We attempted to find a more sustainable solution for performing virtual screening with AutoDock Vina which uses less electricity than computers using typical x64 CPUs.We tested a cluster of ODROID-XU3 Lite computers with ARM CPUs and compared its performance to a server with x64 CPUs.In order to be a viable solution, our cluster needed to perform the screen without sacrificing speed or increasing hardware costs.The cluster completed the virtual screen in a little less time than our comparison server while using just over half the electricity that the server used.Additionally, the hardware for the cluster cost about 38% less than the server, making it a viable solution. CCS Concepts•

Although some colleges and universities have access to parallel computing hardware, none that we are aware of can provide dedicated parallel computing hardware to each student. Instead, institutions often provide shared parallel computing equipment for the students, if they can afford to provide any. It is difficult for students to really get an understanding of the performance of their programs and how they scale when they are using shared equipment that is not dedicated to them and where other students or other users may interfere with their work. The current emphasis on network security at some institutions also prevents some shared resources that students could use from being easily accessible or sometimes accessible at all. We provide a parts list, information, and microSD card images to make a small, affordable compute cluster that each student in a parallel computing course can purchase in lieu of a textbook so each student has their own private compute cluster.

There is a pressing need for a workforce with the modeling and simulation skills associated with computational science. A number of national studies have substantiated those needs with respect to the future competitiveness of USA in research and development, the innovation of new products, and the competitiveness of many industries. Creating computational science programs at academic institutions organized along disciplinary boundaries represents a challenge because aspects of computer science, mathematics, and a science or engineering domain are required parts of any program. Gaining agreement on the associated requirements, integrating the classes with those in the traditional curriculum, and obtaining the necessary support through academic and administrative reviews represent substantial challenges. Clark Atlanta University, the University of Mary Washington, and Southern University are all working on establishing undergraduate or graduate programs in computational science and have had a number of common experiences. Copyright © 2014 John Wiley & Sons, Ltd.

We describe our experiences teaching CPSC 109 - Introduction to Modeling and Simulation, an introductory course that we developed [1]. The course fills one of two quantitative reasoning requirements for the general education program at the University of Mary Washington (UMW) and serves as one of two possible prerequisites for UMW's Computer Science 1 course [2]. It is also intended to serve as a bridge between computer science and other disciplines at UMW, particularly those in the natural and physical sciences. The course is based on the National Computational Science Institute (NCSI) [3] Introduction to Computational Thinking Workshop, but adds in an explicit emphasis on introductory programming concepts for several weeks to ensure adequate preparation for Computer Science 1. We discuss the tools the students use in the course, some assignments, and the projects that students have created at the end of the semester. In addition, we discuss a special version of the course we have created for students in UMW's honors program [4].

HIV, tuberculosis and histoplasmosis are infectious diseases that affect millions of people world-wide. We describe our efforts to find cures for these diseases using the technique of virtual screening to identify possible inhibitors for essential proteins in these organisms using one of the XSEDE supercomputers. We have completed the virtual screens and have found promising compounds for each disease. Cell culture experiments have supported the likelihood of a number of the compounds being effective for treating both histoplasmosis and tuberculosis.

Tuberculosis continues to plague the world with the World Health Organization estimating that about one third of the world's population is infected. Due to the emergence of MDR and XDR strains of TB, the need for novel therapeutics has become increasing urgent. Herein we report the results of a virtual screen of 4.1 million compounds against a promising drug target, DrpE1. The virtual compounds were obtained from the Zinc docking site and screened using the molecular docking program, AutoDock Vina. The computational hits have led to the identification of several promising lead compounds.

As part of a parallel computing course where undergraduate students learned parallel computing techniques and got to run their programs on a supercomputer, one student designed and implemented a sequential algorithm and two versions of a parallel algorithm to solve the knapsack problem.Performance tests of the programs were conducted on the Ranger supercomputer.The performance of the sequential and parallel implementations was compared to determine speedup and efficiency.We observed 82%-86% efficiency for the MPI version and 89% efficiency for the OpenMP version for sufficiently large inputs to the problem.Additionally, we discuss both the student and faculty member's reflections about the experience.

