Physical Sciences and Mathematics Commons^™

Unconventional Computation Including Quantum Computation, Bruce J. Maclennan

Faculty Publications and Other Works -- EECS

Unconventional computation (or non-standard computation) refers to the use of non-traditional technologies and computing paradigms. As we approach the limits of Moore’s Law, progress in computation will depend on going beyond binary electronics and on exploring new paradigms and technologies for information processing and control. This book surveys some topics relevant to unconventional computation, including the definition of unconventional computations, the physics of computation, quantum computation, DNA and molecular computation, and analog computation. This book is the content of a course taught at UTK.

Path Creation By Continuous Flocking As An Example Of A Morphogenetic Programming Language, Bruce J Maclennan

Faculty Publications and Other Works -- EECS

Artificial morphogenesis uses processes inspired by embryology to control massive swarms of robots to assemble complex physical structures. First, we use an example morphogenetic program to illustrate a prototype implementation of morphgen, a morphogenetic programming language. The syntax and semantics are described informally as illustrated by the example program, which is included in its entirety in an appendix. Another appendix includes a complete formal grammar for the current version of the language. Next, we describe the results of a series of experiments with the program, which simulates a continuous swarm of microscopic agents creating paths from an origin to a …

The Synmac Syntax Macroprocessor: Introduction And Manual, Version 5, Bruce J Maclennan

Faculty Publications and Other Works -- EECS

A syntax macroprocessor permits parameterized text substitutions with greater syntactic flexibility than allowed with ordinary macroprocessors. This report describes the \emph{synmac} syntax macroprocessor, which permits arbitrarily delimited macro invocations, and thus allows the definition of new statement and expression forms or even complete languages. Synmac is a computationally complete programming language. We define the synmac macro language, document a prototype implementation, and give examples of its use.

An Exploratory Study Of The Nature And Composition Of Current Library And Information Science Programs In Indian State Universities, Bharat Mehra, Devendra Potnis, Jennifer Morden

Faculty Publications and Other Works -- EECS

This brief article explores the current state of library and information science (LIS) programs in terms of their nature and composition in state universities in India. Preliminary findings were based on a content analysis of representative information regarding LIS education available on the websites of all state universities and colleges that offer LIS programs in India. Findings indicated broad trends in administrative structuring and nomenclature of LIS programs which requires standardization. The type of degrees awarded, the composition of faculty positions, student places per year and student-faculty ratios was also found to be varied among the different institutions. The lack …

A High-Throughput De Novo Sequencing Approach For Shotgun Proteomics Using High-Resolution Tandem Mass Spectrometry, Chongle Pan, Byung H. Park, William H. Mcdonald, Patricia A. Carey, Jillian F. Banfield, Nathan C. Verberkmoes, Robert L. Hettich, Nagiza F. Samatova

Faculty Publications and Other Works -- EECS

Abstract

Background

High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms.

Results

In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were …

Comparison Of Threshold Selection Methods For Microarray Gene Co-Expression Matrices, Bhavesh R. Borate, Elissa J. Chesler, Michael A. Langston, Arnold M. Saxton, Brynn H. Voy

Faculty Publications and Other Works -- EECS

Abstract

Background

Network and clustering analyses of microarray co-expression correlation data often require application of a threshold to discard small correlations, thus reducing computational demands and decreasing the number of uninformative correlations. This study investigated threshold selection in the context of combinatorial network analysis of transcriptome data.

Findings

Six conceptually diverse methods - based on number of maximal cliques, correlation of control spots with expressed genes, top 1% of correlations, spectral graph clustering, Bonferroni correction of p-values, and statistical power - were used to estimate a correlation threshold for three time-series microarray datasets. The validity of thresholds was tested by …

Bridging The Gap Between Systems Biology And Medicine, Gilles Clermont, Charles Auffray, Yves Moreau, David M. Rocke, Daniel Dalevi, Devdatt Dubhashi, Dana R. Marshall, Peter Raasch, Frank Dehne, Paolo Provero, Jesper Tegner, Bruce J. Aronow, Michael A. Langston, Mikael Benson

Faculty Publications and Other Works -- EECS

Abstract

Systems biology has matured considerably as a discipline over the last decade, yet some of the key challenges separating current research efforts in systems biology and clinically useful results are only now becoming apparent. As these gaps are better defined, the new discipline of systems medicine is emerging as a translational extension of systems biology. How is systems medicine defined? What are relevant ontologies for systems medicine? What are the key theoretic and methodologic challenges facing computational disease modeling? How are inaccurate and incomplete data, and uncertain biologic knowledge best synthesized in useful computational models? Does network analysis provide …