Physical Sciences and Mathematics Commons^™

Spring­11: Pdc In Cs1/2 And A Mobile/Cloud Intermediate Mobile/Cloud Intermediate Software Design Course, Joseph P. Kaylor, Konstantin Läufer, Chandra N. Sekharan, George K. Thiruvathukal

Konstantin Läufer

Recent changes in the environment of Loyola University Chicago’s Department of Computer Science include a better differentiation of our four undergraduate majors, growing interest in computing among science majors, and an increased demand for graduates with mobile and cloud skills. In our continued effort to incorporate parallel and distributed computing topics into the undergraduate curriculum, we are focusing on these three existing courses: CS1: In response to a request from the physics department, we started to offer a CS1 section aimed at majors in physics and other hard sciences this spring semester. This section includes some material on numerical methods …

Software Metrics And Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, Nicholas J. Hayward

Konstantin Läufer

Software metrics are a critical tool which provide continuous insight to products and processes and help build reliable software in mission critical environments. Using software metrics we can perform calculations that help assess the effectiveness of the underlying software or process. The two types of metrics relevant to our work is complexity metrics and in-process metrics. Complexity metrics tend to focus on intrinsic code properties like code complexity. In-process metrics focus on a higher-level view of software quality, measuring information that can provide insight into the underlying software development process.

Our aim is to develop and evaluate a metrics dashboard …

Towards Sustainable Digital Humanities Software, George K. Thiruvathukal, Shilpika Shilpika, Nicholas J. Hayward, Saulo Aguiar, Konstantin Läufer

Konstantin Läufer

Our work in software quality for digital humanities was borne of an effort to address sustainable practices in scientific software development, where the speaker (Thiruvathukal) co-authored a position paper on the case for software engineering in scientific software development as part of an all-encompassing strategy to create more sustainable scientific software (an example of a well-known scientific software package is LINPACK). In this position paper, we addressed how “progress in scientific research is dependent on the quality and accessibility of software at all levels". This progress depends on embracing the best traditional--and emergent--practices in software engineering, especially agile practices that …

Building Capable, Energy-Efficient, Flexible Visualization And Sensing Clusters From Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, George K. Thiruvathukal

Konstantin Läufer

We explore the application of clusters of commodity tablet devices to problems spanning a “trilogy” of concerns: visualization, sensing, and computation. We conjecture that such clusters provide a low-cost, energy-efficient, flexible, and ultimately effective platform to tackle a wide range of problems within this trilogy. This is a work in progress, and we now elaborate our position and give a preliminary status report. A wide range of Android tablet devices are available in terms of price and capabilities. “You get what you pay for” w.r.t. display resolution, sensors, and chipset---corresponding to the trilogy. $200 gets one a 1280x800-pixel touch display, …

Metrics Dashboard Services: A Framework For Analyzing Free/Open Source Team Repositories, Shilpika Shilpika, George K. Thiruvathukal, Nicholas Hayward, Konstantin Läufer

Konstantin Läufer

No abstract provided.

Filesystems: Addressing The Last-Mile “Problem” In Services-Oriented/Cloud Computing, George K. Thiruvathukal, Joseph P. Kaylor, Konstantin Läufer

Konstantin Läufer

We have designed and implemented RestFS, a software framework that provides a uniform, configurable connector layer for mapping remote web-based resources to local filesystem-based resources, recognizing the similarity between these two types of resources. Such mappings enable programmatic access to a resource, as well as composition of two or more resources, through the local operating system’s standard filesystem application programming interface (API), script-able file-based command-line utilities, and interprocess communication (IPC) mechanisms. The framework supports automatic and manual authentication.

As part of this talk, we demonstrate a new filesystem that interfaces to the SketchFab.com service to support 3D model visualization. For …

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

Konstantin Läufer

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 …

Design And Implementation Of Triveni: A Process-Algebraic Api For Threads + Events, Christopher P. Colby, Lalita Jategaonkar Jagaeesan, Radhakrishnan Jagadeesan, Konstantin Laufer, Carlos Puchol

Konstantin Läufer

We describe Triveni, a framework and API for integrating threads and events. The design of Triveni is based on an algebra, including preemption combinators, of processes. Triveni is compatible with existing threads standards, such as Pthreads and Java threads, and with the event models structured on the Observer pattern. We describe the software architecture and algorithms underlying a concrete implementation of Triveni in Java. This environment includes specification based testing of safety properties. The results described in the paper have been used to integrate process-algebraic methods into (concurrent) object orientated programming.

Network Technologies Used To Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, George K. Thiruvathukal

Konstantin Läufer

The goal of the Loyola Weather Service (lws) project is to design and build a system of functioning environmental monitoring widgets that can intelligently and autonomously control the environment around them based on set thresholds and triggers. The widgets will also have the ability to aggregate their data and easily display this data in various ways: through a user interface in the room that the widget is placed, via a web application, and programmatically via a RESTful web service.

