NPACI Neuroscience

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First Demonstration of Telemicroscopy was
between NCMIR at San Diego and Chicago at
the Super Computing Convention in 1992 It
involved remote use of the IVEM at UCSD and the
Cray YMP at the San Diego Supercomputer Center
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TELEMICROSCOPY GRID - BASED COMPUTINGREMOTE
ACCESS FOR DATA ACQUISITION AND ANALYSIS
DATA ACQUISITION
DATA ANALYSIS
ADVANCEDCOMPUTER GRAPHICS
NETWORK
MULTI- SCALE DATA- BASES
IMAGING INSTRUMENTS
COMPUTATIONALRESOURCES
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The Login Page The Entrance into the
Portal Single login grants authenticated access
to all applications, resources, and services
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• A Federated Distributed Database for Neuroscience
• A Multimode Multiscale DataGrid
• Interoperates with Gene and Protein databases
  brain map databases of brain anatomy

from Maryann Martone, Amarnath Gupta, Bertram
Ludaescher, Naoko Yamada and Mona Wong
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Tomography Workflow

• Sequence of steps required to acquire, process,
  visualize, and extract useful information from a
  3D volume.
• Problems with non-Portal traditional workflow
• (20) heterogeneous and platform specific tools
  
• Simple shell scripts
• Parallel Grid enabled software
• Commercial software
• Administration is responsibility of the user
• Manual tracking, handling of data
• Advantages of workflow managed by Telescience
  Portal
• Progress through the workflow can be organized
  and tracked
• Automated transparent mechanisms for the flow
  of data
• Centralize tools enhance operations with
  uniform GUIs to improve usability

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Globus Enabled Tomography (Gtomo)
Seleted Resource (s) NCMIR NPACI NASA/IPG NCHC O
saka U.
Gtomo Reader
Gtomo Writer
Data Input
Data Output
Gtomo Driver

• Complete Abstraction of Grid
• No need to manage Globus Certificates
• Simply click resource(s) to use and
• enter biological parameters
• Resources are transparently cross-
• platform, cross-domain

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Grid Services
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Telescience Architecture

• Telescience Portal is composed of many layers
• Layers are modular, allowing for extensions to
  be made to individual layers without disruption
  of the entire system
• Every Layer has its own complexity and
  administration - and previously these headaches
  were passed on to the end-user
• Telescience Portal centralizes all
  administrative details of each layer into a
  single username and passphrase

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TELESCIENCERichly Integrated, End-to-End System
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Building the Pipelines
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Cyber Infrastructure for Telescience

• High Perf. Network in Place
• UCSD to Japan (IPv6)
• UCSD to Sweden
• Gigabit connection to SDSC
• Production Infrastructure for IPv6
• Multiple projects using IPv6 network

• Heterogeneous Distributed Grid Computing
• Blue Horizon, distributed workstations, commodity
  clusters
• Other Computationally Intensive Algorithms
• Additional infrastructure beyond single tilt
  tomography double tilt, BLOBS codes

Broadband Network Connectivity
Computation
Partnership
Large Databases Digital Libraries
People Training

• Brain Data Federation
• Cell level database for tomography data
• Links to databases of larger/smaller structures
• Widely Acknowledged as a Major Success of PACI
  Technologies in Applications to Brain Research
• Model for federation of brain data from high
  field MRI and other imaging methods BIRN

• Global and National Collaborations and Use
• Argentina, Sweden, Japan, etc.
• NASA, Williams College, Montana, Sidwell Friends,
  etc.
• Multi-Access Demonstration
• Neuroscience, SC00, SC01, Sidwell Friends
• IT2000 - 3MeV Osaka and 400KeV UCSD
• Training and Dissemination Events
• Many trainees from middle, upper, undergraduate,
  and graduate school
• Revised training and outreach materials

Instrumentation (large and/or many small)

• Teleinstrumentation
• IVEM (NCMIR), UHVEM (Osaka, JP)
• High Field MRI Centers
• Driving Commercial Efforts to provide
  Telemicroscopy Ready Instruments
• FasTEM, Technai, etc.

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Telescience Portal Welcome Page
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FAST TOMO
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UTILITY of Database Federation for Neuroscience
1. Repository for solved structures in nervous
systems -build a brain -compare structures in
health and disease 2. Make multiresolution
datasets and analysis tools available to the
scientific community - single reconstruction
contains more information than a researcher can
analyze 3. Map protein distributions and gene
expression patterns into a common framework -
build a 3D biochemistry of brain - use to
investigate protein interactions - aid
comparisons between experiments and experimental
conditions 4. Use information to model function
of nervous system
Monte Carlo Simulator of Cellular Physiology -
M-Cell Tom Bartol, Salk Institute Terry
Sejnowski, Salk Institute Joel Stiles, CMU/PSC
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From Telescience to BIRN
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GTOMO Parallel Tomography on THE GRID

• Developed using Globus tool-kit to address
  computational challenges of EM tomography
• Leverages distributed, heterogeneous resources
•  Provides High Performance Computing on demand

Click Here for Movie
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Organism
Macromolecular Complexes, Organelles Cells
Molecules
Genome DBs
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Organism
Macromolecular Complexes, Organelles Cells
Molecules
Genome DBs
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Organism
Macromolecular Complexes, Organelles Cells
Molecules
Genome DBs