Designing your next empirical study on program comprehension (2009)
Massimiliano Di Penta, Eileen Kraemer
The field of program comprehension is characterized by both the continuing development of new tools and techniques and the adaptation of existing techniques to address program comprehension needs for...
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Carlton, Jane M., Dommer, Jennifer, Fischer, Steve, ...
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the...
PlasmoDB: a functional genomic database for malaria parasites (2009)
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Dommer, Jennifer, Fischer, Steve, Gajria, Bindu, ...
PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB...
Laura K. Dillon, Shaohua Xie, Scott D. Fleming, Eileen Kraemer
Empirical studies are important for understanding how well current design methods and notations support development of multi-threaded programs. Unfortunately, concurrency exacerbates an already...
Laura K. Dillon, Eileen Kraemer, Shaohua Xie, Scott D. Fleming
Empirical studies are important for understanding how well current design methods and notations support development of multithreaded programs. Unfortunately, concurrency exacerbates an already...
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Carlton, Jane M., Dommer, Jennifer, Fischer, Steve, ...
© 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids...
BIOINFORMATICS APPLICATIONS NOTE GFPE: gene-finding program evaluation (2008)
Summary: Gene-finding program evaluation (GFPE) is a set of Java classes for evaluating gene-finding programs. A command-line interface is also provided. Inputs to the program include the sequence...
It is generally accepted that concurrency can be difficult for students to reason about and to manage. While some studies provide insight into the nature of these difficulties[6], work remains to be...
Designing your Next Empirical Study on Program Comprehension (2008)
Massimiliano Di Penta, Eileen Kraemer
The field of program comprehension is characterized by both the continuing development of new tools and techniques and the adaptation of existing techniques to address program comprehension needs for...
Token Finding Strategies (2007)
Monitoring distributed computations provides a practical way of learning about and coming to understand a class of applications that are becoming increasingly common. The benefits of distribution...
Delbert Hart, Mihail E. Tudoreanu, Eileen Kraemer
Abstract. One of the greatest challenges facing the software community today is the increasing complexity of software. Complexity limits understanding, making it dicult to evaluate the correctness,...
Why Johnny Won't Visualize (2007)
Eileen Kraemer, Mihail Tudoreanu, Ashley Taylor
Many potential users of program visualization have a strong intuitive belief that visualization is a valuable tool for communicating information about the state and behavior of programs. Yet, in...
Agent Roles in Snapshot Assembly (2007)
Abstract The ability to understand running distributed computations depends on effective monitoring techniques. Monitoring distributed systems entails two primary tasks: collecting data from the...
A Java-based Course in Human-Computer Interaction (2007)
Abstract The ACM/SIGCHI proposed curriculum for Human-Computer Interaction includes four types of HCI courses. The course described in this paper most closely fits the description of the CS1 course,...
Exploratory Visualization of Distributed Computations: A Case Study (2007)
Navin Gupta, Eileen Kraemer, Delbert Hart, Maria Chinwala, David Miller
Exploratory Visualization is an approach for helping users learn about distributed computations without requiring users to examine source code. Instead, visualizations provide intuition about the...
Visualization Tools Creating an Accurate Portrayal of Concurrent Executions (2007)
Eileen Kraemer, John T. Stasko
The authors promote understanding of distributed computations through visualizations featuring reorderable, synchronous, and independent displays. They discuss the necessity of these characteristics...
ApiDB: integrated resources for the apicomplexan bioinformatics resource center (2007)
Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, John Miller, ...
resource center
ApiDB: integrated resources for the apicomplexan bioinformatics resource center (2007)
Aurrecoechea, Cristina, Heiges, Mark, Wang, Haiming, Wang, Zhiming, Fischer, Steve, Rhodes, Philippa, ...
ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The...
CryptoDB: a Cryptosporidium bioinformatics resource update (2006)
Heiges, Mark, Wang, Haiming, Robinson, Edward, Aurrecoechea, Cristina, Gao, Xin, Kaluskar, Nivedita, ...
The database, CryptoDB (http://CryptoDB.org), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and...
Intelligen: A distributed workflow system for discovering protein-protein interactions (2003)
Krys J. Kochut, Jonathan Arnold, Amit Sheth, John Miller, Eileen Kraemer, Budak Arpinar, ...