Putting Type Annotations To Work, Martin Odersky, Konstantin Laufer

Konstantin Läufer

We study an extension of the Hindley/Milner system with explicit type scheme annotations and type declarations. The system can express polymorphic function arguments, user-defined data types with abstract components, and structure types with polymorphic fields. More generally, all programs of the polymorphic lambda calculus can be encoded by a translation between typing derivations. We show that type reconstruction in this system can be reduced to the decidable problem of first-order unification under a mixed prefix.

Automated Systematic Testing For Constraint-Based Interactive Services, Patrice Godefroid, Lalita Jategaonkar Jagadeesan, Radha Jagadeesan, Konstantin Laufer

Konstantin Läufer

Constraint-based languages can express in a concise way the complex logic of a new generation of interactive services for applications such as banking or stock trading, that must support multiple types of interfaces for accessing the same data. These include automatic speech-recognition interfaces where inputs may be provided in any order by users of the service. We study in this paper how to systematically test event-driven applications developed using such languages. We show how such applications can be tested automatically, without the need for any manually-written test cases, and effi- ciently, by taking advantage of their capability of taking unordered …

An Object-Oriented Framework For Userland Filesystem Development, George K. Thiruvathukal, Joseph P. Kaylor, Konstantin Läufer

Konstantin Läufer

Userland filesystems (also known as virtual/installable filesystems) represent a promising direction for interfacing the traditional filesystem concept to specific domain instances (e.g. finance, bioinformatics, astronomy, photo sharing services, etc.) One might initially be inclined to think of filesystems as “old school” or “so 1980s” but their use remains an established practice in computational science and in many business domains, owing to the stability of filesystems interfaces and the continued perception of having great overall performance. While the promise of building one’s own userland filesystems is great, the approach has seen little adoption, owing to the complexity of working with low-level …

Simplifying Domain Modeling And Memory Management In User-Mode Filesystems With The Nofs Framework, Joseph P. Kaylor, Konstantin Läufer, George K. Thiruvathukal

Konstantin Läufer

Transparent access to remote data sets and data arising from web services is a non-trivial challenge to application developers. This early stage work addresses this challenge with NOFS, an object-oriented framework for creating filesystems to support domain specific functionality. While an early stage work, we present a solution to solve the access problem. Our solution greatly simplifies the task of filesystems development by providing the glue code needed between a domain model and the filesystem contract. We demonstrate support for domain models that are larger than physical memory and demonstrate how the concerns of caching can be removed from user-mode …

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

Konstantin Läufer

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Sisl: Several Interfaces, Single Logic, Thomas Ball, Christopher P. Colby, Peter Danielsen, Lalita Jategaonkar Jagadeesan, Radhakrishnan Jagadeesan, Konstantin Laufer, Peter Mataga, Kenneth Rehor

Konstantin Läufer

Modern interactive services such as information and e-commerce services are becoming increasingly more flexible in the types of user interfaces they support. These interfaces incorporate automatic speech recognition and natural language understanding, and include graphical user interfaces on the desktop and web-based interfaces using applets and HTML forms. To what extent can the user interface software be decoupled from the service logic software (the code that defines the essential function of a service)? Decoupling of user interface from service logic directly impacts the flexibility of services, or, how easy they are to modify and extend. To explore these issues, we …

Safe Structural Conformance For Java, Konstantin Laufer, Gerald Baumgartner, Vincent F. Russo

Konstantin Läufer

No abstract provided.

Reference Data Set Of Volcanic Ash Physicochemical And Optical Properties, A. Vogel, S. Diplas, A. J. Durant, A. S. Azar, M. F. Sunding, William I. Rose, A. Sytchkova, C. Bonadonna, K. Krüger, A. Stohl

William I. Rose

Uncertainty in the physicochemical and optical properties of volcanic ash particles creates errors in the detection and modeling of volcanic ash clouds and in quantification of their potential impacts. In this study, we provide a data set that describes the physicochemical and optical properties of a representative selection of volcanic ash samples from nine different volcanic eruptions covering a wide range of silica contents (50–80 wt % SiO2). We measured and calculated parameters describing the physical (size distribution, complex shape, and dense-rock equivalent mass density), chemical (bulk and surface composition), and optical (complex refractive index from ultraviolet to near-infrared wavelengths) …

Chemistry 107 Chemistry For Health Professions Ii Online Fall 2015, David M. Wilson

David Wilson

No abstract provided.

Chemistry 107 Chemistry For Health Professions Ii Online Spring 2015, David M. Wilson

David Wilson

No abstract provided.

