Particle-based and Meshless Methods with Aboria

Aboria is a powerful and flexible C++ library for the implementation of particle-based numerical methods. The particles in such methods can represent actual particles (e.g. Molecular Dynamics) or abstract particles used to discretise a continuous function over a domain (e.g. Radial Basis Functions). Aboria provides a particle container, compatible with the Standard Template Library, spatial search data structures, and a Domain Specific Language to specify non-linear operators on the particle set. This paper gives an overview of Aboria's design, an example of use, and a performance benchmark

An open reproducible framework for the study of the iterated prisoner's dilemma

The Axelrod library is an open source Python package that allows for reproducible game theoretic research into the Iterated Prisoner's Dilemma. This area of research began in the 1980s but suffers from a lack of documentation and test code. The goal of the library is to provide such a resource, with facilities for the design of new strategies and interactions between them, as well as conducting tournaments and ecological simulations for populations of strategies. With a growing collection of 139 strategies, the library is a also a platform for an original tournament that, in itself, is of interest to the game theoretic community. This paper describes the Iterated Prisoner's Dilemma, the Axelrod library and its development, and insights gained from some novel research.Comment: 11 pages, Journal of Open Research Software 4.1 (2016

The C++0x "Concepts" Effort

C++0x is the working title for the revision of the ISO standard of the C++ programming language that was originally planned for release in 2009 but that was delayed to 2011. The largest language extension in C++0x was "concepts", that is, a collection of features for constraining template parameters. In September of 2008, the C++ standards committee voted the concepts extension into C++0x, but then in July of 2009, the committee voted the concepts extension back out of C++0x. This article is my account of the technical challenges and debates within the "concepts" effort in the years 2003 to 2009. To provide some background, the article also describes the design space for constrained parametric polymorphism, or what is colloquially know as constrained generics. While this article is meant to be generally accessible, the writing is aimed toward readers with background in functional programming and programming language theory. This article grew out of a lecture at the Spring School on Generic and Indexed Programming at the University of Oxford, March 2010

Single cell transcriptome analysis using next generation sequencing.

The heterogeneity of tissues, especially in cancer research, is a central issue in transcriptome analysis. In recent years, research has primarily focused on the development of methods for single cell analysis. Single cell analysis aims at gaining (novel) insights into biological processes of healthy and diseased cells. Some of the challenges in transcriptome analysis concern low abundance of sample starting material, necessary sample amplification steps and subsequent analysis. In this study, two fundamentally different approaches to amplification were compared using next-generation sequencing analysis: I. exponential amplification using polymerase-chain-reaction (PCR) and II. linear amplification. For both approaches, protocols for single cell extraction, cell lysis, cDNA synthesis, cDNA amplification and preparation of next-generation sequencing libraries were developed. We could successfully show that transcriptome analysis of low numbers of cells is feasible with both exponential and linear amplification. Using exponential amplification, the highest amplification rates up to 106 were possible. The reproducibility of results is a strength of the linear amplification method. The analysis of next generation sequencing data in single cell samples showed detectable expression in at least 16.000 genes. The variance between samples results in a need to work with a greater amount of biological replicates. In summary it can be said that single cell transcriptome analysis with next generation sequencing is possible but improvements leading to a higher yield of transcriptome reads is required. In the near future by comparing single cancer cells with healthy ones for example, a basis for improved prognosis and diagnosis can be realised

TrusNet: Peer-to-Peer Cryptographic Authentication

Originally, the Internet was meant as a general purpose communication protocol, transferring primarily text documents between interested parties. Over time, documents expanded to include pictures, videos and even web pages. Increasingly, the Internet is being used to transfer a new kind of data which it was never designed for. In most ways, this new data type fits in naturally to the Internet, taking advantage of the near limit-less expanse of the protocol. Hardware protocols, unlike previous data types, provide a unique set security problem. Much like financial data, hardware protocols extended across the Internet must be protected with authentication. Currently, systems which do authenticate do so through a central server, utilizing a similar authentication model to the HTTPS protocol. This hierarchical model is often at odds with the needs of hardware protocols, particularly in ad-hoc networks where peer-to-peer communication is prioritized over a hierarchical model. Our project attempts to implement a peer-to-peer cryptographic authentication protocol to be used to protect hardware protocols extending over the Internet. The TrusNet project uses public-key cryptography to authenticate nodes on a distributed network, with each node locally managing a record of the public keys of nodes which it has encountered. These keys are used to secure data transmission between nodes and to authenticate the identities of nodes. TrusNet is designed to be used on multiple different types of network interfaces, but currently only has explicit hooks for Internet Protocol connections. As of June 2016, TrusNet has successfully achieved a basic authentication and communication protocol on Windows 7, OSX, Linux 14 and the Intel Edison. TrusNet uses RC-4 as its stream cipher and RSA as its public-key algorithm, although both of these are easily configurable. Along with the library, TrusNet also enables the building of a unit testing suite, a simple UI application designed to visualize the basics of the system and a build with hooks into the I/O pins of the Intel Edison allowing for a basic demonstration of the system