Changes between Initial Version and Version 1 of COT08

Timestamp:

Oct 8, 2009, 4:13:31 PM (17 years ago)

Author:

meng

Comment:

--

COT08

@@ +1 @@
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+don't include papers... they will go in the Chimera Software Dev project
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+"Chimera Outreach and Training" subproject for CGL annual report
+
+activities Jun 1, 2007 - May 31, 2008
+---------------------------------------------------------------------------
+
+May 16, 2007
+  Chimera training held at UCSF for Richard Newman who creates visualizations
+  for the Electron Microscopy Data Bank run by the European Bioinformatics
+  Institute.
+  - Tom Goddard
+
+Jun 8, 2007
+  Chimera Release Party - Genentech Hall, UCSF (>100 attendees)
+  A few days before the event, flyers were posted in Genentech Hall and
+  other buildings at the Mission Bay Campus.  Over 100 people attended
+  to learn about Chimera and to enjoy pizza and other refreshments. 
+  Chimera was demonstrated on Mac and Windows computers, both connected 
+  to projectors. Handout materials summarized reasons to try Chimera as a 
+  new user, or to upgrade to the new version from prior versions.  Also
+  handed out were red-cyan stereo glasses, to work with the anaglyph display
+  option, and a short survey about experiences with Chimera and other
+  visualization software.  106 surveys were retrieved.
+  - all Chimera team members
+  
+Jul 16, 2007
+  "What's New in Chimera presentation" - Babbitt group, UCSF (~15 attendees)
+  Advanced features were shown using live demonstrations accompanied by
+  an HTML outline and linked pages. The emphasis was on recently added
+  or improved features, including: raytracing, presets, red-cyan stereo,
+  movie recording options, morphing, clash detection, assignment of charges
+  and other parameters, minimization, rotamer libraries, and sequence 
+  alignment editing.  The web materials were added to the Babbitt group
+  wiki (private).
+  - Elaine Meng and Eric Pettersen
+
+Aug 13, 2007
+  "Introduction to Molecular Visualization" Tutorial at the 
+  Computational Systems Bioinformatics (CSB) conference -
+  University of California, San Diego (8 attendees).  
+  Abstract:
+    Projects such as Structural Genomics are providing increasing numbers
+  of experimental protein and protein-complex structures.  Furthermore, 
+  increasing numbers of theoretical models are being predicted from 
+  primary sequence.  Biologists have an increasing need to understand and 
+  communicate the structures, functions and relationships between these 
+  protein and protein-complex structures.  As a result, molecular 
+  visualization is becoming an important tool for the presentation and 
+  communication of the results of biological experiments and research. 
+  This tutorial will provide a basic foundation for the understanding of 
+  molecular structures through use of visualization tools.
+    Attendees will learn the basics of molecular visualization and will be 
+  provided an overview of available tools and techniques for visualization, 
+  analysis and modeling of protein structure. To make these concepts more 
+  concrete, attendees will be shown the academic program UCSF Chimera in 
+  more detail, and receive instruction in its features and use.  
+  The field of structural biology is still changing, and new techniques 
+  are continually being developed.  Attendees will be shown how they can 
+  add new analysis techniques and their own data to the visualization.
+  - Scooter Morris and Conrad Huang
+
+Oct 22, 2007
+  Two 20-min presentations on work done at the RBVI (each to 8 students)
+  as part of an annual colloquium sponsored by the NSF's Alliances for 
+  Graduate Education and the Professoriate (AGEP).  An example research
+  scenario was illustrated with live demonstrations of Cytoscape and Chimera.
+  AGEP's mission is to increase the number of underrepresented minority
+  students who pursue graduate degrees and careers in the sciences and
+  academia.  The Colloquium is a two-day outreach and informational event 
+  that brings underrepresented undergraduate students to UCSF to learn 
+  about our graduate programs. This year's focus was on programs in 
+  Biophysics, Bioinformatics, and Systems Biology.
+  - Scooter Morris and Elaine Meng
+
+Nov 3, 2007
+  UCSF School of Pharmacy Homecoming lab tours - presentations to groups 
+  of 14 and ~30 alumni on projects of the RBVI, including demonstrations
+  of Cytoscape and Chimera.
+  - Scooter Morris
+
+Nov 14, 2007
+  30-min demo "Interactive Map Visualization with UCSF Chimera"
+  at the NRAMM (National Resource for Automated Molecular Microscopy) 
+  Workshop on advanced topics in EM structure determination,
