Physical Sciences and Mathematics Commons^™

Software Engineering For Science, Jeffrey C. Carver, Neil P. Chue Hong, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Software Engineering for Science provides an in-depth collection of peer-reviewed chapters that describe experiences with applying software engineering practices to the development of scientific software. It provides a better understanding of how software engineering is and should be practiced, and which software engineering practices are effective for scientific software.

The book starts with a detailed overview of the Scientific Software Lifecycle, and a general overview of the scientific software development process. It highlights key issues commonly arising during scientific software development, as well as solutions to these problems.

The second part of the book provides examples of the use of …

Metrics, Software Engineering, Small Systems – The Future Of Systems Development, William L. Honig

Computer Science: Faculty Publications and Other Works

In this talk I will introduce the importance of metrics, or measures, and the role they play in the development of high quality computer systems. I will review some key mega trends in computer science over the last three decades and then explain why I believe the trend to small networked systems, along with metrics and software engineering will define the future of high technology computer based systems.

I first learned about metrics at the Bell System where everything was measured. Metrics can be understood easily if you think of them as measures, for example of calories or salt in …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulous, Konstantin Läufer, George K. Thiruvathukal, Catherine Putonti

Computer Science: Faculty Publications and Other Works

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …