Biophysical Society 2005
NIH NCRR Exhibitor Booth Talks and Demos

Booth #123

Time Slot

Sunday

Monday

Tuesday

10:00-11:00

NBCR: Jessica Swanson
End-point free energy calculations of FK506BP

NBCR: John Mongan
Constant pH MD in generalized Born implicit solvent

NBCR: David Zhang & Nathan Baker
Continuum rate calculation by solving the steady-state Smoluchowski equation

11:00-12:00

NBCR: Wilfred Li
Grid infrastructure for biomedical applications

NBCR: Sarah Healy
A 3D gating law for stretch-activated currents in the rabbit left ventricle

NBCR: Jeffrey J. Saucerman
Modeling the proarrhythmic effects of a KCNQ1 gene mutation

12:00-13:00

NBCR: Michel Sanner
Python-based molecular viewing and visual programming environment

NBCR: Michele Sanner
Python-based molecular viewing and visual programming environment

NRCAM: Ion I. Moraru
Overview of the Virtual Cell Model Building and Simulation Framework

13:00-14:00

RBVI: Dan Greenblatt, John "Scooter" Morris
DASH (and other tools)

RBVI: Tom Goddard
New Features in Chimera

RBVI: Scott Pegg
The Structure-Function Linkage Database

14:00-15:00

NRCAM: Ion I. Moraru
Overview of the Virtual Cell Model Building and Simulation Framework

NRCAM: James C. Schaff
Cytoskeletal-Mediated Transport in the Virtual Cell Modeling Framework

NCMI: Irina I. Serysheva
Visualizing Pore-lining Alpha Helices in RyR1 by Single Particle Cyro-EM

15:00-16:00

NCMI: Matthew L. Baker
Software Tools for Subnanometer Resolution Electron Cryomicroscopy

NCMI: Michael F. Schmid
Visualization of Actin Conformational Variation in Acrosomal Bundle from Limulus Sperm

SCI: Frank Sachse & Jeroen Stinstra
SCIRun/BioPSE

16:00-17:00

RMMB: Elizabeth Villa
Multiscale Simulation of Gene Regulation

RMMB: Emad Tajkhorshid
How so fast, yet Selective.

RMMB: Tim Isgro
Visualizaing a Trip Through the Nuclear Pore

Abstracts

Title:
DASH (and other tools)
Presenter: Dan Greenblatt & John "Scooter" Morris
Abstract:
The focus of the Resource for Biocomputing, Visualization and Informatics (RBVI) is the development of innovative computational and visualization-based data analysis methods into easy-to-use software tools for use by the biological research community. Here we present several of these tools, including a data-sharing framework and two general-purpose software libraries targeted at facilitating the research process.

Our DASH (DAta SHaring) infrastructure meets the data-sharing needs of collaborative team-based research projects by managing updates within a distributed set of data sources. DASH has a robust yet lightweight event-processing engine, which matches arbitrary âeventsâ (a series of attribute / value pairs) to registered âhandlersâ based on configurable criteria. A graphical user interface will enable users to describe multi-step computational pipelines in terms of the data and processing protocols involved. DASH monitors registered data for changes, and then automatically invokes the appropriate processing pipeline(s). We describe the overall design of the DASH system and the application of a preliminary DASH implementation to a collaborative pharmacogenomics research project involving several dozen researchers located at different sites.

The Multiloader’ library provides a generic mechanism for easily converting data between Python programming language objects and Extensible Markup Language (XML) representations via a simple API. Multiloader easily integrates with pre-existing Python code, enabling you to harness the power of XML without the need for writing customized parsers. A third tool, ‘WidgetPy’, is a comprehensive set of HTML form widgets that are easily managed through a Python interface. WidgetPy eliminates the drudgery of coding HTML forms. Instead you simply specify which form elements are required, and define Python objects to hold the form’s data. WidgetPy then renders the form in HTML and populates the Python objects upon form submission.

The full presentation is also available.

Title:
New Features in Chimera
Presenter: Tom Goddard
Abstract:
The RBVI develops and distributes a highly extensible interactive molecular graphics program called UCSF Chimera. It is used for analysis of proteins, nucleic acids, volumetric and sequence data and for creating publication images. It provides a rich set of capabilities including hydrogen bond identification, molecular surface calculation, viewing multiple sequence alignments and associated structures, distance and angle measurements, volumetric display and model building, lenses, screening docked ligands, and multi-party remote viewing and control. We will show four new features: 1) nucleotide display as slabs for showing unusual stacking interactions, base orientations, and ring puckers, 2) a tool for rendering arbitrary atom and residue properties, 3) multiple resolution display of virus capsids or other large molecular complexes, and 4) a facility for making turn-key presentations for teaching. These new tools are examples of Chimera extensions. Chimera was designed from the start to enable advanced users and RBVI staff to easily add new capabilities using the Python programming language. We currently include about 40 extensions in our distribution. Chimera is free for academic use and runs on Windows, Macintosh, Linux, and other Unix platforms (www.cgl.ucsf.edu/chimera).
Title:
The Structure-Function Linkage Database (SFLD)
Presenter: Scott Pegg
Abstract:
The Structure-Function Linkage Database (SFLD) provides highly curated information about the relationships between protein structure and function. The SFLD currently focuses on enzymes, using a superfamily-centric organization designed to allow users to easily investigate how conserved folds and active sites are able to perform a wide variety of chemical reactions. The information within the SFLD includes sequences, structures, enzyme reactions (including partial reactions), the specific residues of each enzyme which participate in the reaction (and their role when known), hidden Markov models based on family and superfamily classifications, and literature references. In an effort to make assignments of function, superfamily, etc. transparent, assignment evidence codes and extensive metadata are easily accessible. Users can search the database using a sequence (useful in determining the function of a newly sequenced enzyme), a full or partial reaction (useful in identifying a template for enzyme engineering), or through a variety of keyword searches. The SFLD is freely available via a web interface at http://sfld.rbvi.ucsf.edu.