Bounds on edit metric codes with combinatorial DNA constraints

The design of a large and reliable DNA codeword library is a key problem in DNA based computing. DNA codes, namely sets of fixed length edit metric codewords over the alphabet {A, C, G, T}, satisfy certain combinatorial constraints with respect to biological and chemical restrictions of DNA strands. The primary constraints that we consider are the reverse--complement constraint and the fixed GC--content constraint, as well as the basic edit distance constraint between codewords. We focus on exploring the theory underlying DNA codes and discuss several approaches to searching for optimal DNA codes. We use Conway's lexicode algorithm and an exhaustive search algorithm to produce provably optimal DNA codes for codes with small parameter values. And a genetic algorithm is proposed to search for some sub--optimal DNA codes with relatively large parameter values, where we can consider their sizes as reasonable lower bounds of DNA codes. Furthermore, we provide tables of bounds on sizes of DNA codes with length from 1 to 9 and minimum distance from 1 to 9.

RelMDD-A Library for Manipulating Relations Based on MDDs

Relation algebras is one of the state-of-the-art means used by mathematicians and computer scientists for solving very complex problems. As a result, a computer algebra system for relation algebras called RelView has been developed at Kiel University. RelView works within the standard model of relation algebras. On the other hand, relation algebras do have other models which may have different properties. For example, in the standard model we always have L;L=L (the composition of two (heterogeneous) universal relations yields a universal relation). This is not true in some non-standard models. Therefore, any example in RelView will always satisfy this property even though it is not true in general. On the other hand, it has been shown that every relation algebra with relational sums and subobjects can be seen as matrix algebra similar to the correspondence of binary relations between sets and Boolean matrices. The aim of my research is to develop a new system that works with both standard and non-standard models for arbitrary relations using multiple-valued decision diagrams (MDDs). This system will implement relations as matrix algebras. The proposed structure is a library written in C which can be imported by other languages such as Java or Haskell.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Incorporating Language Skills Strategies into Library Instruction for ESL Students

a self-reflection study of the incorporation of language skills strategies in speaking, listening, reading, and writing in a library instruction classroom setting

Is Library Database Searching a Language Learning Activity?

A qualitative research study that asked international students how they thought of words to enter into a library database to see if language learning was also involved.

We All Have an Accent: Welcoming International Students to the Library

an overview of ways to make international students feel welcome in the library

Library Open Access publishing funds

Presentation on scope, successes and challenges facing library Open Access publishing funds delivered at the Canadian Association of Learned Journals meeting at Congress 2014, Brock University, St. Catharines, ON, Canada. Focus on Canada but also some info on the U.S.

Collegial Self-Governance for Professional Librarians: A Look at the Advantages of the Establishment of a Library Council and its Role in the Lives of the Librarians in the Brock University Faculty Association

The ability to perform collegial governance is a cornerstone of modern universities in the United States and Canada. This idea of governance is well practiced among faculty members but is not often practiced to the same extent with librarians in those same institutions. In this chapter, I will look at a popular form of collegial governance called the Library Council. Further, I will examine how the Library Council at Brock University has enabled librarians there to perform meaningful collegial self-governance.

Copyright in the Stacks: The Chilling Effects of Unclear Copyright Interpretations in the Canadian Academic Library

Presented at the Annual Conference of the Canadian Political Science Association, Brock University, St. Catharines, Ontario, May 27, 2014