Automated unit-level testing with heuristic rules

Software testing plays a significant role in the development of complex software systems. Current testing methods generally require significant effort to generate meaningful test cases. The QUEST/Ada system is a prototype system designed using CLIPS to experiment with expert system based test case generation. The prototype is designed to test for condition coverage, and attempts to generate test cases to cover all feasible branches contained in an Ada program. This paper reports on heuristics sued by the system. These heuristics vary according to the amount of knowledge obtained by preprocessing and execution of the boolean conditions in the program

The development of a program analysis environment for Ada

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

Motivation: A global map of transcription factor binding sites (TFBSs) is critical to understanding gene regulation and genome function. DNaseI digestion of chromatin coupled with massively parallel sequencing (digital genomic footprinting) enables the identification of protein-binding footprints with high resolution on a genome-wide scale. However, accurately inferring the locations of these footprints remains a challenging computational problem

Advisory Committee:

After many years, support for multithreading has been integrated into main-stream programming languages. Inclusion of this feature brings with it a need for a clear and direct explanation of how threads interact through memory. Pro-grammers need to be told, simply and clearly, what might happen when their programs execute. Compiler writers need to be able to work their magic without interfering with the promises that are made to programmers. Java’s original threading specification, its memory model, was fundamentally flawed. Some language features, like volatile fields, were under-specified: their treatment was so weak as to render them useless. Other features, including fields without access modifiers, were over-specified: the memory model prevents almost all optimizations of code containing these “normal ” fields. Finally, some features, like final fields, had no specification at all beyond that of normal fields; no additional guarantees were provided about what will happen when they are used. This work has attempted to remedy these limitations. We provide a clear and concise definition of thread interaction. It is sufficiently simple for programmers to work with, and flexible enough to take advantage of compiler and processor-level optimizations. We also provide formal and informal techniques for verifying that the model provides this balance. These issues had never been addressed for any programming language: in addressing them for Java, this dissertation provides a framework for all multithreaded languages. The work described in this dissertation has been incorporated into the version 5.0 of the Java programming language