Eileen Kraemer

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Molecules to Maps: Tools for Visualization and Interaction in Computational Biology

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Proceedings of the 1st ACM international workshop on Empirical assessment of software engineering languages and technologies: held in conjunction with the 22nd IEEE/ACM International Conference on Automated Software Engineering (ASE) 2007

Automated software engineering, Nov 5, 2007

Societal Factors that Impact Retention and Graduation of Underrepresented Computer Science Undergraduates

Lack of diversity and high dropout rates among underrepresented students plague the CS discipline... more Lack of diversity and high dropout rates among underrepresented students plague the CS discipline. We developed, administered, and validated survey scales measuring social factors that impact the retention and graduation of underrepresented CS undergrads at two institutions. Results revealed significant differences between students who identify as men vs. women in terms of computing identity and confidence, and between black and nonblack students in terms of familiarity with future opportunities.

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Session details: Modeling methodology A: parallel and distributed methods III

Winter Simulation Conference, Dec 5, 2004

<title>Automatic presentation of running programs</title>

Proceedings of SPIE, May 3, 2001

This paper presents a technique for automatically generating graphical presentations of a program... more 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 computation by creating a specification of the program's entities and properties of interest. We identify three goals for visualizations that display consecutive computation states, known as program visualizations. First, a visualization must present all of the entities and properties described by viewers and no other information. Second, the graphical representations assigned to various program entities must be sufficiently distinctive to permit views to easily recognize entities of different types, despite similarities in graphical characteristics denoting common properties of those entities. Third, to maintain continuity of the animation over time, graphical elements used to present one state of the program must be reserved and subsequently used to represent the same or similar entities or properties in other states. Based on these goals, we have developed an algorithm that assigns graphical objects to each program entity of interest. The algorithm relies on a characterization of the available graphical objects and attributes to determine the graphical elements that best display the data contained in the entities and their properties. For views that have a greater number of properties than the available number of graphical elements, we have developed heuristics for deciding which properties can be depicted by overloading the same graphical attribute. The automatic presentation is flexible and permits viewers to intervene and determine entirely or partly the graphical design of a visualization.

VisIOn

VisIOn (Interactive Visualization Ontology) is a web application designed to categorize and store... more VisIOn (Interactive Visualization Ontology) is a web application designed to categorize and store information about Software Visualization (SV) systems, in a way that can be easily searched and used for comparison. VisIOn will allow users and developers to quickly find systems related to their needs or interests. Also, this site will serve as a collection point for information about SV tools through which developers can disseminate their work and make it available to their target community in a timely manner. VisIOn incorporates attributes identified in earlier taxonomies but emphasizes the notion of effectiveness. In the context of Software Visualization, we define effectiveness as how well a system can be used by an SV designer to communicate information to the SV viewer. In developing an SV ontology, we seek to clarify the meaning of effectiveness in the SV domain and to reconcile the terminology introduced in various SV taxonomy papers. In related work, we are conducting studies that we hope will help reduce some of the subjectivity and difficulty involved in rating the effectiveness of SV systems and of visualizations created using these systems.

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Network Visualization and Assessment of Student Reasoning About Conditionals

Understanding the thought processes of students as they progress from initial (incorrect) answers... more Understanding the thought processes of students as they progress from initial (incorrect) answers toward correct answers is a challenge for instructors, both in this pandemic and beyond. This paper presents a general network visualization learning analytics system that helps instructors to view a sequence of answers input by students in a way that makes student learning progressions apparent. The system allows instructors to study individual and group learning at various levels of granularity. The paper illustrates how the visualization system is employed to analyze student responses collected through an intervention. The intervention is BeginToReason, an online tool that helps students learn and use symbolic reasoning-reasoning about code behavior through abstract values instead of concrete inputs. The specific focus is analysis of tool-collected student responses as they perform reasoning activities on code involving conditional statements. Student learning is analyzed using the visualization system and a post-test. Visual analytics highlights include instances where students producing one set of incorrect answers initially perform better than a different set and instances where student thought processes do not cluster well. Post-test data analysis provides a measure of student ability to apply what they have learned and their holistic understanding. CCS CONCEPTS • Human-centered computing → Graph drawings; Information visualization; Visualization systems and tools; Empirical studies in visualization.

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Wang H: PlasmoDB: a functional genomic database for malaria parasites

PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides... more 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 belongs to a family of genomic resources that are housed under the EuPathDB (http:// EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories-annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.

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Supporting exploratory visualization of distributed computations

Visualizing distributed computations is a challenging endeavor. My research on exploratory visual... more Visualizing distributed computations is a challenging endeavor. My research on exploratory visualization has investigated how to effectively and efficiently enable interactions with running distributed computations. My approach has focused on both what the needs of the user are and how the user can guide the process. The realization that the user often wants only a small percentage of the computation's state at any particular time dramatically shifts the emphasis of tool development from low level optimizations to configurability and flexibility. With such a system the user may forsake post-mortem analysis of short executions in favor of dynamic interactions with running distributed computations that are both large and long-running. To demonstrate and quantify the benefits of exploratory visualization I have designed and built the PathFinder system. PathFinder creates visualizations based on consistent global snapshots created using a new class of algorithms developed as part of this research. While traditional monitoring and steering systems have treated data collection and consistency issues monolithically, PathFinder regards them as orthogonal. PathFinder has also served as a testbed to investigate the impact software agents can have on monitoring and steering.

Session details: Software visualization applications

EuPathDB: a portal to eukaryotic pathogen databases. Nucleic acids research

EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic ... more EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recentlyimplemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.

format_quoteThe current version of EuPathDB provides genomic data access for 22 species, improving functional genomics for eukaryotic pathogens.format_quote

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Tool-Aided Learning of Code Reasoning with Abstraction in the CS Curriculum

Informatics in Education, 2021

Computer science students often evaluate the behavior of the code they write by running it on spe... more Computer science students often evaluate the behavior of the code they write by running it on specific inputs and studying the outputs, and then apply their comprehension to a more general understanding of the code. While this is a good starting point in the student's career, successful graduates must be able to reason analytically about the code they create or encounter. They must be able to reason about the behavior of the code on arbitrary inputs, without running the code. Abstraction is central for such reasoning. In our quest to help students learn to reason abstractly and develop logically correct code, we have developed tools that rely on a verification engine. Code involves assignment, conditional, and loop statements, along with objects and operations. Reasoning activities involve symbolic reasoning with simple assertions and design-by-contract assertions such as pre-and post-conditions as well as loop invariants with data abstractions. Students progress from tracing and reading code to the design and implementation of code, all relying on abstraction for verification. This paper reports some key results and findings from associated studies spanning several years.

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Shulei Sun

This thesis describes the development of a knowledge-based system to evaluate forested land for a... more This thesis describes the development of a knowledge-based system to evaluate forested land for availability of wildlife habitat. NED is an acronym derived from “Northeast Decision Model”. The NED DSS, a collection of software products, was created to help resource managers to build up goals, access current and potential conditions, and create long-term, landscape-level management plans for forest properties in the eastern United States. An initial version of NED had been released, which achieved only part of the functions we hope eventually to capture in NED. Throughout this thesis, I will focus on the wildlife component of NED and its successors. I will describe the weakness of first version in four aspects: 1) intelligent module manager, 2) data management, 3) reporting utility, and 4) knowledge representation. Then, I will discuss how we implement solutions to these problems.

Teaching the Design-by-Contract Concept in a Software Engineering Course Using RESOLVE

ACM SIGSOFT Software Engineering Notes, 2018

Design by contract (DBC) is a key concept in software engineering. The RESOLVE language and envir... more Design by contract (DBC) is a key concept in software engineering. The RESOLVE language and environment support the teaching and learning of DBC concepts. However, students encounter obstacles in fully achieving the desired educational outcomes. Some of these obstacles are related to the complexity of the content. Additional appropriate exercises can help to address these obstacles. Other obstacles are related to features of the environment and documentation. We propose a variety of interventions to address these obstacles, including potential revisions to the environment, updates to the documentation, and the creation of additional instructional materials.

[email protected] October 16, 1993

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School of Engineering & Applied Science

Molecules to Maps: Tools for Visualization and Interaction in Computational Biology

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Eileen Kraemer

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