Visit Booth 920 for information, presentations and demos from —
Biomedical Computation, Visualization, Imaging, and Informatics Resources of the
National Center for Research Resources
Neuroscience 2004 Oct 23 – 27, 2004 San Diego, CA
Laboratory of Neuro Imaging (LONI), UCLA
Sunday, Oct 24, 2004 10:30 am – 11:30 am; 3:00 pm – 4:00 pm
Title: Neuroimaging and Brain Mapping in the Laboratory of Neuro Imaging
Presenter: Ivo Dinov
Abstract: Protocols, algorithms and tools for high resolution image acquisition, preprocessing,
analysis and visualization are becoming increasingly widely needed/used with the recent advancement of
the software, hardware, mathematical and computational sciences. The Laboratory of Neuro Imaging
(LONI) is designing, engineering, deploying and validating new models and computational tools for
interpreting neuroimaging and brain mapping data. LONI is a multidisciplinary team of faculty, postdocs,
students, researchers and staff with expertise in a wide range of fields from physics, mathematics, biology,
medicine, chemistry and engineering to psychology and psychiatry.
LONI research involves: normal brain development and aging, schizophrenia, autism, drug abuse
(methamphetamine, alcohol, cocaine), multiple sclerosis and others. Data processed in the LONI lab
include MRI, MRA, MRS, fMRI, DTI, PET/SPECT, OIS and neurogenetic data of various populations and
across the mammalian species. LONI is an NCRR and NCBC research center. LONI web-page:
http://www.loni.ucla.edu/
Center for Bioelectric Field Modeling, Simulation, and Visualization,
Scientific Computing and Imaging Institute (SCI), U of Utah
Monday, Oct 25, 2004 10:30 am – 11:30 am; 3:00 pm – 4:00 pm
Title: SCIRun: A Visual Programming Environment for Integrated Scientific Computing
Presenter: David Weinstein, Greg Jones
Abstract: SCIRun is a software architecture that facilitates the development of both software tools
and end-user applications. At its most core level, SCIRun provides a set of high-performance computing
libraries, a set of tools for developing new modular components, and a platform for integrating disparate
tools into a common application. Atop this core, SCIRun has a graphical programming interface called a
Network Editor.
Using this Network Editor layer, users can instantiate and connect modular components, set and
query algorithm parameters, and group and label components to manage complexity. Most recently, we
have added an even higher-level "PowerApp" interface to SCIRun for wrapping and customizing dataflow
networks into seamless end-user applications. In this presentation, we will overview how we have applied
the SCIRun environment to neuroscience applications, including the forward and inverse EEG problem,
and the visualization of volumetric and diffusion tensor imaging data. We will conclude our presentation
with several live SCIRun demos.
National Biomedical Computation Resource (NBCR), UCSD
Sunday, Oct 24, 2004 1:00 pm – 2:00 pm
Title: Complex query and data integration tools in scientific workflow
Presenter: Amarnath Gupta
Abstract: As in many other fields of science, computational methods in molecular biology need to
intersperse information access and algorithm execution in a computational workflow. Users often find
difficulties when transferring data between data sources and applications. In most cases there is no standard
solution for workflow design and execution and tailored scripting mechanisms are implemented in a case
by case basis. We present a general purpose ‘programmable integrator’ that can access information from a
variety of sources in a coordinated manner. Its usefulness in complex bioinformatics applications is claimed
and supported by some application examples.
