Changes between Initial Version and Version 1 of COT16

Timestamp:

Jun 15, 2016, 10:47:02 AM (10 years ago)

Author:

meng

Comment:

--

COT16

@@ +1 @@
+
+----
+2015/2016 report
+
+----
+
+March 24, 2015
+ 
+  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.
+
+ * Sam Hertig
+
+March 26, 2015
+ 
+  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.
+
+ * Tom Goddard, Thao Do, Megan Riel-Mehan, Kara Helmke, Michael Broeker, Graham Johnson
+
+April 7, 2015
+
+  Introduction to Cytoscape course given at UCSF (2 hours).  30 participants, 4 hours prep time.
+
+ * Scooter Morris
+
+April 21, 2015
+
+  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.
+
+  * Eric Pettersen
+
+April 21-May 7, 2015
+
+    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.
+
+  * Patricia Babbitt, Eyal Akiva, Gemma Holliday, Shoshana Brown
+
+June 2, 2015
+
+  American Microbiology Society meeting, New Orleans. Superfamily analysis and protein similarity networks. 10 hours prep. 60 attendees.
+
+  * Patsy Babbitt
+
+July 6-17, 2015
+
+  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.
+
+  * Tom Goddard
+
+July 11, 2015
+  ''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.
+
+  * Scooter Morris
+
+July 13, 2015
+
+  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.
+
+  * Tom Goddard, Elaine Meng
+
+July 14, 2015
+
+  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.
+
+  * Patsy Babbitt
+
+July 16, 2015
+   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.
+
+  * Scooter Morris
+
+July 20, 2015
+    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.
+
+  * Scooter Morris
+
+July 23, 2015
+
+  29th Annual Symposium of the Protein Society, Barcelona, Spain. Superfamily analysis with the SFLD and protein similarity networks. 15 hours prep time, 150 attendees.
+
+  * Patsy Babbitt
+
+August 4, 2015
+
+  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.
+
+  * Tom Goddard
+
+August 24, 2015
+
+  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.
+
+  * Tom Goddard, Graham Johnson, Kara Helmke, Dyche Mullins, Lillian Fritz-Laylin, Wendell Lim
+
+September 16, 2015
+
+  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.
+
+  * Graham Johnson, Tom Goddard, Megan Riel-Mehan
+
+September 28 - October 3, 2015
+  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.
+
+ * Scooter Morris
+
+October 2, 2015
+
+  San Francisco State University, San Francisco, CA.  Presentation on superfamily analysis with protein similarity networks. 12 hours prep, 30 attendees.
+
+  * Patsy Babbitt
+
+November 2, 2015
+
+  San Francisco State University, San Francisco, CA.  Diversity Outreach Talk on superfamily analysis with protein similarity networks. 20 hours prep, 35 attendees.
+
+  * Patsy Babbitt
+
+November 20, 2015
+
+    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]
+
+  * Scooter Morris, Eric Pettersen, Elaine Meng 
+
+January 2016
+
+  Presentation on SFLD data including multiple sequence alignments. InterPro Consortium Meeting, EMBL-EBI, Hinxton, UK. 20 attendees. 5 hours preparation.
+
+  * Gemma Holliday 
+
+February 3, 2016
+
+  Presentation on SFLD and similarity networks for Sakanari lab meeting at UCSF. 10 hours prep, 15 attendees.
+
+  * Patsy Babbitt
+
+February 12 and 19, 2016
+
+  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.
+
+  * Tom Goddard
+
+March 25, 2016
+
+  University of Maryland, College Park, MD. Presentation on superfamily analysis with protein similarity networks. 18 hours prep time, 60 attendees.
+
+  * Patsy Babbitt
+
+April 14, 2016
+
+  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.
+
+  * Gemma Holliday
+
+May 2, 2016
+
+  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.
+
+  * Tom Goddard, Megan Riel-Mehan
+
+June 14, 2016
+
+  Zika virus Chimera demonstration for 18 San Francisco high school students taking part in the [http://sep-sfhi.ucsf.edu UCSF Public Health Investigators] 4 week program.  Showed 3d printing, cryoEM and atomic models, protein structure, crawling neutrophils, stereo visualization and oculus rift virtual reality.  Two 45 minute demonstrations.  8 hours preparation.
+
+  * Tom Goddard
+