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

PList-based Divide and Conquer Parallel Programming

This paper details an extension of a Java parallel programming framework – JPLF. The JPLF framework is a programming framework that helps programmers build parallel programs using existing building blocks. The framework is based on {em PowerLists} and PList Theories and it naturally supports multi-way Divide and Conquer. By using this framework, the programmer is exempted from dealing with all the complexities of writing parallel programs from scratch. This extension to the JPLF framework adds PLists support to the framework and so, it enlarges the applicability of the framework to a larger set of parallel solvable problems. Using this extension, we may apply more flexible data division strategies. In addition, the length of the input lists no longer has to be a power of two – as required by the PowerLists theory. In this paper we unveil new applications that emphasize the new class of computations that can be executed within the JPLF framework. We also give a detailed description of the data structures and functions involved in the PLists extension of the JPLF, and extended performance experiments are described and analyzed

Estimating the Algorithmic Complexity of Stock Markets

Randomness and regularities in Finance are usually treated in probabilistic terms. In this paper, we develop a completely different approach in using a non-probabilistic framework based on the algorithmic information theory initially developed by Kolmogorov (1965). We present some elements of this theory and show why it is particularly relevant to Finance, and potentially to other sub-fields of Economics as well. We develop a generic method to estimate the Kolmogorov complexity of numeric series. This approach is based on an iterative "regularity erasing procedure" implemented to use lossless compression algorithms on financial data. Examples are provided with both simulated and real-world financial time series. The contributions of this article are twofold. The first one is methodological : we show that some structural regularities, invisible with classical statistical tests, can be detected by this algorithmic method. The second one consists in illustrations on the daily Dow-Jones Index suggesting that beyond several well-known regularities, hidden structure may in this index remain to be identified

Performance Improvements of Common Sparse Numerical Linear Algebra Computations

Manufacturers of computer hardware are able to continuously sustain an unprecedented pace of progress in computing speed of their products, partially due to increased clock rates but also because of ever more complicated chip designs. With new processor families appearing every few years, it is increasingly harder to achieve high performance rates in sparse matrix computations. This research proposes new methods for sparse matrix factorizations and applies in an iterative code generalizations of known concepts from related disciplines. The proposed solutions and extensions are implemented in ways that tend to deliver efficiency while retaining ease of use of existing solutions. The implementations are thoroughly timed and analyzed using a commonly accepted set of test matrices. The tests were conducted on modern processors that seem to have gained an appreciable level of popularity and are fairly representative for a wider range of processor types that are available on the market now or in the near future. The new factorization technique formally introduced in the early chapters is later on proven to be quite competitive with state of the art software currently available. Although not totally superior in all cases (as probably no single approach could possibly be), the new factorization algorithm exhibits a few promising features. In addition, an all-embracing optimization effort is applied to an iterative algorithm that stands out for its robustness. This also gives satisfactory results on the tested computing platforms in terms of performance improvement. The same set of test matrices is used to enable an easy comparison between both investigated techniques, even though they are customarily treated separately in the literature. Possible extensions of the presented work are discussed. They range from easily conceivable merging with existing solutions to rather more evolved schemes dependent on hard to predict progress in theoretical and algorithmic research

Resource Bounded Immunity and Simplicity

Revisiting the thirty years-old notions of resource-bounded immunity and simplicity, we investigate the structural characteristics of various immunity notions: strong immunity, almost immunity, and hyperimmunity as well as their corresponding simplicity notions. We also study limited immunity and simplicity, called k-immunity and feasible k-immunity, and their simplicity notions. Finally, we propose the k-immune hypothesis as a working hypothesis that guarantees the existence of simple sets in NP.Comment: This is a complete version of the conference paper that appeared in the Proceedings of the 3rd IFIP International Conference on Theoretical Computer Science, Kluwer Academic Publishers, pp.81-95, Toulouse, France, August 23-26, 200

Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George Ellis (eds.), Cambridge University Pres