Monday, Oct 25; Wednesday, Oct 27, 2004 1:00 pm – 2:00 pm
Title: Advanced computational tools and resources from NBCR
Presenter: Wilfred Li
Abstract: NBCR’s mission is to conduct, catalyze, and enable biomedical research by harnessing
forefront computational and information technologies. The key aim of the resource is to provide transparent
access to the new and emerging grid infrastructure that will deliver integrated compute, data, physical,
experimental, and human resources to biomedical scientists investigating a wide range of medically
important problems spanning scales of biological organization from small molecule drug design and
comparative genomics to diagnostic brain imaging and cardiovascular disease. The technology research and
development activities of NBCR involve collaborations among researchers at UCSD, the San Diego
Supercomputer Center, Cal-(IT)2, and The Scripps Research Institute, and Washington University, Saint
Louis. Core research projects include Integrative Modeling of Subcellular Processes: 1) Application to
Synaptic Activity and Pharmaceutical Discovery 2) Data Integration and Analytic Tools for Molecular
Sequences 3. Structurally and Functionally Integrated Modeling of Cell and Organ Biophysics 4) Creating
Visualization Environments for Multi-Scale Biomedical Modeling 5) Grid Computing and Analysis for
Multi-scale Biomedical Applications
Tuesday, Oct 26, 2004 10:30 am – 11:30 am
Title: Exploration of Macromolecular Electrostatics with APBS/PMV Tools
Presenter: Robert Konecny
Abstract: Electrostatics plays a central role in many biological processes. Continuum electrostatics
methods and particularly numerical solutions to the Poisson-Boltzmann equation (PBE) have been shown
to provide valuable insights into molecular interactions and function. Adaptive Poisson-Boltzmann Solver
(APBS), state of the art software package for studying molecular electrostatic potentials has been recently
interfaced with a powerful molecular viewing environment the Python Molecule Viewer (PMV). This
provides an integrated environment for studying electrostatic properties of molecular system at different
scales - from small molecules to extended macromolecular systems. Demonstration will include application
of PBS/PMV to acetylcholinesterase, an important enzyme which participates in a signal transduction
process.
Tuesday, Oct 26, 2004 1:00 pm – 2:00 pm; 3:00 pm – 4:00 pm
Title: Python-based molecular viewing and visual programming environment
Presenter: Sophie Coon, Michel Sanner
Abstract: Vision is a visual-programming environment in which a user can interactively build
networks describing novel combinations of computational methods, and yielding new visualizations of their
data without actually writing code. Nodes can be defined or modified interactively during a session and be
saved. Multiple networks can be loaded at the same time. Sub-networks can be encapsulated in Macro
nodes. Many of the nodes available in the Vision's library expose the functionality of the same packages
used to develop Python Molecular Viewer (PMV). PMV has most of the features usually expected in a
molecule viewer, but is dynamically extensible, i.e., new commands can be developed independently and
placed in libraries. We’ll describe the use and extensibility of these tools in neuroscience applications.
Wednesday, Oct 27, 2004 10:30 am – 11:30 am
Title: Rocks Distributed Computing Clusters
Presenter: Nadya Williams
Abstract: Commodity clusters are becoming everyday compute engines that offer a very good
price/performance ratio. Without a scalable ``cluster'' management strategy, the favorable economics of
clusters are offset by the additional on-going personnel costs involved to ``care and feed'' for the machine.
The complexity of cluster management (e.g., determining if all nodes have a consistent set of software)
often overwhelms part-time cluster administrators, who are usually domain application scientists. The
Rocks Clusters philosophy is driven by a single goal: make clusters easy. "Easy" includes deployment,
management, upgrade and scalability. Rocks Clusters help to deliver the computational power of clusters to
a wide range of scientific users, making stable and manageable parallel computing platforms available for
diverse scientific computations and applications. Recent development in Rocks adds support of molecular
visualization applications such as PMV within a cluster environment.
2
National Center for Microscopy and Imaging Research (NCMIR),
UCSD
Sunday - Wednesday, Oct 24 - 27, 2004 9:30 am – 10:30 am; 4:00 pm – 5:00 pm
Title: The Telescience Portal for Advanced Tomography Applications
Presenter: S. Peltier, A. Lin, T. Molina, K. Ung, G. Yang, L. Dai, M. Wong, D. Lee, G. Hand, M.E.
Martone, M. H. Ellisman
Abstract: The application of electron tomography to cell biology has led to important insights into
the 3D fine structure of subcellular processes and organelles. Tomography has been particularly useful for
studying relatively large, multi-component structures such as the Golgi apparatus, mitochondria, and
synaptic complexes. When combined with very powerful high voltage electron microscopes, tomography
has also provided high resolution quantitative views of extended structures such as neuronal dendrites in
very thick sections (4 µm) at electron microscopic resolution. The utility of tomography is twofold: first, it
provides 3D examination of subcellular structure without the need for serial section analysis; second,
because the computed slices through the tomographic volumes can be much thinner than is possible to
produce by physical sectioning, it reveals structural detail in the range of 5-30 nm that tends to be obscured
in conventional thin sections. Tomographic analysis has forced re-assessment of long-standing views of
organelles such as mitochondria and the Golgi apparatus and as the technique advances, additional insights
are likely forthcoming.1
Electron tomography is an expensive technique, both in terms of the instruments used and the
computational resources required. The three major high voltage electron microscope resources in the
United States, San Diego, Boulder and Albany, all are actively engaged in tomographic research and offer
this important technology to the scientific community at large. However, travel can be a major impediment
for many researchers due to the expense and time away from the laboratory. At the National Center for
Microscopy and Imaging Research (NCMIR), along with our research program on electron tomography, we
are working to increase access to tomographic resources through the Internet.