Malaria continues to affect millions of people annually. With the rise of drug resistant strains, the need for alternative treatments has become increasingly urgent. Recently, PfUCHL3 was identified as an essential deubiquitinating enzyme. The increasing number of drug target structures being solved has increased the feasibility of utilizing a structural comparative approach to identifying novel inhibitors. Using AutoDock Vina, we recently screened the NCI library of about 320,000 compounds against the crystal structure of PfUCHL3. The top hits were subsequently screened against its human ortholog UCHL3 as to identify compounds that could specifically target the PfUCHL3 over its human counterpart. This method was used to identify small molecule inhibitors that can preferentially inhibit the parasitic enzyme. Several compounds were identified that demonstrated significant binding affinity preference for the malaria target over the human enzyme. Two of these compounds demonstrated ng/mL activity.

The ever-increasing amount of computational power available has made it possible to use docking programs to screen large numbers of compounds to search for molecules that inhibit proteins. This technique can be used not only by pharmaceutical companies with large research and development budgets and large research universities, but also at small liberal arts colleges with no special computing equipment beyond the desktop PCs in any campus' computer laboratory. However, despite the availability of significant quantities of compute time available to small colleges to conduct these virtual screens, such as supercomputing time available through grants, we are unaware of any small colleges that do this. We describe the experiences of an interdisciplinary research collaboration between faculty in the Chemistry and Computer Science Departments in a chemistry course where chemistry and biology students were shown how to conduct virtual screens. This project began when the authors, who had been collaborating on drug discovery research using virtual screening, decided that the virtual screening process they were using in their research could be adapted to fit in a couple of lab periods and would complement one of the instructors’ courses on medicinal chemistry. The resulting labs would introduce students to the virtual screening portion of the drug discovery process.

This study investigates which factors cause college student to express an interest in participating in what we classify as nontraditional community service opportunities. The particular form of community service that we examine-participation in a volunteer computing project-differs from traditional forms of college student volun-teerism in that it involves no face-to-face contact with others, requires a minimal time commitment, is a small part of a highly technical enterprise and focuses on the global rather than the local community. We find that some of the variables that explain participation in traditional forms of community service, in particular belief that one can make a difference, also explain a penchant for nontraditional participation. We also discover that there are some unique influences on the willingness of students to do community service in this alternative form. Finally, we explore the pathways by which the influence of personal characteristics operate in order to address how and why these factors matter in promoting nontraditional forms of community service.

Computation has become an accepted technique for scientists, mathematicians, economists, and others to learn about complex phenomena that might otherwise be impractical or impossible to study. Computational science uses modeling to create a simplified view of the phenomenon being studied and simulation to see how the phenomenon will behave over time under given conditions [1]. Computational science is used for pharmaceutical development, weather forecasting, predicting the behavior of the stock market, studying disasters like the oil spill that occurred in the summer of 2010, and many other things. A number of colleges and universities have majors in computational science [2, 3, 4, 5, 6, 7, 8].

Volunteer computing is a distributed computing model where a large problem requiring the computational power of a supercomputer can be solved by thousands or millions of personal computers. In volunteer computing, people allow their personal computers to work together on a large problem when the computers are not otherwise in use. The owners of the computers are not compensated for the use of their computers. As volunteer computing has become an accepted way to solve large problems, the number of volunteer computing projects has increased significantly over the years. However, as the number of volunteer computing projects increases, the participation in volunteer computing must increase to allow volunteer computing to remain a viable way to solve large problems. We studied the reasons that people do not participate in order to determine how participation can be increased. We found that the likelihood of people participating in such projects was not affected by how these projects were described. We also collected information about factors that influenced the subjects' decisions.

In this demo, I will present an activity that I use to introduce computational thinking in my non-majors course and outreach talks at high schools. I do this by first talking about what modeling and simulation are and why they are useful. Following this explanation, I introduce a variant of a problem about Alice and Bob. In the original problem, Alice and Bob take turns flipping a coin until one of them gets heads and wins. If Alice goes first, what is the probability that she wins? In class, I introduce this variant of the problem: "Bob suggests to Alice that they play a game. They will take turns flipping a coin until one of them wins by getting heads. The winner will then receive a dollar from the loser. If Bob says he will always let Alice go first, should Alice play the game?" While this problem is trivial for those comfortable with basic probability and familiar with geometric sequences, most of my students who are not computer science majors are not comfortable with math. Thus, I explain that although the problem can be solved with some math, instead we should first model the problem. Once we have modeled the problem, I have my students get some intuition by pairing off and having each pair play the game 20 times. I collect the results and discuss how so few trials are not sufficient to draw conclusions. Finally, I run a simulation that runs the game one million times and demonstrates that Alice should win 2/3 of the time and thus should play the game.

