NPACI Alpha Project: Telescience for Advanced Tomography Applications

1
NPACI Alpha Project Telescience for Advanced
Tomography Applications
Abel W. Lin National Center for Microscopy and
Imaging Research University of California, San
Diego
https//telescience.ucsd.edu
2
The Telescience Vision
A combination of several independent technologies
integrated for the application of biological
tomography in a way that fosters collaboration.
3
Testbed for the Project ? Electron Tomography

• Derive 3D information about a sample from a
  series of 2D projections.
• Perfect application for driving the integration
  of technologies
• Computation and data intensive
• Requires increased access to unique, expensive
  instrumentation
• Requires advanced visualization tools for
  segmentation
• and analysis of the data
• Detailed process well suited for collaboration
• Demand from neuroscience community for
  accelerated
• population of databases of biological structure

HVEM
3D Model of the Node of Ranvier
4
Grid Networked Resources enable High-Throughput
Scientific Environment
Growing data sizes require (960 MB -gt 90 GB
Volumes) require massive computational and
distributed storage resources Experiments
require multiple geographically distributed
resources
Data Computation
Data Archival
Data Acquisition
Grid Middleware is the software stack that
enables the Grid
Data Visualization
Database
Telescience Portal A web-based application
environment that extends the Grid to the user
via a single username and password
5
Telescience Portal
6
Telescience Architecture
Telescience Portal

Applications / Instruments
Java Grid Interface
GridPort ToolKit
SRB
DataCutter
Globus
NWS
NPACkage
Physical Resources

• Telescience Portal is composed of many layers
• Layers are modular, allowing for extension of
  each layers with great disruption to the entire
  system
• Due to layered Telescience architecture,
  expansion of services does not cause any Portal
  downtime. New services simply appear for use.

Telescience Portal centralizes all
administrative details of each layer into a
single username and passphrase
7
Login Page
8
Telescience Portal Tomography Workflow
9
Example Data from Grid to NIH ImageJ
10
Grid Services
11
Telemicroscopy via VidCon2
12
Globus Enabled Tomography (Gtomo)

• No need to manage Globus Certificates
• Simply click resource(s) to use and enter
  biological parameters
• Resources are transparently cross-platform,
  cross-domain
• Gtomo has been launched 160 times since Aug
  2002
• NCHC resources used 83 times since its
  integration in Sept 2002

The Grid is abstracted away from the end user
13
Image Processing
JFido
JViewer
Pre-processing Utilities (ie. Fiducial marking,
cropping, normalization) general 2D image viewer
3D contour visualization morphological
measurements
14
NCHC Automatic - Segmentation

• Data Input / Output to SRB
• Job is initiated via Portal but computation is
  on NCHC compute resource
• Output Formats vrml, Open Inventor, IvI Vis
  Browser

15
NCHC Surface Rendering Browser
16
Database Integration
17
SRB Collection Browser
18
(No Transcript)
19
Wireless Access

• Web based technologies lets us take advantage of
  commodity technologies.
• Anywhere, anytime access.
• Uniform Internet interface.

20
Telescience and Education
Sidwell Friends School Washington, DC
21
Telescience incorporated into the classroom

• Students have been collaborating with NCMIR in
  San Diego using a 400,000 volt Transmission
  Electron Microscope (shown at right)

A 3-D reconstruction done by a student during a
summer internship
22
Curricular Impact

• The collaboration thus far has
• Introduced students to the cyberinfrastructure
  (advanced networking, computational resources,
  image processing, and computer graphics) as well
  as neurobiology
• Expanded students understanding of microscopy
  and imaging science
• Provided intern opportunities
• Facilitated scientific presentations
• Involved Telescience Portal and Tomography Tools

23
Project Participants

• Telescience Participants
• Telemicroscopy and Project Integration National
  Center for Microscopy and Imaging Research
  (Ellisman)
• Globus Information Sciences Institute,
  University of Southern California (Kesselman)
• GridPort San Diego Supercomputer Center (Mock)
  Texas Advanced Computing Center (Thomas)
• Storage Resource Broker (SRB) San Diego
  Supercomputer Center (Moore, Rajasekar)
• Cell-Centered Database University of California
  San Diego (Martone, Gupta), Montana State
  University (Jacobs)
• Interactive Collaboration Environments Center
  for Computational Visualization, University of
  Texas (Bajaj)
• Application-Level Scheduling (AppLeS) and Network
  Weather Service (NWS) University of California
  San Diego (Berman), University of California
  Santa Barbara (Wolski)
• International Collaborators
• Advanced Networking and Computation Cybermedia
  Center, Osaka University, Japan (Shimojo,
  Akiyama)
• 3 MeV Microscopy Center for UHVEM, Osaka
  University, Japan (Mori)
• Visualization and Computation National Center
  for High-Performance Computing (NCHC), Taiwan
  (Lin)
• Global Networking Collaborators
• Internet-2 Abilene IPv6 Backbone (Almes,
  Corbató) 10Gigabit US Backbone
• SURFnet 10Gigabit Amsterdam Network
• Tyco/IEEAF 10 Gigabit POS Lambda between US
  and SURFnet
• APAN/Transpac OC12 Between Pacific Northwest
  Gigapop Seattle and Toyko