In the new millennium biology has gone through a paradigm shift with the advent of Genomics, the study of the structure, function, and evolution of whole genomes. The term “genomics ” was coined...
GFPE: gene-finding program evaluation (2003)
Summary: Gene-finding program evaluation (GFPE) is a set of Java classes for evaluating gene-finding programs. A command-line interface is also provided. Inputs to the program include the sequence...
A Study of the Performance of Steering Tasks under Spatial Transformation of Input (2002)
Mihail E Tudoreanu, Eileen Kraemer
Indirection exists between the virtual objects that form the computer interface and the input devices through which the user interacts to manipulate these objects. This paper studies the effect of...
Empirical evidence that algorithm animation promoted understand of distributed algorithms (2002)
Mihail E. Tudoreanu, Rong Wu, Ashley Hamilton-taylor, Eileen Kraemer
Previous studies of program visualization have generally failed to provide convincing support for the benefits of algorithm animation in promoting the understanding of computations. This paper...
Algorithm Animation Beneficial in Understanding Distributed Algorithms (2002)
Mihail E. Tudoreanu, Rong Wu, Ashley Hamilton-Taylor, Eileen Kraemer
Previous studies of program visualization have failed to provide convincing support for the benefits of algorithm animation in promoting the understanding of computations. This paper presents a study...
Automatic Presentation of Running Programs (2001)
Mihail E Tudoreanu, Eileen Kraemer
This paper presents a technique for automatically generating graphical presentations of a program execution. Viewers can customize the presentation and examine particular aspects of the running...
Mobile Agents for Monitoring Distributed Systems (2001)
Delbert Hart, Mihail Tudoreanu, Eileen Kraemer
Mobile agents can be employed to help a system adapt to diverse conditions and provide functionality that would otherwise be cumbersome and perhaps in-feasible. The benets of mobile agents though are...
An analysis of gene-finding programs for Neurospora crassa (2001)
Kraemer, Eileen, Wang, Jian, Guo, Jinhua, Hopkins, Samuel, Arnold, Jonathan
Motivation: Computational gene identification plays an important role in genome projects. The approaches used in gene identification programs are often tuned to one particular organism, and accuracy...
Consistency Considerations in the Interactive Steering of Computations (1999)
Interactive steering can be helpful in understanding and managing parallel and distributed systems. Multiple approaches to the implementation of steering systems are under investigation or in...
Balancing Consistency and Lag in Transaction-Based Computational Steering (1998)
Eileen Kraemer, Delbert Hart, Gruia-Catalin Roman
Computational steering, the interactive adjustment of application parameters and allocation of resources, is a promising technique for higher-productivity simulations, finer-grained optimization of...
Interactive Visual Exploration of Distributed Computations (1997)
Delbert Hart, Eileen Kraemer, Gruia-catalin Roman
Program understanding is central to the development of distributed computations, from the initial coding phase, through testing and debugging, to maintenance and support. Our goal is to support...
Interactive program steering is a promising technique for improving the performance of parallel and distributed applications. Steering decisions are typically based on visual presentations of some...
Interactive Visual Exploration of Distributed Computations (1997)
Delbert Hart, Eileen Kraemer, Gruia-catalin Roman
Program understanding is central to the development of distributed computations, from the initial coding phase, through testing and debugging, to maintenance and support. Our goal is to support...
An Architecture for Monitoring, Visualization, and Control and Gigabit Networks (1997)
Guru Parulkar, Douglas Schmidt, Eileen Kraemer, Jonathan Turner, Anshul Kantawala
In this paper, we outline a design of a highly scalable network monitoring, visualization and control system (NMVC) system with advanced algorithmic and human-in-the-loop capability. This capability...
Using Snapshot Streams to Support Visual Exploration (1997)
Delbert Hart, Eileen Kraemer, Gruia-catalin Roman
The non-determinism, complexity, and size of distributed software systems present significant difficulties for designers and maintainers. Visualization can help alleviate these difficulties through...
Using Snapshot Streams to Support Visual Exploration (1997)
Delbert Hart, Eileen Kraemer, Gruia-catalin Roman
The non-determinism, complexity, and size of distributed software systems present significant difficulties for designers and maintainers. Visualization can help alleviate these difficulties through...
