CPEG Reseach Activities An Overview Guang R Gao

CPEG Reseach Activities – An Overview Guang R. Gao Computer Architecture and Parallel Systems Laboratory Dept. of Electrical and Computer Engineering University of Delaware ggao@capsl. udel. edu 1/15/2022 capslbioinfor. ppt 1

CPEG Faculty • • • John Elias Guang R. Gao Dave Mills Fouad Kiamilev Kevin Theobald Peter Warter (Emeritus) 1/15/2022 capslbioinfor. ppt 2

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 1/15/2022 capslbioinfor. ppt 3

John Elias: Research Interests • Neuromorphic Engineering – Silicon neurons – Neurocomputation • User Interfaces (collaboration with Prof. Westerman) – Gesture based – Multi-hand Multi-finger – Unified (touch, voice, force, gesture, etc. ) 1/15/2022 capslbioinfor. ppt 4

Professors Westerman and Elias: The Finger. Board • 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 1/15/2022 capslbioinfor. ppt 5

Finger. Board Product Concept 1/15/2022 capslbioinfor. ppt 6

Finger. Board Product Concept 1/15/2022 capslbioinfor. ppt 7

Kiamilev: Active Projects • • 1/15/2022 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) capslbioinfor. ppt 8

CVORG: CMOS for VLSI Opto-Electronics Group Prof. Fouad Kiamilev, Jeremy Ekman, Premanand Chandramani, Ping Gui, Xiaoqing Wang, Muhammad Fikri, Amitava Bhaduri 12 Gbit/sec PCI NIC for workstation clusters. Demonstrated communication between 2 dell workstations in Q 4/2000. Funding Source: Darpa MTO Partners: Honeywell, Sun, Intel 10 Gbit/sec Si. Ge circuits and advanced communication and power-saving protocols for parallel optical links. Funding Source: Darpa MTO, ITO Partners: Raytheon, Mayo Clinic, BAE 32 -port 12 Gbit/sec/port router using MCM and freespace optical interconnect. Funding: Darpa Partners: Honeywell 4 mm 1/15/2022 capslbioinfor. ppt 9

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 1/15/2022 capslbioinfor. ppt 10

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 1/15/2022 EARTH (Efficient Architecture for Running Threads) divides processing between a COTS "Execution Unit" and a custom "Synchronization capslbioinfor. ppt 11 Unit"

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 1/15/2022 capslbioinfor. ppt 12

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 1/15/2022 Embedded System and Applications capslbioinfor. ppt 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 1/15/2022 Data collection & Organization Information Mining & Discovery Database Modeling Simulation/ Emulator Result presentation/visualization capslbioinfor. ppt 15

CAPSL Bioinformatics Portal Service Model. . . User-n CAPSL BIOINFOR Web Interface CAPSL HPC Bioinformatic toolbox EARTH Technology 1/15/2022 CAPSL internal Database High-Performance Parallel Computing Servers capslbioinfor. ppt High-speed Network User-1 User-2 Public Resources External Private Resources 16

High-Performance Bioinformatic Toolset/Testbed Modeling/Simulation/Emulation Multiple Sequence Alignment & Visualization Sequence Database & Tools Expression Analysis & Visualization Array Database & tools Pathway Analysis & Visualization Pathway Database & tools A Sketch of CAPSL Bioinformatic Tool Development 1/15/2022 capslbioinfor. ppt 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 1/15/2022 capslbioinfor. ppt 18

BIO Transcript expression Profiles across perturbation series Arterial Baroreceptors m. RNA in identified cell type Cardiac Ganglion Heart and Peripheral Vasculature (a) Intercellular Level Principal Neuron and other homeostatic control neurons NTS Inter NA/DMN Cardiorespiratory control circuit (b) Signaling Pathway MICRO Threaded programs receptor BIOMEX Engine High-speed net 1/15/2022 p 1 p 3 p 2 p 4 K+ BIOMEX Platform Bioinformatics Server Ca 2+ messenger Visualization Server Threaded Algorithm for ODE/PDE implementation Modeled by ODE dr = f(p) - Vr dt (c) Gene Network DNA m. RNA Protein dp = Lr - Up dt DNA m. RNA Protein INFO Bio. MEX Model and Testbed capslbioinfor. ppt 19

New Bioinformatics Courses • ELEG 667 -13: Discovery Informatics : fall 2000 (with Prof. Javier Garcia-Frias ) • ELEG 667 -13: 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. ) 1/15/2022 capslbioinfor. ppt 20

Industry Connections • Du. Pont • Astro. Zenica • Others 1/15/2022 capslbioinfor. ppt 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 1/15/2022 capslbioinfor. ppt 22