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RBVI Workshops and Training
The RBVI provides several types of training on the tools we develop,
from presentations at conferences to intensive workshops
at UCSF or other sites. In addition, there are many online
Chimera tutorials and
Cytoscape tutorials,
some developed for specific workshops, others as standalone materials.
Selected training events are listed below, with links to associated materials
where available. See also
Upcoming Workshops (below) and
Selected Presentations.
| Event |
Date |
Topics |
| Northern California Society for Microscopy meeting, UCSF |
Nov 15 2012 |
Viewing and analyzing microscopy data with Chimera; map segmentation
[HTML] |
| Macromolecular Interactions course, UCSF BP204 |
Oct 17 2012 |
Chimera structural analysis and comparison; contacts and H-bonds,
superposition, morphing, building multimers, working with sequences |
| Cytoscape workshop at NIH, Bethesda, MD |
Oct 4 2012 |
Network visualization and analysis with Cytoscape
[workshop materials] |
| Chimera workshop at NIH, Bethesda, MD |
Oct 2-3 2012 |
Introduction to Chimera, structure analysis, sequence-structure tools,
EM density analysis, publication images and movies
[workshop materials] |
| Bay Area cryo-EM meeting, Santa Cruz |
Aug 27 2012 |
Making movies in Chimera,
morphing EM maps and molecular structures of ParM
[HTML] |
| Chimera training via WebEx for graduate students
in structural and computational biology, Baylor College of Medicine |
Aug 14 2012 |
Chimera visualization of protein structures and sequences
(dipeptide epimerase) and covering multiple length scales,
from atoms to cells (T-cell tomography and termite gut EM)
|
| Chimera hands-on training by teleconference,
cryoEM workshop at the
National University of Singapore |
Jul 12 2012 |
Electron tomography segmentation, molecule display, fitting; Q & A
[HTML] |
| Chimera training for the DeGrado group at UCSF |
Jul 3 2012 |
Chimera structural analysis and comparison; H-bonds, superposition,
morphing, attributes, working with sequences, density display,
making movies; Q & A |
| Chimera workshop at the University of Missouri |
Apr 28 2012 |
Molecular visualization and analysis |
| Cytoscape workshop at the University of Missouri |
Apr 27 2012 |
Network visualization and analysis |
| Cytoscape tutorial at
the Swiss Institute of Bioinformatics, Lausanne |
Mar 12-13 2012 |
Network visualization and analysis |
| Chimera tutorial at
VIZBI 2012
(EMBO Visualizing Biological Data conference),
Heidelberg, Germany |
Mar 5 2012 |
Basics of molecular visualization and animation |
| Cytoscape developer tutorial at
VIZBI 2012,
Heidelberg, Germany |
Mar 5 2012 |
Cytoscape plugin development |
| Chimera hands-on training at Indiana University |
Dec 1 2011 |
Building an α-crystallin model using EM and X-ray data;
Chimera Q & A |
| Chimera hands-on tutorial at Purdue University |
Nov 30 2011 |
Building a ParM filament using an EM map and X-ray structure |
| Enzyme Function
Initiative November-December meeting |
Nov 30 2011 |
New features in the Structure-Function Linkage Database |
| Macromolecular Interactions course, UCSF BP204 |
Sep 30 2011 |
Chimera structural analysis and comparison; contacts and H-bonds,
superposition, morphing, building multimers, working with sequences |
| Introduction to Bioinformatics course, UCSF BMI206 |
Sep 23 2011 |
Enzyme annotation using protein similarity networks in Cytoscape |
| Introduction to Bioinformatics course, UCSF BMI206 |
Sep 21 2011 |
Introduction to the Structure-Function Linkage Database |
| 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria |
Jul 16 2011 |
Analysis and visualization of biological networks with Cytoscape
[PDF] |
| Seminar at the Swiss Institute of Bioinformatics,
Lausanne, Switzerland |
Jul 11-12 2011 |
Analysis and visualization of biological networks with Cytoscape
[PDF] |
| Gordon Conference on “Three Dimensional Electron Microscopy,”
Colby-Sawyer College, NH |
Jun 26-Jul 1 2011 |