Interactive Visual Exploration of Distributed Computations (1997)
Delbert Hart Eileen, Eileen Kraemer, Gruia-catalin Roman
Program understanding is central to the development of distributed computations, from the initial coding phase, through testing and debugging, to maintenance and support. Our goal is to support...
Interactive program steering is a promising technique for improving the performance of parallel and distributed applications. Steering decisions are typically based on visual presentations of some...
An Architecture for Monitoring, Visualization and Control of Gigabit Networks (1997)
Guru Parulkar, Douglas Schmidt, Eileen Kraemer, Jonathan Turner, Anshul Kantawala
We propose a network monitoring, visualization and control system (NMVC) that ensures adequate quality of service to network users while maintaining high network resource utilization. The main...
Online Displays of Parallel Programs: Problems and Solutions (1997)
Greg Eisenhauer, Weiming Gu, Eileen Kraemer, Karsten Schwan, John Stasko
The continuous display of information derived from on-line monitoring presents problems that are more difficult to resolve than those associated with off-line displays. Handling these problems...
Interactive Steering of Simulated Annealing (1996)
Combinatorial optimization problems involve the selection of an arrangement of discrete objects (a state) from a discrete, finite space of mutually exclusive states. The goal is to select the...
Falcon: On-line monitoring and steering of large-scale parallel programs (1995)
Weiming Gu, Greg Eisenhauer, Eileen Kraemer, Karsten Schwan, John Stasko, Jeffrey Vetter
Abstract-- Falcon is a system for on-line monitoring and steering of large-scale parallel programs. The purpose of such interactive steering is to improve its performance or to affect its execution...
The collection of global snapshots is an essential task in the monitoring and interactive steering of distributed systems. In the PathFinder exploratory visualization system we have implemented...
Toward Flexible Control of the Temporal Mapping from Concurrent Program Events to Animations (1994)
Eileen Kraemer, John T. Stasko
As parallel and distributed computers become more widely available and used, the already important process of understanding and debugging concurrent programs will take on even greater importance. We...
Issues in Visualization for the Comprehension of Parallel Programs (1994)
Eileen Kraemer, John T. Stasko
Parallel and distributed computers are becoming more widely used. Thus, the comprehension of parallel programs is increasingly important. Understanding parallel programs is more challenging than...
Issues in Visualization for the Comprehension of Parallel Programs (1994)
Eileen Kraemer, John T. Stasko
Parallel and distributed computers are becoming more widely used. Thus, the comprehension of parallel programs is increasingly important. Understanding parallel programs is more challenging than...
A Methodology for Building Application-Specific Visualizations of Parallel Programs (1993)
John T. Stasko, Eileen Kraemer
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...
Applying Program Visualization Techniques to Aid Parallel and Distributed Program Development (1991)
William F. Appelbe, John T. Stasko, Eileen Kraemer
Parallel and distributed programming is intrinsically more difficult than sequential programming, yet few effective tools or methodologies have been developed to help programmers understand the...
CryptoDB: a Cryptosporidium bioinformatics resource update
Heiges, Mark, Wang, Haiming, Robinson, Edward, Aurrecoechea, Cristina, Gao, Xin, Kaluskar, Nivedita, ...
The database, CryptoDB (), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed...
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.
Xu, Zheng, Lance, Britton, Vargas, Claudia, Arpinar, Budak, Bhandarkar, Suchendra, Kraemer, Eileen, ...
A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits...
CryptoDB: a Cryptosporidium bioinformatics resource update
Heiges, Mark, Wang, Haiming, Robinson, Edward, Aurrecoechea, Cristina, Gao, Xin, Kaluskar, Nivedita, ...
The database, CryptoDB (), is a community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium. CryptoDB integrates whole genome sequence and annotation with expressed...
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.
Xu, Zheng, Lance, Britton, Vargas, Claudia, Arpinar, Budak, Bhandarkar, Suchendra, Kraemer, Eileen, ...
A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits...
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
Aurrecoechea, Cristina, Heiges, Mark, Wang, Haiming, Wang, Zhiming, Fischer, Steve, Rhodes, Philippa, ...
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...
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Carlton, Jane M., Dommer, Jennifer, Fischer, Steve, ...
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the...
PlasmoDB: a functional genomic database for malaria parasites
Aurrecoechea, Cristina, Brestelli, John, Brunk, Brian P., Dommer, Jennifer, Fischer, Steve, Gajria, Bindu, ...
PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB...