Design Review 1

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Design Review 1

• Viral Infection
• Group 8
• Anya Castillo, Adam Hartman,
• Shambhavi Patel, Colby Ranger

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Design Review 1 Synopsis

• Design Goals
• Design Exploration Plan
• Implementation Plan
• Verification, Integration, and Test Plan
• Demonstration Plan
• Division of Labor
• Schedule

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Design Goals

• Use-case The design is meant to be used for
  situations in which human presence is not
  desirable and where there may be limited
  communications bandwidth
• E.g. A biohazard exposure site

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Design Goals

• Major use-case issues addressed by design
  innovations
• - Limited communications bandwidth USB mass
  storage device preloaded with database
• - Desire for no human presence remote alert
  system that will upload findings to a web server
  control of the system through the same, or a very
  similar, server
• Success measurements
• - Correct findings viewable from a remote
  location via the Internet while still providing
  local notification
• - Ability to compare query against entire
  database without requiring an update from the
  main database but allow updates from the database
  to the system if requested

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Design Exploration Plan Overview

• Architecture
• - Find neighbor words function and remote alert
  system on ARM vs. Nios
• Search Algorithm
• - Optimization of string matching and BLOSUM62
  matrix calculations
• User Interface
• - Local input via a terminal vs. remote input
  via the Internet
• - Available interface commands (start, stop,
  update database, et cetera)
• Remote Alert System
• - Running a small server on the Nios vs.
  updating a page on a remote server

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Architecture Exploration

• Find neighbor words on Nios and run alert system
  on ARM
• - Pros no inter-chip communications required to
  send neighbor word results to correct
  destination ARM can devote all resources to
  alert system processing
• - Cons Nios is already responsible for large
  tasks server may not be streamlined (or even
  plausible) for execution on the ARM alert
  information must be sent to the Nios before it
  reaches the Internet
• Find neighbor words on ARM and run alert system
  on Nios
• - Pros ARM has strong integer computation
  abilities (this is good for table accesses)
  direct interface on Nios between alert system and
  Ethernet connection
• - Cons increased communication between Nios and
  ARM

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Architecture Exploration Design 1
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Architecture Exploration Design 2
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Search Algorithm Exploration

• Analyze various string matching methods
• - Naïve no pre-processing O((n m 1)m)
  search time
• - Knuth-Morris-Pratt T(m) pre-processing time
  T(n) search time finite state machine
  implementation
• - Boyer-Moore O(m) pre-processing time average
  O(n/m) and worst O(nm) search time
• - where m length of query and n length of
  searchable string
• Optimize operations dealing with BLOSUM62 table
• - Store smaller subset of the whole table
• - Do pre-processing to cull certain calculations
• - Write code which prevents repetitive
  calculations

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User Interface Exploration

• Local Input
• - Pros ease of implementation fast reactions
  to commands
• - Cons requires human presence at the site
• Remote Input
• - Pros allows commands to be sent without
  requiring human presence at the site
• - Cons more difficult to implement system may
  react slowly to these commands depending on
  implementation
• Commands research which types of commands would
  be useful/necessary

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Remote Alert System Exploration

• Running a server on the Nios
• - Pros easy to update necessary files many
  users can log in to view results
• - Cons requires greater bandwidth requires
  significantly more space on chip for hardware
• Using Nios to update files on a remote server
• - Pros requires less bandwidth, chip area, and
  processing power ease of implementation
• - Cons relies on dependability of remote
  server extra work required to send findings to
  multiple users

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Implementation Plan

• Explore various design options
• Simulation in C of code for each component
• - ARM, DSP, Nios, microcontroller
• Define interfaces
• Port C simulations to hardware and add interfaces
• Implement peripherals
• - Ethernet, USB storage, LCD
• Interconnection of components
• System testing and verification

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Verification

• Components
• - DSP, ARM, microcontroller
• - simulation and verification in C
• - port code to hardware
• - test in isolation
• - Nios
• - simulation and verification in C
• - port code to hardware and Verilog
• - test Verilog portions with custom testbenches
• - test complete Nios system in isolation

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Verification

• Components
• - USB mass storage device
• - verify read/write capabilities in isolation
• - LCD
• - verify write and animation capabilities in
  isolation
• - Ethernet
• - verify communications between Nios and PC via
  loopback tests

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Integration

• Individual components will be added one by one to
  the complete system after evaluation of
  interfaces
• Outputs from neighboring components may be
  simulated in order to test an individual
  component in the system
• All components in current system must be
  interfaced and correct communication must be
  verified before additional components are added
• - This allows incremental debugging that will
  prevent masking of problems in later steps of
  integration
• Upon integration of all components, the system
  will be tested with the baseline database
• Upon correctly handling the baseline database,
  larger databases will be tested with the system

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Demonstration Plan

• C code for nucleotide to amino acid conversion
• - Works toward overall goal of DSP development
• - Find the amino acid for any given sequence of
  nucleotides based on the given table written as
  a console program
• C code for find_neighbor_words part of BLASTP
• - Works toward overall goal of algorithm
  development
• - Find all neighbor words for any query based on
  the BLOSUM62 table written as a console program
• Initial LCD connection
• - Works toward overall goal of peripheral
  implementation
• - Allow characters to be written to the LCD

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Demonstration Plan

• Initial Ethernet connection
• - Works toward overall goal of peripheral
  implementation
• - Allow data to be sent between PC and Nios
• Research use of the USB interface
• - Works toward overall goal of peripheral
  implementation
• - Allows for remainder of schedule to become
  well defined
• Plan implementation of remote alert system
• - Works toward overall goal of design innovation
• - Explore potential designs and choose the best
  one define interfaces for that design

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Division of Labor

• Adam Find word hits , extend hits, and find
  best match implementation on the Nios
• Anya USB interface and local alert system
• Colby Remote alert system
• Shambhavi Signal processing, nucleotide to amino
  acid, and integration of components

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Schedule