+  November 10-16, 2007, The Scripps Research Institute, La Jolla, CA.
+  http://nramm.scripps.edu/seminars/2007/cryoem/ 
+  - Tom Goddard
+
+December 6, 2007
+  Chimera Release Party and RBVI Open House (2-5 pm in Genentech Hall N453, 
+  UCSF Mission Bay) for local researchers and students to meet the Chimera 
+  developers, see demonstrations and discuss features, tour the RBVI 
+  facilities, and share refreshments.
+  - Chimera team
+
+December 17, 2007
+  Chimera demonstration for Greg Farrington, executive director of the
+  California Academy of Sciences, and Bruce Alberts, professor of
+  biochemistry and biophysics, UCSF.
+  - Tom Goddard
+
+Feb 3-5, 2008
+  Chimera demonstrations at the NCRR booth, 2008 Biophysical Society 
+  Annual Meeting, Long Beach, CA.  Summaries:
+
+Title: Introduction to the UCSF Chimera molecular modeling package
+Presenter: Scooter Morris
+Abstract:
+UCSF Chimera is a program for interactive molecular graphics and modeling. 
+It provides standard graphics features as well as more unique, domain-specific 
+tools; the menu and command-line interfaces provide a rich and overlapping 
+set of functionality. The Introduction to Chimera shows frequently used 
+coloring and display options, including molecular representations such as 
+ribbons, "pipes and planks," surfaces, and abstract renderings of nucleotides. 
+Other general features shown are distance measurements, bond angle rotations, 
+H-bond identification, and display of the corresponding amino acid and/or 
+nucleotide sequences. Attributes such as B-factors and hydrophobicities can be 
+rendered visually with colors, atomic radii, and "worm" thickness. 
+Chimera includes detailed user documentation and is available for Windows, 
+Linux, Mac OS X (with X11), IRIX, and Tru64 Unix. Chimera is free for 
+academic, government, and non-profit use and can be downloaded from 
+http://www.cgl.ucsf.edu/chimera
+
+Title: New Features in UCSF Chimera
+Presenter: Elaine Meng, Eric Pettersen
+Abstract:
+UCSF Chimera is an interactive molecular graphics program with a wide 
+variety of features. Applications include structure analysis (hydrogen 
+bonding, contacts, clashes), structure superposition and comparison, 
+ensemble analysis (trajectory playback, ensemble clustering), analysis in 
+the context of other types of data (sequence alignments, density maps), 
+and making high-quality images and movies.
+
+Recently added features include display and incorporation of amino acid 
+sidechain rotamers from backbone-dependent and -independent libraries, 
+creation of "morph trajectories" between different conformations of a protein 
+or even different proteins, and generating shadowed images with POV-Ray, 
+which is embedded in Chimera. We will demonstrate these features as well 
+as other features (whether new or not) upon request.
+
+Title: Visualizing 3-D Electron Microscopy Data with UCSF Chimera
+Presenter: Thomas Goddard
+Abstract:
+I'll demonstrate some new capabilities of the UCSF Chimera visualization 
+program ( www.cgl.ucsf.edu/chimera) including tracing surfaces of intracellular
+membranes or virus layers in electron microscopy density maps, extracting 
+density within surfaces, slicing tomography data at arbitrary angles to 
+show nuclear pores, and displaying data cross-sections as topographic 
+relief surfaces.
+
+UCSF Chimera is an interactive molecular graphics program for analysis of 
+proteins, nucleic acids, volumetric and sequence data. and for creating 
+publication images. The density map display and analysis capabilities are 
+being developed for studying single particle reconstructions and EM tomography.
+
+Feb 6, 2008
+  Chimera presentation for discussion session on tomographic software,
+  National Center for X-ray Tomography, Lawrence Berkeley National 
+  Laboratory, CA.
+  - Tom Goddard
+
+Apr 4, 2008
+  Chimera demonstration showing electron microscopy data and crowded 
+  cellular environments to three high school visitors.
+  - Tom Goddard
+
+Apr 14, 2008
+  Chimera demonstration for post-doc and programmer from the National 
+  Center for X-ray Tomography (at LBNL), showing  stereo visualization, 
+  force feedback and 3D input devices, head tracking, and lenticular images.
+  - Tom Goddard
+
+Apr 17, 2008
+  Demonstration of Chimera to a dozen students from Lincoln High School.
+  - Tom Goddard
+
+Apr 24, 2008
+  Kids at UCSF Day. Two 90-minute sessions with up to 10 elementary- and
+  middle-school-age children, on the theme: "What causes colds and flu?  
+  See, hold and feel these bugs using 3 dimensional computer virtual reality." 
+  Interactive molecular graphics with Chimera and paper models of 
+  viral capsids will be used.
+  - Tom Goddard, Elaine Meng
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+