We have demonstrated previously that it is possible to control our JEOL 4000EX intermediate voltage
electron microscope (IVEM) through a web-based system written in Java that provides interactive and
collaborative video guided remote control and data acquisition from a web browser.2 This system is
actively used by a large number of collaborators including researchers in Oregon studying synaptic
structure.3 Since its inception, the Telemicroscopy system has been refined and expanded to several
instruments in the US, Japan, and Korea. A new generalized remote instrumentation system is currently
deployed and serves as a cornerstone of a more ambitious effort, entitled Telescience, which is creating a
set of tools to allow researchers to go seamlessly through the steps required to create tomographic images
using the high voltage electron microscopes, from acquisition to analysis. Central to this effort is the
Telescience web portal4.
The Telescience Portal represents a conglomeration of tools necessary for a biologist to perform a
complete tomographic reconstruction from any Internet capable location. More than just a collection of
individual applications, the Portal provides transparent workflow and data management, simple intuitive
interfaces to grid enabled computation and data distribution, remote instrumentation via Telemicroscopy, as
well as utilities that allow for increased collaboration between researchers. Telescience tools are evolving
to make data management and computationally related tasks, transparent to the user. This tightly integrated
Telescience system is designed to increase the throughput of data acquisition and processing, and
ultimately improve the accuracy of the final data product.
The typical tomographic volume of a multi-component structure such as a synapse is extremely
data-rich and contains more information than is analyzed by a given researcher. The Telescience Portal
incorporates access to a Cell Centered Database (http://ccdb.ucsd.edu) of neuronal structure containing
tomographic volumes and confocal datasets as well as information on the distribution of various proteins.
Through the CCDB, users have access to computed tomographic volumes, segmented structures,
measurements, and analysis information targeting protein distribution. Using analysis tools provided in the
Telescience Portal, users can download these volumes and utilize them according to their individual needs.
1
Perkins, G. and Frey, T. (2000) Micron, 31, 97-111.
2
Hadida-Hassan, M., et al., (1999) J. Struct. Biol. 125: 235-245.
3
Lenzi, D., et al. (1999) J. Neurosci. 19:119-132.
4
Peltier, S., et al. (2001) J. Parallel Distr. Comp. 63(5): 539 – 550.
3
Booth 920: Presentations and demos from LONI, SCI, NBCR & NCMIR: Neuroscience 2004 participating members of the
Biomedical Computation, Visualization, Imaging, and Informatics Resources of the
National Center for Research Resources
Sunday 24-Oct Monday 25-Oct Tuesday 26-Oct Wednesday 27-Oct
From To
9:30 10:30 NCMIR:
The Telescience Portal for Advanced Tomography Applications
(Lin, Yang, Peltier)
10:30 11:30 LONI: SCI: NBCR: NBCR:
Neuroimaging and Brain SCIRun: A Visual Exploration of Macromolecular Rocks Distributed
Mapping in the Labohratory of Programming Environment Electrostatics with APBS/PMV Computing Clusters
Neuro Imaging for Integrated Scientific Tools (Williams)
(Dinov) Computing (Konecny)
(Weinstein, Jones)
11:30 13:00 Lunch/Open session
13:00 14:00 NBCR: NBCR: NBCR: NBCR:
Complex query and data Advanced computational tools and Python-based molecular viewing Advanced computational tools and
integration tools in scientific resources from NBCR and visual programming resources from NBCR
workflow (Li) environment (Li)
(Gupta) (Coon)
14:00 15:00 Open session/demo
15:00 16:00 LONI: SCI: NBCR: NBCR:
Neuroimaging and Brain SCIRun: A Visual Python-based molecular viewing Advanced computational tools and
Mapping in the Laboratory of Programming Environment and visual programming resources from NBCR
Neuro Imaging for Integrated Scientific environment (Li)
(Dinov) Computing (Sanner)
(Weinstein, Jones)
16:00 17:00 NCMIR: NCMIR:
The Telescience Portal for Advanced Tomography Applications Cell Centered DataBase
(Lin, Yang, Peltier) (Martone)
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