Scientific Programming Research Articles

CSM 2017 Orthopaedic Section Platform Presentations (Abstracts OPL1–OPL64)

CSM 2017 Orthopaedic Section Platform Presentations (Abstracts OPL1–OPL64)

Rigid Body Sampling and Individual Time Stepping for Rigid-Fluid Coupling of Fluid Simulation

In this paper, we propose an efficient and simple rigid-fluid coupling scheme with scientific programming algorithms for particle-based fluid simulation and three-dimensional visualization. Our approach samples the surface of rigid bodies with boundary particles that interact with fluids. It contains two procedures, that is, surface sampling and sampling relaxation, which insures uniform distribution of particles with less iterations. Furthermore, we present a rigid-fluid coupling scheme integrating individual time stepping to rigid-fluid coupling, which gains an obvious speedup compared to previous method. The experimental results demonstrate the effectiveness of our approach.

Increasing Exposure to Programming: A Comparison of Demographic Characteristics of Students Enrolled in Introductory Computer Science Programming Courses vs. a Multidisciplinary Data Analysis Course

Upward trends in programming careers and increases in programming in less traditionally computer-oriented occupations threaten to further increase the current underrepresentation of both females and individuals from racial minority groups in these disciplines. Using administrative data (2009 – 2014), the present study compares demographic characteristics of students enrolled in a course that introduced programming: a multidisciplinary data analysis course, an introductory programming course, or an introductory computer science (CS) gateway course. The multidisciplinary data analysis course enrolled significantly more female students and students with lower Math SAT scores. Females were overrepresented in the data analysis course and underrepresented in the introductory programming and CS gateway courses relative to the larger campus community, with similar findings for underrepresented minority students. Less emphasis on traditional approaches to introductory programming and increased interdisciplinary opportunities to tackle real world questions may be one way to improve access to programming experiences for students from a wider range of educational, social and economic backgrounds.

Comparing Programmer Productivity in Openacc and Cuda : An Empirical Investigation

OpenACC has been touted as a API designed to make GPGPU programming accessible to scientific programmers, but to date, no studies have attempted to verify this quantitatively. In this paper, we conduct an empirical investigation of program productivity comparisons between OpenACC and CUDA in the programming time, the execution time and the analysis of independence of OpenACC model in high performance problems. Our results show that, for our programs and our subject pool, this claim is true. We created two assignments called Machine Problem 3(MP3) and Machine Problem 4(MP4) in the classroom environment and instrumented the WebCode website developed by ourselves to record details of students’ coding process. Three hypotheses were supported by the statistical data: for the same parallelizable problem, (1) the OpenACC programming time is at least 37% shorter than CUDA; (2) the CUDA running speed is 9x faster than OpenACC; (3) the OpenACC development work is not significantly affected by previous CUDA experience

Whose banner are we waving? Exploring STEM partnerships for marginalized urban youth

This case study examines after school programming in citizen science from the perspective of Critical Race Theory. During the course of enacting community outreach projects this data was used to examine the positioning of experts, student, and teachers within the program. This study explores the role of race and ethnicity, and the ways in which marginalization can manifest itself with black urban youth and teachers. Implications for partner selection and training are addressed.

Tracking students' performance to assess correlations among computer science programming series courses

The objective of this paper is to investigate the relationships among a series of computer programming courses and the impact of a basic programming class upon the subsequent advanced programming courses. It describes a direct measure that kept track of the performance of 195 students over eight semesters within a series of computer science programming courses. Analysis of these correlations shows that, in a series programming courses, student performance in the basic programming class can predict their performance in a data structures course. However, the performance of the students in the advanced level programming course is not substantially predicted by basic programming.

Optical eye simulator for laser dazzle events.

An optical simulator of the human eye and its application to laser dazzle events are presented. The simulator combines optical design software (ZEMAX) with a scientific programming language (MATLAB) and allows the user to implement and analyze a dazzle scenario using practical, real-world parameters. Contrary to conventional analytical glare analysis, this work uses ray tracing and the scattering model and parameters for each optical element of the eye. The theoretical background of each such element is presented in relation to the model. The overall simulator's calibration, validation, and performance analysis are achieved by comparison with a simpler model based uponCIE disability glare data. Results demonstrate that this kind of advanced optical eye simulation can be used to represent laser dazzle and has the potential to extend the range of applicability of analytical models.

Design considerations for a large-scale image-based text search engine in historical manuscript collections

Abstract This article gives an overview of design considerations for a handwriting search engine based on pattern recognition and high-performance computing, “Monk”. In order to satisfy multiple and often conflicting technological requirements, an architecture is used which heavily relies on high-performance computing, interactivity, and a Posix file-access model for the scientific programmers. The resulting system is able to handle billions of image files, in the order of petabytes of storage capacity, with a single mount point. Monk is operational since the year 2009.

Development, Implementation, and Outcomes of an Equitable Computer Science After-School Program: Findings From Middle-School Students

Current policy efforts that seek to improve learning in science, technology, engineering, and mathematics (STEM) emphasize the importance of helping all students acquire concepts and tools from computer science that help them analyze and develop solutions to everyday problems. These goals have been generally described in the literature under the term computational thinking. In this article, we report on the design, implementation, and outcomes of an after-school program on computational thinking. The program was founded through a partnership between university faculty, undergraduates, teachers, and students. Specifically, we examine how equitable pedagogical practices can be applied in the design of computing programs and the ways in which participation in such programs influence middle school students' learning of computer science concepts, computational practices, and attitudes toward computing. Participants included 52 middle school students who voluntarily attended the 9-week after-school program, as well as four undergraduates and one teacher who designed and implemented the program. Data were collected from after-school program observations, undergraduate reflections, computer science content assessments, programming products, and attitude surveys. The results indicate that the program positively influenced student learning of computer science concepts and attitudes toward computing. Findings have implications for the design of effective learning experiences that broaden participation in computing. (Keywords: computational thinking, programming, middle school, mixed methods)

OPR

The ability to reproduce a parallel execution is desirable for debugging and program reliability purposes. In debugging (13), the programmer needs to manually step back in time, while for resilience (6) this is automatically performed by the the application upon failure. To be useful, replay has to faithfully reproduce the original execution. For parallel programs the main challenge is inferring and maintaining the order of conflicting operations (data races). Deterministic record and replay (R&R) techniques have been developed for multithreaded shared memory programs (5), as well as distributed memory programs (14). Our main interest is techniques for large scale scientific (3; 4) programming models.

Engaging youth of color in applied science education and public health promotion

ABSTRACTParticipation in inquiry-based science education, which focuses on student-constructed learning, has been linked to academic success. Whereas the benefits of this type of science education are evident, access to such high-quality science curriculum and programming is not equitable. Black and Latino students in particular have less access to supplementary science programming, and fewer opportunities to engage in inquiry-based education. This paper describes outcomes associated with an inquiry-based out-of-school time science education program, Nuestro Futuro: Applied Science Education to Engage Black and Latino Youth (NFASE), which sought to build the capacity of middle school students of color to ‘think’ like health scientists from diverse disciplinary perspectives. The program was designed with the intent of (1) improving student attitudes toward and motivation for science and (2) increasing active and engaged citizenship (AEC). NFASE students explored health inequity and the social determinants of health locally and engaged in developing health promotion, outreach and education efforts targeted to their peers, parents/families, and community. Interest in the program was high overall, but implementation was not without challenges. Although evaluation outcomes indicate that there were no statistically significant changes in science-related attitudes or motivation, students reported significant increases in neighborhood social connection, as well as overall AEC.

The Scientific Programming Integrated Degree Program – A Pioneering Approach to Join Theory and Practice

While already established in other disciplines, integrated degree programs have become more popular in computer science and mathematical education in Germany as well over the last few years. These programs combine a theoretical education and a vocational training. The bachelor degree course “Scientific Programming”, offered at FH Aachen University of Applied Sciences, is such an integrated degree program. It consists of 50% mathematics and 50% computer science. It incorporates the MATSE (MAthematical and Technical Software dEveloper) vocational training in cooperation with research facilities and IT companies located in and nearby Aachen, Jülich and Cologne.This paper presents the general concept behind integrated degree programs in Germany and the Scientific Programming educational program in particular. A key distinguishing feature of this concept is the continuous combination of theoretical education at university level with practical work experience at a company. In this fashion, students end up being very well positioned for the labor market, and companies educate knowledgeable staff familiar with their products and processes. Additionally students are able to earn two degrees in three years, which is a rare approach for computer science programs in Germany. Therefore, Scientific Programming offers an important contribution towards reducing the shortage in advanced software development and engineering on the German labor market.

ELECTRONIC SPECTRUM OF THE I2MOLECULE: A BRIEF INTRODUCTION TO SCIENTIFIC PROGRAMMING

This study proposes an activity to introduce scientific programming. In particular, the multidisciplinary concepts of scientific programming, quantum mechanics, and spectroscopy are presented in the study of the electronic spectrum of the I2 molecule. We use Python programming language and the IPython command shell, in particular, for their user friendliness and versatility.

Equalization Technique for Balancing the Modulation Ratio Characteristics of the Single-Phase-to-Three-Phase Matrix Converter

Three-phase system has numerous advantages over the single-phase system in terms of instantaneous power, stability, and cost. Three-phase systems are not available in every location particularly in remote rural areas, hill stations, low voltage distribution homes, and so forth. Having a system that is capable of converting directly the readily available single-phase system to three phases will have greater usability in various applications. The routine techniques adopted in the direct ac-ac single-phase-to-three-phase converters do not yield the best desired outputs because of their complexity in the segregation process and bidirectional nature of the input signal. Other initiatives use ac-dc-ac converters which are huge and costly due to dc link energy storage devices. Further, none of these systems provide a convincing result in producing the standard three-phase output voltages that are 120° away from each other. This paper proposes an effective direct ac-ac single-phase-to-three-phase conversion technique based on space vector pulse width modulation based matrix converter system that produces a convincing three-phase output signals from a single-phase source with balanced modulation index characteristics. The details of the scientific programming adopted on the proposed technique were presented.

Impact of Automated Software Testing Tools on Reflective Thinking and Student Performance in Introductory Computer Science Programming Classes

The goal of this research was to investigate the effects of automated testing software on levels of student reflection and student performance. This was a self-selecting, between subjects design that examined the performance of students in introductory computer programming classes. Participants were given the option of using the Web-CAT software-testing tool to evaluate their computer code. Student self-reported levels of reflection were measured using reflective thinking survey.

Engagement and knowledge building in an afterschool STEM Club: analyzing youth and facilitator posting behavior on a social networking site

Social networking sites (SNSs) are popular technologies used frequently among youth for recreational purposes. Increasing attention has been paid to the use of SNSs in educational settings as a way to engage youth interest and encourage academically productive discussion. Potential affordances of using SNSs for education include knowledge building, collaborative communities, and the ability to document and share processes and designs. In this study, the SNS, Edmodo, is examined as an educational tool used with Studio STEM. Results indicated that youth appropriated Edmodo to exhibit engagement and articulate knowledge through reciting facts, acknowledging learning, and documenting progress with the guidance of instructors and facilitators. Based on results, we suggest that efforts to include SNSs in integrative science, technology, engineering, and mathematics programming for youth prioritize consistent monitoring and guidance by supportive and more knowledgeable others as this serves to develop community and encourage youth engagement.

Racial/Ethnic and Gender Equity Patterns in Illinois High School Career and Technical Education Coursework

This study analyzed high school Career and Technical Education (CTE) enrollments in Illinois, with comparisons to national data when possible, by career cluster and pathway and with respect to gender and racial/ethnic makeup of students. Enrollment patterns in Science, Technology, Engineering, and Math (STEM) CTE programming were emphasized. Gender and ethnicity-based inequities were found in certain areas and more equitable patterns were apparent in others. Of concern, student enrollment in courses fitting within STEM pathways included substantially greater male than female participation (64.1% male vs. 35.9% female), whereas other pathways showed the reverse enrollment pattern (45.0% male and 55.0% female). With respect to ethnicity, all subgroups except White students were underrepresented in CTE programming in general. The underrepresentation was exacerbated for all but Asian students when concerning STEM CTE programming. Considering implications, we recommend heightened focus, support, and goal setting concerning equity of CTE programming.