Volunteer computing projects have been used to make significant advances in knowledge since the 1990s. These projects use idle CPU cycles donated by people to solve computationally intensive problems in medicine, the sciences and other disciplines. It is important to use the donated cycles as efficiently as possible because participation in volunteer computing is low and the number of volunteer computing projects keeps increasing. Task retrieval policies, policies describing when a volunteered computer requests additional work from a server, can have an effect on the number of wasted CPU cycles and consequently, the number of tasks completed by clients. We present the results of simulating different task retrieval policies for clients under realistic conditions, including clients running on computers with one single-core CPU, clients running on computers with multi-core CPUs, and clients running on computers that are put into a power save mode by environmentally conscious owners.

A method of handling appliances on a sea bottom for the operation and maintenance of well heads in off-shore oil field or other working plants making use of an articulated column resting on the sea bed substantially about the site of said appliances or well heads, wherein the improvement consists in the use of at least one tubular elongated structure extending along said column in parallel relation to the axis thereof, the inside of said structure serving the purpose of guiding said appliances and related means cooperating therewith and also of forming a passage-way for the remote control cables and other transmission or connecting means in particular for operating the well heads.

Volunteer computing projects rely on volunteers running clients on their computers that contribute to projects when the computers' owners allow them to. These projects allow people to solve problems that were previously too computationally intensive to solve. However, due to the relatively small fraction of the population that participates in volunteer computing projects, it's very important to use the donated CPU cycles as efficiently as possible. Volunteer computing clients use two different methods to retrieve tasks: retrieving one task at a time when the client has no more work to do or retrieving multiple tasks at once and storing them in a buffer. We simulate these different task retrieval policies to compare the number of tasks completed by clients using the different policies. Our simulations showed that clients that retrieve one task at a time complete more tasks than clients that retrieve multiple tasks at once and buffer them. Our simulations also showed that there was not a significant gain in the amount of work that could be completed by devising a more complicated adaptive policy.

This paper gives an overview of XML formal models, summarizes database engineering practices, problems and their evolution. We focus on categorical aspects of XML formal models. Many formal models such as XML Data Model, XQuery Data Model or Algebra for XML can be described in terms of category theory. This kind of description allows to consider generic properties of these formalisms, e. g. expressive power, optimization, reduction or translation between them, among others. These properties are rather crucial to comparison of different XML formal models and to consequent decision which formal system should be used to solve a concrete problem. This work aim is to be the basis for further research in the area of XML formal models where category theory is applied.

Boyer-Moore-Horspool (BMH) algorithm is commonly used to solve text searching problems. In this paper is used to solve the constraint subset of XPath queries offering effective algorithm to resolve such queries. XML can be grasp as text file contains tags and its content; that kind of view to XML is used in this work. We constraint XML document content and possible XPath que- ries. This work focus on key ideas and problems appertaining XPath queries execution using text search algorithm BMH.

Volunteer computing is a form of distributed computing where projects attempt to accomplish some goal, using volunteered computational resources instead of paying for the resources [1]. Volunteer computing projects are being used for a wide range of computationally intensive scientific and mathematical goals, ranging from searching for evidence of extraterrestrial intelligence to searching for cures to cancer and other diseases, to finding Mersenne prime numbers [1, 2, 3]. Due to the computational demands of volunteer computing projects, it is desirable to find additional sources of volunteer computing power. In order to be a viable source of volunteer computing power, a platform must be able to provide enough CPU cycles to make it worth the effort to port volunteer computing applications to that platform. Video game consoles have become increasingly powerful computers over the last 30 years, and the number of video game consoles sold and their computational power combined with their network capability makes them a potentially good platform for volunteer computing. We devise an experiment to test the potential usefulness of video game consoles for volunteer computing and compare the time it takes a video game console and several different computers to do the same amount of work for an example project.