Designing, Conducting, and Analyzing Empirical Studies

LED08 is concerned with the role of diagrams in communication between engineers. Evaluation is at the heart of an engineering approach to designing and/or selecting diagrams that are well-suited to a particular task. In this talk I will survey several methods for conducting empirical studies of such diagrams, discuss approaches to analysis, review several studies that we have conducted, and summarize the lessons learned in the process

Groundwork for the Development of Testing Plans for Concurrent Software

While multi-threading has become commonplace in many application domains (e.g., embedded systems, digital signal processing (DSP), networks, IP services, and graphics), multi-threaded code often requires complex co-ordination of threads. As a result, multi-threaded implementations are prone to subtle bugs that are difficult and time-consuming to locate. Moreover, current testing techniques that address multi-threading are generally costly while their effectiveness is unknown. The development of cost-effective testing plans requires an in-depth study of the nature, frequency, and cost of concurrency errors in the context of real-world applications. The full paper will lay the groundwork for such a study, with the purpose of informing the creation of a parametric cost model for testing multi-threaded software. The current version of the paper provides motivation for the study, an outline of the full paper, and a bibliography of related papers

A Methodology for Building Application-Specific Visualizations of Parallel Programs

Visualization of computer programs, particularly parallel programs, promises to help programmers better understand, develop, and debug their code, especially if the visualizations are relatively easy to create. We have developed a visualization methodology being used as a component in a comprehensive parallel program visualization system. The focus of the system is on application-specific user-tailored program views. An application-specific visualization of a parallel program presents the inherent application domain, semantics, and data being manipulated by the program in a manner natural to one's understanding of the program. In this paper we discuss why application-specific views are necessary for program debugging, and we list several requirements and challenges that a system for applicationspecific viewing should meet. The visualization methodology that we introduce includes primitives for designing smooth animation scenarios, and most importantly, for allowing designers to visualize or showcase the concurrency exhibited by parallel programs

Toward a task model of concurrent software maintenance

This paper describes a first step toward developing a methodology for the maintenance of concurrent software that incorporates best practices in design and verification. Specifically, we describe our plan for using the think-aloud method to study the strategies, goals, and intentions of contemporary practitioners engaged in the maintenance of concurrent software. The method will yield a task model that details the specific tasks practitioners undertake while so engaged. Initially, we will conduct the study with graduate students in a formal-methods course at Michigan State University. Copyright 2007 ACM

A novel framework to guide antibiotic stewardship nursing practice.

BACKGROUND: There is a pervasive view among some nurses and health care disciplines that antibiotic stewardship (AS) is solely a physician or pharmacist responsibility. There is an urgent need to alter this view so that nurses can seize every opportunity to prevent patient harm from antibiotics and optimize antibiotic use. One challenge to achieving full nurse engagement as equal members of the AS team is lack of an organizing framework to illustrate relationships of phenomena and concepts inherent to adoption of AS nursing practices. METHODS: We sought to create a framework derived from the peer-reviewed literature, systematic and scoping reviews, and professional standards, consensus statements and white papers. The emerging framework went through multiple iterations as it was vetted with nurse clinicians, scholars and educators, physicians, pharmacists, infection preventionists and AS subject matter experts. RESULTS: Our evidence-based Antibiotic Stewardship Nursing Practice SCAN-P Framework provides the much-needed context and clarity to help guide local-level nurses to participate in and lead AS nursing practice. CONCLUSIONS: Nurses worldwide are ideally situated to provide holistic person-centered care, advocate for judicious use of antibiotics to minimize antibiotic resistance, and be AS educators of their patients, communities and the general public. The Antibiotic Stewardship Nursing Practice SCAN-P Framework provides a tool to do so

ApiDB: integrated resources for the apicomplexan bioinformatics resource center

ApiDB () represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as a database in its own right, but as a single web-based point of entry that unifies access to three major existing individual organism databases (, and CryptoDB.org), and integrates these databases with data available from additional sources. Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases

EuPathDB: the eukaryotic pathogen database

ABSTRACT EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNAseq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010

TriTrypDB: a functional genomic resource for the Trypanosomatidae

TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ‘User Comments’ may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate