Workshop on Teaching Computational Science (WTCS) Session 1

Time and Date: 10:15 - 11:55 on 3rd June 2015

Room: M201

Chair: Alfredo Tirado-Ramos

117 Developing a Hands-On Course Around Building and Testing High Performance Computing Clusters [abstract]
Abstract: We describe a successful approach to designing and implementing a High Performance Computing (HPC) class focused on creating competency in building, configuring, programming, troubleshooting, and benchmarking HPC clusters. By coordinating with campus services, we were able to avoid any additional costs to the students or the university. Students built three twelve-unit independently-operating clusters. Working groups were formed for each cluster and they installed the operating system, created users, connected to the campus network and wrote a variety of scripts and parallel programs while documenting the process. We describe how we solved unexpected problems encountered along the way. We illustrate through pre- and post-course surveys that students gained substantial knowledge in fundamental aspects of HPC through the hands-on approach of creating their own clusters.
Karl Frinkle, Mike Morris
269 Interactively Exploring the Connection between Bidirectional Compression and Star Bicoloring [abstract]
Abstract: The connection between scientific computing and graph theory is detailed for a particular problem called bidirectional compression. This scientific computing problem consists of finding a pair of seed matrices in automatic differentiation. In terms of graph theory, the problem is nothing but finding a star bicoloring of a suitably defined graph. An interactive educational module is designed and implemented to illustrate the connection between bidirectional com- pression and star bicoloring. The web-based module is intended to be used in classroom to illustrate the intricate nature of this combinatorial problem.
M. Ali Rostami, Martin Buecker
651 Scientific Workflows with XMDD: A Way to Use Process Modeling in Computational Science Education [abstract]
Abstract: Process models are well suited to describe in a formal but still intuitive fashion what a system should do. They can thus play a central role in problem-based computational science education with regard to qualifying students for the design and implementation of software applications for their specific needs without putting the focus on the technical part of coding. eXtreme Model Driven Design (XMDD) is a software development paradigm that explicitly focuses on the What (solving problems) rather than on the How (the technical skills of writing code). In this paper we describe how we apply an XMDD-based process modeling and execution framework for scientific workflow projects in the scope of a computer science course for students with a background in natural sciences.
Anna-Lena Lamprecht, Tiziana Margaria
152 Teaching Science Using Computationally-Based Investigations [abstract]
Abstract: Wofford College has initiated a computational laboratory course, Scientific Investigations Using Computation, which satisfies one of its Bachelor of Science requirements. In the course, which one professor teaches, students explore important concepts in science and, using computational tools, implement the scientific method to gain a better understanding of the natural world. Before the first class for a topic, which usually takes one week, students read a module by the authors of this abstract. Some of the topics are the carbon cycle, global warming, disease, adaptation and mimicry, fur patterns, membranes, gas laws, chemical kinetics, and enzyme kinetics. Each module includes a discussion of the topic, quick review questions, points of inquiry for further investigation, and references. In class, students take an online quiz from the quick review questions and complete an enriching activity related to the topic. Typically, in pairs or larger groups, students are assigned points of inquiry to investigate, develop, and present for subsequent periods in the week. A topic culminates in a three-hour laboratory, where students perform experiments at computers using the agent-based modeling tool NetLogo and the spreadsheet Excel. NetLogo, which is free to download, includes numerous computational models that have levels for Interface to run the simulation and view the results, Information about the model, and Code, which the user can view and change. Laboratory guidelines by the authors lead the students through the material in a step-by-step fashion. As well as conducting experiments computationally, the students modify the code to refine the models. Thus, the class examines scientific topics using the scientific method and various resources, gains an appreciation of the utility of computational simulations, and starts to learn to program and to think algorithmically.
Angela Shiflet and George Shiflet
158 DNA and普通話(Mandarin): Bringing introductory programming to the Life Sciences and Digital Humanities [abstract]
Abstract: The ability to write software (to script, to program, to code) is a vital skill for students and their future data-centric, multidisciplinary careers. We present a ten-year effort to teach introductory programming skills in domain-focused courses to students across divisions in our liberal arts college. By creatively working with colleagues in Biology, Statistics, and now English, we have designed, modified, and offered six iterations of two courses: “DNA” and “Computing for Poets”. Larger percentages of women have consistently enrolled in these two courses vs. the traditional first course in the major. We share our open source course materials and present here our use of a blended learning classroom that leverages the increasing quality of online video lectures and programming practice sites in an attempt to maximize faculty-student interactions in class.
Mark Leblanc, Michael Drout

Workshop on Teaching Computational Science (WTCS) Session 2

Time and Date: 14:10 - 15:50 on 3rd June 2015

Room: M201

Chair: Angela Shiflet

3 DAEL Framework: A New Adaptive E-learning Framework for Students with Dyslexia [abstract]
Abstract: This paper reports on an extensive study conducted on the existing frameworks and relevant theories that lead to a better understanding of the requirements of an e-learning tool for people with dyslexia. The DAEL framework has been developed with respect to four different dimensions: presentation, hypermediality, acceptability and accessibility, and user experience. However, there has been no research on the different types of dyslexia and the dyslexic user’s viewpoint as they affect application design. Therefore, in this paper a framework is proposed which would conform to the standards of acceptability and accessibility for dyslexic students. We hypothesise that an e-learning application, which will adopt itself according to individuals’ dyslexia types, will advantage the dyslexics’ individuals in their learning process.
Aisha Alsobhi, Nawaz Khan, Harjinder Rahanu
632 Approach to Automation of Cloud Learning Resources’ Design for Courses in Computational Science Based on eScience Resources with the Use of the CLAVIRE Platform [abstract]
Abstract: Abstract This paper describes the set of methods and cloud tools used to simplify the rapid design of learning resources for courses in computational science. We have developed and added new tools to our cloud platform – CLAVIRE – to simplify and speed up the sharing of scientific executable resources, design and implementation of courses’ structure and virtual learning labs, and preparation of the text resources for the theoretical part of the course and the case studies and seminars. We have applied our approach to design a course in eScience tchnologies based on the sequences of application packages and cloud services developed for task solving in different application domains and integrated into the CLAVIRE platform. Our approach allows us to significantly speed up the design and implementation of learning resources, and does not reduce the value of teachers’ (experts’) participation.
Alexey Dukhanov, Tamara Trofimenko, Maria Karpova, Lev Bezborodov, Alexey Bezgodov, Anna Bilyatdinova, Anna Lutsenko
248 An Introduction Course in the Computational Modeling of Nature [abstract]
Abstract: To meet the requirement of a course in computational thinking for a minor in Informational Technology, an introductory course in computational modeling of nature was developed. Influenced by the modeling course developed by Dickerson at Middlebury College, the computational science textbook by Shiflet and Shiflet, and my own work on partial differential equation models, this course contains the development of three kinds of models of phenomena in nature. These three kinds of models are agent-based models using the language of NetLogo, simple finite difference models using the system dynamics option of NetLogo, and complex finite difference models using the language of C++. The natural phenomena modeled include some standard ones (ants following pheromone trails, the interaction of sheep and wolves, erosion due to rainfall, and the spread of malaria) and some non-standard ones (the 7-day creation of the world, 3 dogs playing games, and formation of stripes and spots in the skins of animals). The emphasis of the course is on the modeling process instead of on programming with modeling as a thread. A distinguishing feature is that, because students spend significant time with three different modeling techniques, they are able to compare and critique these models.
Kathie Yerion
403 How Engineers deal with Mathematics solving Differential Equations [abstract]
Abstract: Numerical methods are tools for approximating solutions to problems that may have complicated developments or cannot be solved analytically. In engineering studies, students have to face problems from other disciplines such as structural or rock mechanics, biology, chemistry or physics. Prior to solving these problems it is important to define and adopt a rational framework. The students of fourth course out of five, of the bachelor’s degree in Computer Sciences or Industrial Engineering at the University of Salamanca (Spain), they learn mathematics solving real problems with the help of their acquired interdisciplinary knowledge. We have proposed the students a term project that summarizes some of the knowledge and skills acquired during the course. We will describe in this study the software and specific applications that will be use during the whole course.
Araceli Queiruga Dios, Ascensión Hernández Encinas, Angel Martin Del Rey, Jesus Martin-Vaquero, Juan José Bullón Pérez, Gerardo Rodríguez Sánchez
116 TSGL: A Thread Safe Graphics Library for Visualizing Parallelism [abstract]
Abstract: Multicore processors are now the standard CPU architecture, and multithreaded parallel programs are needed to take full advantage of such CPUs. New tools are needed to help students learn how to design and build such parallel programs. In this paper, we present the thread-safe graphics library (TSGL), a new C++11 library that allows different threads to draw to a shared Canvas, which is updated in approximate real-time. Using TSGL, instructors and students can create visualizations that illustrate multithreaded behavior. We present three multithreaded applications that illustrate the use of TSGL to help students see and understand how an application is using parallelism to speed up its computation.
Joel Adams, Patrick Crain, Mark Vander Stel
26 Education in Computational Sciences [abstract]
Abstract: The last two decades have witnessed an enormously rapid development of computational technologies which have undoubtedly affected all the fields of human activities, including education. In fact, computational science is one of the most evolving profile study programmes at technical universities nowadays. This article thus focuses on the description of the key content courses, curricula and degrees offered within the study programmes at the Faculty of Informatics and Management of the University of Hradec Kralove, Czech Republic. Moreover, this study characterizes teaching and learning of university computational professionals with a special focus on core competences such as an ability to identify and solve problems, knowledge of analytical methods, or operating systems, but also on active and passive knowledge of English since English as lingua franca can help these professionals together with other core competences succeed in the job market after their graduation.
Petra Poulova, Blanka Klimova