Fake Run-Time Selection of Template Arguments in C++

C++ does not support run-time resolution of template type arguments. To circumvent this restriction, we can instantiate a template for all possible combinations of type arguments at compile time and then select the proper instance at run time by evaluation of some provided conditions. However, for templates with multiple type parameters such a solution may easily result in a branching code bloat. We present a template metaprogramming algorithm called for_id that allows the user to select the proper template instance at run time with theoretical minimum sustained complexity of the branching code.Comment: Objects, Models, Components, Patterns (50th International Conference, TOOLS 2012

Philosophy of Computer Science: An Introductory Course

There are many branches of philosophy called “the philosophy of X,” where X = disciplines ranging from history to physics. The philosophy of artificial intelligence has a long history, and there are many courses and texts with that title. Surprisingly, the philosophy of computer science is not nearly as well-developed. This article proposes topics that might constitute the philosophy of computer science and describes a course covering those topics, along with suggested readings and assignments

Odeint - Solving ordinary differential equations in C++

Many physical, biological or chemical systems are modeled by ordinary differential equations (ODEs) and finding their solution is an every-day-task for many scientists. Here, we introduce a new C++ library dedicated to find numerical solutions of initial value problems of ODEs: odeint (www.odeint.com). odeint is implemented in a highly generic way and provides extensive interoperability at top performance. For example, due to it's modular design it can be easily parallized with OpenMP and even runs on CUDA GPUs. Despite that, it provides a convenient interface that allows for a simple and easy usage.Comment: 4 pages, 1 figur

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Investigating grid computing technologies for use with commercial simulation packages

As simulation experimentation in industry become more computationally demanding, grid computing can be seen as a promising technology that has the potential to bind together the computational resources needed to quickly execute such simulations. To investigate how this might be possible, this paper reviews the grid technologies that can be used together with commercial-off-the-shelf simulation packages (CSPs) used in industry. The paper identifies two specific forms of grid computing (Public Resource Computing and Enterprise-wide Desktop Grid Computing) and the middleware associated with them (BOINC and Condor) as being suitable for grid-enabling existing CSPs. It further proposes three different CSP-grid integration approaches and identifies one of them to be the most appropriate. It is hoped that this research will encourage simulation practitioners to consider grid computing as a technologically viable means of executing CSP-based experiments faster

Supporting simulation in industry through the application of grid computing

An increased need for collaborative research, together with continuing advances in communication technology and computer hardware, has facilitated the development of distributed systems that can provide users access to geographically dispersed computing resources that are administered in multiple computer domains. The term grid computing, or grids, is popularly used to refer to such distributed systems. Simulation is characterized by the need to run multiple sets of computationally intensive experiments. Large scale scientific simulations have traditionally been the primary benefactor of grid computing. The application of this technology to simulation in industry has, however, been negligible. This research investigates how grid technology can be effectively exploited by users to model simulations in industry. It introduces our desktop grid, WinGrid, and presents a case study conducted at a leading European investment bank. Results indicate that grid computing does indeed hold promise for simulation in industry