Global, sequential, and symmetric fitting of structures into EM density;
Chimera Q & A |
| Cytoscape training, UCSF |
Jun 8 2011 |
Using Cytoscape with proteomics data |
| Enzyme Function
Initiative May meeting |
May 24 2011 |
New features in the Structure-Function Linkage Database |
| Cytoscape Retreat, San Diego, CA |
May 19 2011 |
Using Cytoscape and selected plugins |
| Workshop on Visualizing Biological Data (VIZBI) 2011, Broad Institute, Cambridge, MA |
Mar 19 2011 |
Using Cytoscape and clusterMaker, structureViz, chemViz, and nodeCharts plugins |
| EMAN single particle reconstruction workshop, University of Houston, TX |
Mar 14-17 2011 |
Chimera EM tools including fitting, symmetry, presentation graphics
[PDF]
[data zip]
[video]
|
| Chimera training in protein engineering course, UC Berkeley, CA |
Oct 27 2010 |
Chimera structural analysis, morphing, trajectories, sequences, rotamers, building multimers, stereo |
| Chimera training for Department of Computational and Systems Biology, University of Pittsburgh, PA |
Sep 29 2010 |
Chimera demonstration and “Getting Started” tutorial |
| Macromolecular Interactions course, UCSF BP204 |
Sep 29 2010 |
Chimera structural analysis, working with sequences, morphing, attribute display, building multimers |
| Enzyme Function Initiative (EFI) meeting, UCSF |
Aug 16 2010 |
2-hour tutorial on using SFLD and working with networks in Cytoscape
[PDF] (text-only) |
| Computational Systems Bioinformatics (CSB) conference, Stanford, CA |
Aug 16 2010 |
Analysis and visualization of biological networks with Cytoscape |
| Cytoscape Developer Retreat, Ann Arbor, MI |
Jul 18 2010 |
2-hour introductory user tutorial, demonstration of plugin CyCommandHandlers |
| Summer School 2010, Universitat Autonoma de Barcelona, Spain |
Jun 16-17 2010 |
Python programming and Chimera
[PDF] |
| Cytoscape training for Burlingame group, UCSF |
Mar 17 2010 |
Network visualization and analysis with Cytoscape |
| Automated Molecular Imaging (AMI) forum, Scripps Research Institute, La Jolla, CA |
Feb 11 2010 |
Chimera segmentation and fitting capabilities |
| Cytoscape training for Cell Signaling Technologies, Salem, MA |
Feb 1 2010 |
Network visualization and analysis with Cytoscape |
| Introduction to Bioinformatics course, UCSF BMI206 |
Oct 23 2009 |
Cytoscape and the structureViz plugin |
| EMBO practical course, Grenoble, France |
Oct 20 2009 |
Combining EM and X-ray data for structure determination of large complexes
[HTML]
[PDF]
[data zip]
|
| Macromolecular Interactions course, UCSF BP204A |
Sep 30 2009 |
Chimera structural analysis, working with sequences, morphing, attribute display, building multimers |
| EMBO European School of Genetic Medicine course |
Sep 22 2009 |
Analysis of biological networks with Cytoscape |
| American Chemical Society National Meeting, COMP, Washington, DC |
Aug 19 2009 |
Chimera structural analysis, morphing, presentation graphics |
| UCSF Library Course Series: UCSF Chimera |
Mar-May 2009 |
Seven 2-hour sessions (details below) |
| Asia-Pacific Congress on Electron Tomography |
Feb 1 2009 |
Interactive visualization of spikes, pores, and cages with Chimera |
| Automated Molecular Imaging (AMI) forum, Scripps Research Institute, La Jolla, CA |
Jan 23 2009 |
Chimera tools for electron tomography |
UCSF Library Chimera and Cytoscape Series
Molecular Visualization with UCSF Chimera: Getting Started
This session will go over the basics of molecular visualization and
provide an introduction to how to use UCSF Chimera to load, visualize,
and manipulate protein structures. Topics include: installing Chimera;
Chimera menus and commands; fetching protein structures from ModBase
and PDB; selections and actions; depictions; key tools: Side View,
Model Panel, and the Selection Panel; and saving your work: sessions
and images.
Participants should have a basic understanding of protein structure.
All participants will receive a CD with UCSF Chimera installers for
Mac, PC, and Linux as well as example files and additional exercises.
