Patsy Babbitt
+
+May 30, 2013
+
+  EFI Meeting, Albert Einstein College of Medicine, New York. SFLD representative node networks and Cytoscape. 12 hrs prep. 60 attendees.
+
+ * Shoshana Brown, Eyal Akiva
+
+June 25, 2013
+
+  Chimera tutorial at the University of Dundee.  25 attendees.  12 hours prep time.
+
+ * Scooter Morris
+
+June 27, 2013
+
+  Seminar on RBVI Cytoscape apps: chemViz, structureViz, and the MPI app RINAlyzer at the University of Dundee.  40 attendees, 14 hours prep time.
+
+ * Scooter Morris
+
+July 20, 2013
+  
+  International Society for Computational Biology, 3DSig: Structural Bioinformatics and Computational Biophysics,
+  Berlin, Germany. Keynote speech on the SFLD, similarity networks, and functionally diverse enzyme superfamilies.
+  15 hours prep, 55 attendees.
+
+  * Patsy Babbitt
+
+July 21, 2013 
+
+  International Society for Computational Biology, Automated Function Prediction SIG. The SFLD, similarity networks, and 
+  functionally diverse enzyme superfamilies. 10 hours prep, 35 attendees.
+
+  * Patsy Babbitt
+
+July 22, 2013
+
+  27th Symposium of the Protein Society, Boston. Poster presentation on the glutathione S-transferase (GST) superfamily in the SFLD. 7 hours prep, ~20 visitors.
+
+ * Eyal Akiva
+
+July 25, 2013
+
+  [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.
+
+ * Tom Goddard, Scooter Morris
+
+July 25, 2013
+
+  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.
+
+ * Scooter Morris, Tom Ferrin
+
+August 2, 2013
+
+  GlaxoSmithKline, Philadelphia, PA. The SFLD, similarity networks, and functionally diverse enzyme superfamilies.
+  12 hours prep, 30 attendees.
+
+  * Patsy Babbitt
+
+August 27-28, 2013
+
+  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.
+
+ * Scooter Morris, Tom Goddard, Conrad Huang, Eric Pettersen, Elaine Meng, Greg Couch
+
+August 29, 2013
+
+  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.
+
+ * Scooter Morris
+
+September 18, 2013
+
+  6th Beilstein Symposium on Experimental Standard Conditions of Enzyme Characterizations (ESCEC), Rüdesheim, Germany. 
+  The SFLD, similarity networks, and functionally diverse enzyme superfamilies. 20 hours prep, 30 attendees.
+ 
+ * Patsy Babbitt
+
+September 19, 2013
+
+  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.
+
+ * Tom Goddard
+
+October 5, 2013
+
+  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.
+
+ * Shoshana Brown, Patsy Babbitt, Gemma Holliday
+
+October 9, 2013
+
+  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.
+
+ * Elaine Meng, Eric Pettersen
+
+October 10-11, 2013
+
+  Training at UCSF on Pythoscape and sequence similarity networks for two members of the Fetrow group (from Wake Forest University). Prep time 16 hours.
+
+ * Patsy Babbitt, Gemma Holliday, Jeff Yunes, Susan Mashiyama, Rebecca Davidson, Jack Yu
+
+October 22-25, 2013
+
+  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.
+
+ * Scooter Morris
+
+October 28, 2013
+
+  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.
+
+ * Scooter Morris
+
+November 21, 2013
+
+  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.
+
+ * Tom Goddard
+
+January 6-11, 2014
+
+  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.
+
+ * Gemma Holliday, Patsy Babbitt
+
+February 7, 2014
+
+  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.
+
+ * Tom Goddard
+
+February 14, 2014
+
+  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.
+
+ * Tom Goddard
+
+February 16-18, 2014
+
+  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.
+
+ * Tom Goddard, Matt Dougherty
+
+February 20, 2014
+
+  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.
+
+ * Matt Dougherty, Tom Goddard, Al Conde, Tom Ferrin
+
+February 21, 2014 
+
+  New England Biolabs, Ipswich, MA. The SFLD, similarity networks, and functionally diverse enzyme superfamilies.
+  12 hours prep, 25 attendees.
+
+  * Patsy Babbitt
+
+March 5, 2014
+
+  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.
+
+ * Tom Goddard
+
+March 10-11, 2014
+
+  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.
+
+ * Scooter Morris
+
+April 8, 2014
+
+  International Society for Biocuration, Toronto, Canada. Plenary lecture on the SFLD, similarity networks, and functionally diverse
+  enzyme superfamilies. 20 hours prep, 80 attendees (anticipated).
+
+ * Patsy Babbitt
+
+April 10, 2014
+
+  Texas A&M University, Dept. of Biochemistry & Biophysics, College Station, TX. Seminar on the SFLD, similarity networks, and 
+  functionally diverse enzyme superfamilies. 15 hours prep, 40 attendees (anticipated).
+
+ * Patsy Babbitt
+
+April 11, 2014
+
+  ADVANCE Center Speaker Series, Texas A&M University. The SFLD, similarity networks, and functionally diverse enzyme superfamilies.
+  8 hours prep, 25 attendees (anticipated). 
+
+ * Patsy Babbitt
+
+April 12, 2014
+
+  2014 Texas Protein Folders & Function Meeting, Cleveland, TX. Keynote speech on the SFLD, similarity networks, and 
+  functionally diverse enzyme superfamilies. 18 hours prep, 60 attendees (anticipated).
+
+ * Patsy Babbitt