Observation And Modeling Of Gravity Wave Propagation Through Reflection And Critical Layers Above Andes Lidar Observatory At Cerro Pachón, Chile, Bing Cao, Christopher J. Heale, Yafang Guo, Alan Z. Liu, Jonathan B. Snively

Jonathan B. Snively

A complex gravity wave event was observed from 04:30 to 08:10 UTC on 16 January 2015 by a narrow-band sodium lidar and an all-sky airglow imager located at Andes Lidar Observatory (ALO) in Cerro Pachón (30.25∘S, 70.73∘W), Chile. The gravity wave packet had a period of 18–35 min and a horizontal wavelength of about 40–50 km. Strong enhancements of the vertical wind perturbation, exceeding10 m s−1, were found at ∼90 km and ∼103 km, consistent with nearly evanescent wave behavior near a reflection layer. A reduction in vertical wavelength was found as the phase speed approached the background wind speed …

Numerical Modeling Of A Multiscale Gravity Wave Event And Its Airglow Signatures Over Mount Cook, New Zealand, During The Deepwave Campaign, C. J. Heale, K. Bossert, J. B. Snively, D. C. Fritts, P. -D. Pautet, M. J. Taylor

Jonathan B. Snively

A 2-D nonlinear compressible model is used to simulate a large-amplitude, multiscale mountain wave event over Mount Cook, NZ, observed as part of the Deep Propagating Gravity Wave Experiment (DEEPWAVE) campaign and to investigate its observable signatures in the hydroxyl (OH) layer. The campaign observed the presence of a �x = 200 km mountain wave as part of the 22nd research flight with amplitudes of >20 K in the upper stratosphere that decayed rapidly at airglow heights. Advanced Mesospheric Temperature Mapper (AMTM) showed the presence of small-scale (25–28 km) waves within the warm phase of the large mountain wave. The …

Nonlinear Ionospheric Responses To Large-Amplitude Infrasonic-Acoustic Waves Generated By Undersea Earthquakes, M. D. Zettergren, J. B. Snively, A. Komjathy, O. P. Verkhoglyadova

Jonathan B. Snively

Numerical models of ionospheric coupling with the neutral atmosphere are used to investigate perturbations of plasma density, vertically integrated total electron content (TEC), neutral velocity, and neutral temperature associated with large-amplitude acoustic waves generated by the initial ocean surface displacements from strong undersea earthquakes. A simplified source model for the 2011 Tohoku earthquake is constructed from estimates of initial ocean surface responses to approximate the vertical motions over realistic spatial and temporal scales. Resulting TEC perturbations from modeling case studies appear consistent with observational data, reproducing pronounced TEC depletions which are shown to be a consequence of the impacts of …

Peremajaan Kebun Rakyat, Antara Sumsel

aang sbd

Applying A Resources Framework To Analysis Of The Force And Motion Conceptual Evaluation, Trevor I. Smith, Michael C. Wittmann

Trevor I. Smith

We suggest one redefinition of common clusters of questions used to analyze student responses on the Force and Motion Conceptual Evaluation. Our goal is to propose a methodology that moves beyond an analysis of student learning defined by correct responses, either on the overall test or on clusters of questions defined solely by content. We use the resources framework theory of learning to define clusters within this experimental test that was designed without the resources framework in mind. We take special note of the contextual and representational dependence of questions with seemingly similar physics content. We analyze clusters in ways …

Student Understanding Of Taylor Series Expansions In Statistical Mechanics, Trevor I. Smith, John R. Thompson, Donald B. Mountcastle

Trevor I. Smith

One goal of physics instruction is to have students learn to make physical meaning of specific mathematical expressions, concepts, and procedures in different physical settings. As part of research investigating student learning in statistical physics, we are developing curriculum materials that guide students through a derivation of the Boltzmann factor using a Taylor series expansion of entropy. Using results from written surveys, classroom observations, and both individual think-aloud and teaching interviews, we present evidence that many students can recognize and interpret series expansions, but they often lack fluency in creating and using a Taylor series appropriately, despite previous exposures in …

Comparing Three Methods For Teaching Newton’S Third Law, Trevor I. Smith, Michael C. Wittmann

Trevor I. Smith

Although guided-inquiry methods for teaching introductory physics have been individually shown to be more effective at improving conceptual understanding than traditional lecture-style instruction, researchers in physics education have not studied differences among reform-based curricula in much detail. Several researchers have developed University of Washington–style tutorial materials, but the different curricula have not been compared against each other. Our study examines three tutorials designed to improve student understanding of Newton’s third law: the University of Washington’s Tutorials in Introductory Physics (TIP), the University of Maryland’s Activity-Based Tutorials (ABT), and the Open Source Tutorials (OST) also developed at the University of Maryland. …

First-Principles And Model Simulation Of All-Optical Spin Reversal, Thomas F. George, G.P. Zhang, Z. Babyak, Y. Xue, Y. H. Bai

Thomas George

The Diseños Project: A Geospatial Visualization Of The Environmental History Of California, 1769-1892, Rubén Mendoza

Rubén Mendoza

No abstract provided.

Trust And Prior Experience In Human-Robot Interaction, Tracy L. Sanders, Keith R. Macarthur, William Volante, Gabriella M. Hancock, Thomas Macgillivray, William T. Shugars, Peter A. Hancock

Keith Reid MacArthur

Causal Inference In A Big Data World: The Roadmap, Laura Balzer

Laura B. Balzer

No abstract provided.