Behavioral types in programming languages

A recent trend in programming language research is to use behav- ioral type theory to ensure various correctness properties of large- scale, communication-intensive systems. Behavioral types encompass concepts such as interfaces, communication protocols, contracts, and choreography. The successful application of behavioral types requires a solid understanding of several practical aspects, from their represen- tation in a concrete programming language, to their integration with other programming constructs such as methods and functions, to de- sign and monitoring methodologies that take behaviors into account. This survey provides an overview of the state of the art of these aspects, which we summarize as the pragmatics of behavioral types

A Programming Language for Web Service Development

There is now widespread acceptance of Web services and service-oriented architectures. But despite the agreement on key Web services standards there remain many challenges. Programming environments based on WSDL support go some way to facilitating Web service development. However Web services fundamentally rely on XML and Schema, not on contemporary programming language type systems such as those of Java or .NET. Moreover, Web services are based on a messaging paradigm and hence bring forward the traditional problems of messaging systems including concurrency control and message correlation. It is easy to write simple synchronous Web services using traditional programming languages; however more realistic scenarios are surprisingly difficult to implement. To alleviate these issues we propose a programming language which directly supports Web service development. The language leverages XQuery for native XML processing, supports implicit message correlation and has high level join calculus-style concurrency control. We illustrate the features of the language through a motivating example

Study of Tools Interoperability

Interoperability of tools usually refers to a combination of methods and techniques that address the problem of making a collection of tools to work together. In this study we survey different notions that are used in this context: interoperability, interaction and integration. We point out relation between these notions, and how it maps to the interoperability problem. We narrow the problem area to the tools development in academia. Tools developed in such environment have a small basis for development, documentation and maintenance. We scrutinise some of the problems and potential solutions related with tools interoperability in such environment. Moreover, we look at two tools developed in the Formal Methods and Tools group1, and analyse the use of different integration techniques

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