Scooter Morris & Conrad Huang
Tuesday March 31, 2009 10am-12pm Mission Bay Community Center Library
Analyzing and Comparing Structures with UCSF Chimera
This session will cover general structure visualization and analysis
with Chimera. Topics include: identifying hydrogen bonds and contacts;
measuring distances and angles, rotating bonds; viewing amino acid
sidechain rotamers, "mutating" residues; displaying attributes such as
B-factor and residue hydrophobicity; superimposing and comparing structures,
morphing; viewing NMR ensembles and molecular dynamics trajectories.
Participants should have some knowledge of protein structure and
molecular graphics, but expertise with Chimera is not required.
Participants are encouraged to bring structures of interest
(or note their Protein Data Bank IDs for retrieval in the lab) as
"real-life" examples to supplement the provided exercises.
Elaine Meng & Scooter Morris
Tuesday April 7, 2009 10am-12pm Mission Bay Community Center Library
Course materials
Exploring Sequence-Structure Relationships with UCSF Chimera
This session will cover working with protein sequence alignments
together with 3D structures. Topics include:
customizing alignment appearance in Chimera;
sequence-structure association and crosstalk;
calculating sequence conservation and displaying it on structures;
matching (superimposing) structures using an alignment;
comparing structures of the same protein or different but related proteins;
creating sequence alignments in Chimera;
other sources of sequence alignments.
Participants should have some experience using Chimera and a basic
understanding of protein structure and sequence alignments.
Participants are encouraged to bring data on systems of interest
(structure IDs, and if available, corresponding sequence alignments)
as "real-life" examples to supplement the provided exercises.
Elaine Meng & Eric Pettersen
Tuesday April 14, 2009 10am-12pm Mission Bay Community Center Library
Course materials
Electron Microscope Tomography in UCSF Chimera
This course provides hands-on training exploring electron tomography
maps. You'll learn to trace membranes, mask and extract structures,
filter data, and fit models in cellular tomograms containing microtubules,
nuclear pores, vesicles and assorted subcellular structures. Chimera
map capabilities are also useful for single-particle EM reconstructions
and x-ray crystallography maps and researchers studying those data types
may benefit from this course.
Participants should have familiarity with Chimera.
Tom Goddard
Tuesday April 21, 2009 10am-12pm Mission Bay Community Center Library
Course materials
Publication-Quality Images with UCSF Chimera
This session provides hands-on training for creating images for journal
articles and presentations. You will be introduced to the myriad of
options to enhance your graphics: presets, depth cueing, transparency,
silhouette edges, lighting, shininess, text labels, clipping and
capping, color choices, raytracing, supersampling, subdivision quality,
transparent backgrounds for image compositing, ribbon styles, stereo
pairs, fish eye views, ambient occlusion, and lenticular images. Then
you'll try some of these techniques on your own data (downloaded or
brought on a flash drive or CD) or with example data we provide.
Participants should have familiarity with Chimera.
Greg Couch
Tuesday April 28, 2009 10am-12pm Mission Bay Community Center Library
Course materials
Movie Making with UCSF Chimera
This course provides hands-on training creating movies of molecular
models for journal articles and presentations. You'll create an animation
showing a ligand binding to a receptor with morphing between unbound and
bound states. Titling, movie encoding, animation commands, and
effects (edging highlighting, shininess, smoothing) will be covered.
Participants should have familiarity with Chimera.
Tom Goddard
Tuesday May 5, 2009 10am-12pm Mission Bay Community Center Library
Course materials
Customizing and Tailoring UCSF Chimera
This session will cover methods for customizing Chimera for specific
tasks and projects, writing command scripts, and programming Chimera
in Python. Other topics will be covered based on attendees interests.
Please send mail to rbvi-workshopscgl.ucsf.edu if you would like to
see a specific topic covered in depth. Possible topics include (but are
not limited to): per-frame scripting of molecular dynamics trajectories;
using the Demo Editor; adding user-defined headers to sequence alignments;
writing Chimera extensions or commands.
Participants should have hands-on experience with Chimera.
Eric Pettersen & Conrad Huang
Tuesday May 12, 2009 10am-12pm Mission Bay Community Center Library
Upcoming Workshops Offered by the RBVI
The RBVI offers workshops covering the use of the technology and
tools we have developed as part of various research projects. Workshops
are held at UCSF or at institutions with a significant enough user base
to make it feasible for us to send a team to the users rather than
bringing the users to UCSF.
We have no workshops scheduled at this time.
If you are interested in hosting a workshop
at your institution, please contact us: rbvi-workshops@cgl.ucsf.edu.
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