Efficient Solutions of Kepler’s Equation via Hybrid and Digital Approaches

The solution of Kepler’s equation is accomplished via families of hybrid and table lookup techniques. A new arithmetic operation timing approach with general application to scientific programming is used to accurately estimate performance of each Kepler’s equation solution technique. The hybrid approaches couple a power series expansion starting approximation with nine different types of higher-order corrective step methods. The resulting computationally efficient non-iterative methods avoid “if” statements and directly yield in-plane Euler rotation angles necessary to map orbit elements to orbital position. The best-performing of the nine hybrid methods are up to two times faster than the original efficient Laguerre iterative method and achieve worst-case resultant true anomaly accuracies down to machine precision at 3 × 10−11° for eccentricities up to 0.999999. This matches or exceeds the performance of iterative methods and translates to less than three micro-meters at GEO altitude. Meanwhile, six digital approaches were explored, with the best table lookup approach boasting a ten-fold speed increase with a worst-case accuracy of 1 × 10−6° (154 mm) for an eccentricity of 0.999999. These combinations of accuracy and speed performance make both the hybrid and table lookup approaches well-suited for in-line incorporation into a wide range of low- to high-fidelity semi-analytic orbit propagators and multi-threaded or vector programming languages and computing hardware (GPUs, etc.). And finally, a new operator-based computational timing technique is designed and employed to estimate the performance of math-laden computer programs, with sample application to all of the aforementioned Kepler’s equation solution techniques.

Updates from the Neuro-Oncology Section of the 2015 American Neurological Association Annual Meeting.

American Neurological Association Annual Meeting, Chicago, IL, USA, 27-29 September 2015 The American Neurological Association (ANA) held its annual meeting in Chicago, IL, USA on 27-29 September 2015. The Scientific Programming Advisory Committee was chaired by Dr. S Pleasure from the University of California-San Francisco (CA, USA). The Neuro-Oncology session, chaired by Dr. A Pruitt from the University of Pennsylvania (PA, USA) and cochaired by Dr. J Laterra from Johns Hopkins University (MD, USA), was held on 27 September 2015. Speakers included Dr. D Wainwright (Northwestern University, IL, USA), Dr. N Kolb (University of Utah, UT, USA), Dr. A Nath (NINDS/NIH, MD, USA), Dr. D Franz (Cincinnati Children's Hospital, OH, USA) and Dr. R Lukas (University of Chicago, IL, USA). A summary of key presentations from the Neuro-Oncology section of the 2015 American Neurological Association annual meeting is reported. Preclinical and clinical advances in the use of immunotherapies for the treatment of primary and metastatic CNS tumors are covered. Particular attention is paid to the enzyme indoleamine dioxygenase and the immune checkpoints CTLA4 and PD1 and their ligands. Specific nervous system toxicities associated with novel immunotherapies are also discussed. The recent success of targeting the mTOR pathway in the neurocutaneous syndrome tuberous sclerosis is detailed. Finally, important early steps in our understanding of the common toxicity of chemotherapy induced neuropathy are reviewed.

The Omics Revolution in Agricultural Research.

The Agrochemicals Division cosponsored the 13th International Union of Pure and Applied Chemistry International Congress of Pesticide Chemistry held as part of the 248th National Meeting and Exposition of the American Chemical Society in San Francisco, CA, USA, August 10–14, 2014. The topic of the Congress was Crop, Environment, and Public Health Protection; Technologies for a Changing World. Over 1000 delegates participated in the Congress with interactive scientific programming in nine major topic areas including the challenges and opportunities of agricultural biotechnology. Plenary speakers addressed global issues related to the Congress theme prior to the daily technical sessions. The plenary lecture addressing the challenges and opportunities that omic technologies provide agricultural research is presented here. The plenary lecture provided the diverse audience with information on a complex subject to stimulate research ideas and provide a glimpse of the impact of omics on agricultural research.