Detection and reconstruction of error control codes for engineered and biological regulatory systems. Metadata

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Title

  • Main Title Detection and reconstruction of error control codes for engineered and biological regulatory systems.

Creator

  • Author: May, Elebeoba Eni
    Creator Type: Personal
  • Author: Rintoul, Mark Daniel
    Creator Type: Personal
  • Author: Johnston, Anna Marie
    Creator Type: Personal
  • Author: Pryor, Richard J.
    Creator Type: Personal
  • Author: Hart, William Eugene
    Creator Type: Personal
  • Author: Watson, Jean-Paul
    Creator Type: Personal

Contributor

  • Sponsor: United States. Department of Energy.
    Contributor Type: Organization

Publisher

  • Name: Sandia National Laboratories
    Place of Publication: United States

Date

  • Creation: 2003-10-01

Language

  • English

Description

  • Content Description: A fundamental challenge for all communication systems, engineered or living, is the problem of achieving efficient, secure, and error-free communication over noisy channels. Information theoretic principals have been used to develop effective coding theory algorithms to successfully transmit information in engineering systems. Living systems also successfully transmit biological information through genetic processes such as replication, transcription, and translation, where the genome of an organism is the contents of the transmission. Decoding of received bit streams is fairly straightforward when the channel encoding algorithms are efficient and known. If the encoding scheme is unknown or part of the data is missing or intercepted, how would one design a viable decoder for the received transmission? For such systems blind reconstruction of the encoding/decoding system would be a vital step in recovering the original message. Communication engineers may not frequently encounter this situation, but for computational biologists and biotechnologist this is an immediate challenge. The goal of this work is to develop methods for detecting and reconstructing the encoder/decoder system for engineered and biological data. Building on Sandia's strengths in discrete mathematics, algorithms, and communication theory, we use linear programming and will use evolutionary computing techniques to construct efficient algorithms for modeling the coding system for minimally errored engineered data stream and genomic regulatory DNA and RNA sequences. The objective for the initial phase of this project is to construct solid parallels between biological literature and fundamental elements of communication theory. In this light, the milestones for FY2003 were focused on defining genetic channel characteristics and providing an initial approximation for key parameters, including coding rate, memory length, and minimum distance values. A secondary objective addressed the question of determining similar parameters for a received, noisy, error-control encoded data set. In addition to these goals, we initiated exploration of algorithmic approaches to determine if a data set could be approximated with an error-control code and performed initial investigations into optimization based methodologies for extracting the encoding algorithm given the coding rate of an encoded noise-free and noisy data stream.
  • Physical Description: 42 p.

Subject

  • Keyword: Dna
  • STI Subject Categories: 99 General And Miscellaneous//Mathematics, Computing, And Information Science
  • Keyword: Exploration
  • Keyword: Transcription
  • Keyword: Approximations
  • STI Subject Categories: 59 Basic Biological Sciences
  • Keyword: Rna
  • Keyword: Linear Programming
  • Keyword: Communications
  • Keyword: Optimization
  • Keyword: Detection
  • Keyword: Algorithms
  • Keyword: Engineers
  • Keyword: Genetics
  • Keyword: Design

Collection

  • Name: Office of Scientific & Technical Information Technical Reports
    Code: OSTI

Institution

  • Name: UNT Libraries Government Documents Department
    Code: UNTGD

Resource Type

  • Report

Format

  • Text

Identifier

  • Report No.: SAND2003-3963
  • Grant Number: AC04-94AL85000
  • DOI: 10.2172/918239
  • Office of Scientific & Technical Information Report Number: 918239
  • Archival Resource Key: ark:/67531/metadc889138