1. CPEG Reseach Activities – An Overview
Guang R. Gao
Computer Architecture and Parallel Systems Laboratory
Dept. of Electrical and Computer Engineering
University of Delaware
9/18/2018
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2. CPEG Faculty John Elias Guang R. Gao Dave Mills Fouad Kiamilev
Kevin Theobald
Peter Warter (Emeritus)
9/18/2018
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3. Research Areas Traditional Computer Engineering Research Areas:
Computer Networking (Mills)
VLSI Design for Optical Comm. (Kiamilev)
Computer Systems, Compilers and Software (Gao)
Neuromorphic Engineering and User Interfaces (Elias)
Computer Architecture and Hardware (Theobald)
High-Performance Computing for Biotechnology
9/18/2018
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4. John Elias: Research Interests
Neuromorphic Engineering
Silicon neurons
Neurocomputation
User Interfaces (collaboration with Prof. Westerman)
Gesture based
Multi-hand and Multi-finger
Unified (touch, voice, force, gesture, etc.)
9/18/2018
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5. Professors Westerman and Elias: The FingerBoard
Integrates typing, mouse, and gesture input.
Touch sensitive surface images multiple fingers and multiple hands.
Gesture used to control graphics, text, and apps.
Commercialization underway
9/18/2018
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6. FingerBoard Product Concept
9/18/2018
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7. FingerBoard Product Concept
9/18/2018
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8. Kiamilev: Active Projects
Honeywell (DARPA VLSI Photonics)
Lockheed (DARPA STAB)
Mayo (DARPA VLSI Photonics)
GMU (DARPA P-WASSP)
OE Consortium East Coast (DARPA)
GORE Photonics (IR&D)
SUN Microsystems (IR&D)
Xilinx (Teaching equipment grant)
9/18/2018
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9. CVORG: CMOS for VLSI Opto-Electronics Group
Prof. Fouad Kiamilev, Jeremy Ekman, Premanand Chandramani, Ping Gui, Xiaoqing Wang, Muhammad Fikri, Amitava Bhaduri
12Gbit/sec PCI NIC for workstation clusters. Demonstrated communication between 2 dell workstations in Q4/2000.
Funding Source: Darpa MTO
Partners: Honeywell, Sun, Intel
10Gbit/sec SiGe circuits and advanced communication and power-saving protocols for parallel optical links.
Funding Source: Darpa MTO, ITO
Partners: Raytheon, Mayo Clinic, BAE
32-port 12Gbit/sec/port router using MCM and free-space optical interconnect.
Funding: Darpa
Partners: Honeywell
4 mm
9/18/2018
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10. Mills: Research Projects
Autonomous Configuration and Authentication in Very Large Networks
Simulation of Very Large Networks
CAKRD/DARTnet Collaboration
Network Time Synchronization Project
Precision Time Synchronization
Fault-Tolerance Time Synchronization
9/18/2018
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11. Kevin B. Theobald
Models for parallel computation based on two-level multithreading
Evolutionary path to effective MPP for irregular applications on COTS processors
Hardware prototype SU being developed for cluster of 16 PCs
EARTH (Efficient Architecture for Running Threads) divides processing between a COTS "Execution Unit" and a custom "Synchronization Unit"
9/18/2018
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12. Gao: Research Projects
Execution model for the HTMT Petaflop Architectures
High-Performance Compiler Infrastructure
Power-Aware Software Optimization for Embedded Architectures
Architecture/Compiler Design Issues for Single-Chip Multiprocessors
High-Performance Visualization
9/18/2018
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13. Core Intellectual Capacity -- An Overview
Bio/Medical
applications
Core Technology/Asset
Discovery Informatics
EARTH Technology
Programming tools
Runtime software
Hardware
Compiler Technology
Retargeting
Tools
HPC System
and
Applications
Embedded System
and
Applications
9/18/2018
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14. Computation Biology/Bioinformatics Overview
focus:
Parallelization of
certain key
information
mining and
discovery
algorithm
High-performance
modeling and
simulation tools
- Virual reality visualization tools
Data collection
&
Organization
Information
Mining
&
Discovery
Database
Modeling
Simulation/
Emulator
Result presentation/visualization
9/18/2018
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15. CAPSL Bioinformatics Portal Service Model
User-1
User-2
User-n
. . .
CAPSL BIOINFOR Web Interface
Public
Resources
CAPSL HPC
Bioinformatic
toolbox
CAPSL internal
Database
High-speed Network
External
Private
Resources
High-Performance
Parallel
Computing
Servers
EARTH
Technology
9/18/2018
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16. A Sketch of CAPSL Bioinformatic Tool Development
High-Performance Bioinformatic Toolset/Testbed
Modeling/Simulation/Emulation
Multiple
Sequence
Alignment
&
Visualization
Expression
Analysis
&
Visualization
Pathway
Analysis
&
Visualization
Sequence
Database
&
Tools
Array
Database
&
tools
Pathway
Database
&
tools
A Sketch of CAPSL Bioinformatic Tool Development
9/18/2018
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17. Pilot Research Projects
Discovery Informatics
sequence similarity search
structure homology search (MSA, SNP, etc.)
pattern discovery for arrays
Predictive Modeling and Simulation
biological pathway modeling and simulation
protein structure prediction
Visulaization
9/18/2018
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18. BioMEX Model and Testbed
Transcript expression Profiles
across perturbation series
Arterial
Baroreceptors
Cardiac Ganglion
Heart and
Peripheral Vasculature
mRNA in
identified cell type
(a) Intercellular Level
Principal Neuron and other
homeostatic control neurons
NTS
Inter NA/DMN
Cardiorespiratory control circuit
(b) Signaling Pathway
Ca2+
MICRO
messenger p3
Threaded
programs p1 p2
receptor p4 K+
BIOMEX
Platform
Modeled by ODE dr dt dp
(c) Gene Network
BIOMEX
Engine
Threaded
Algorithm
for ODE/PDE
implementation
DNA
= f(p) - Vr
mRNA
Protein
High-speed net
DNA
mRNA
Protein
= Lr - Up
Bioinformatics
Server
Visualization
Server
BioMEX Model and Testbed
INFO
9/18/2018
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19. New Bioinformatics Courses
ELEG : Discovery Informatics : fall 2000 (with Prof. Javier Garcia-Frias )
ELEG : Discovery Informatics II: Spring 2001 (With Prof. Javier Garcia-Frias)
ECE/DBI Joint Distinguished Seminar: IBM Blue Gene Project (M. Snir)
Other ECE/CAPSL seminars (NCBI, Fox Chase, etc.)
9/18/2018
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20. Industry Connections DuPont AstroZenica Others 9/18/2018
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21. Summary
Multi-discipline team for novel algorithms, modeling and visualization methods
In-house high-performance computing capability for joint research with collaborators
New education activities tighted into rigorous research programs
9/18/2018
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