Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

The syntax of DRAGOON: Evaluation and recommendations

Several different ways to add linguistic support for object-oriented programming to the Ada programming language have been proposed and developed in recent years. The Distributable Reusable Ada Generated from an Object-Oriented Notation (DRAGOON) language is one such Ada extension. The DRAGOON syntax is described for classes, objects, and inheritance, and the syntax is evaluated against the following five criteria: readability, writeability, lack of ambiguity, ease of translation, and consistency with existing Ada syntax. The evaluation reveals several deficiencies in the notation. A revised syntax that corrects these deficiencies is proposed

Building an interactive 3D animation system

The continued improvement and proliferation of graphics hardware for workstations and personal computers has brought increasing prominence to a newer style of software application program. This style relies on fast, high quality graphics displays coupled with expressive input devices to achieve real-time animation and direct-manipulation interaction metaphors. Such applications impose a rather different conceptual approach, on both the user and the programmer, than more traditional software. The application program can be thought of increasingly as a virtual machine, with a tangible two or three dimensional appearance, behavior and tactile response. Dynamic graphics techniques are now considered essential for making computers easier to use, and interactive and graphical interfaces that allow the presentation and the direct manipulation of information in a pictorial form is now an important part of most of modern graphics software tools211-24

Rethinking Complexity: Vladimir Shukhov’s Steel Lattice Structures

This paper is a critical review on advantages and disadvantages of contemporary digital architecture, in retrospect to Vladimir Shukhov's design techniques, applied in the early 20th century. After investigating Shukhov's structural systems, this paper explores the relationship between performance and form, questioning the necessity of high-complexity structures. It will present unpublished archive material of his early work and stimulate a valuable discussion by comparing it with contemporary projects designed by renowned architects. The study on Shukhov focuses on his tessellation method of double-curved surfaces using simple standardized elements. The study of present digital approaches revolves around leading architects using computational tools (e.g. Foster and Partners, Buro Happold and Arup), who have materialized high complexity structures composed by irregular units. Our findings highlight advantages and disadvantages of contemporary computational approaches

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

Programming language trends : an empirical study

Predicting the evolution of software engineering technology trends is a dubious proposition. The recent evolution of software technology is a prime example; it is fast paced and affected by many factors, which are themselves driven by a wide range of sources. This dissertation is part of a long term project intended to analyze software engineering technology trends and how they evolve. Basically, the following questions will be answered: How to watch, predict, adapt to, and affect software engineering trends? In this dissertation, one field of software engineering, programming languages, will be discussed. After reviewing the history of a group of programming languages, it shows that two kinds of factors, intrinsic factors and extrinsic factors, could affect the evolution of a programming language. Intrinsic factors are the factors that can be used to describe the general desigu criteria of programming languages. Extrinsic factors are the factors that are not directly related to the general attributes of programming languages, but still can affect their evolution. In order to describe the relationship of these factors and how they affect programming language trends, these factors need to be quantified. A score has been assigued to each factor for every programming language. By collecting historical data, a data warehouse has been established, which stores the value of each factor for every programming language. The programming language trends are described and evaluated by using these data. Empirical research attempts to capture observed behaviors by empirical laws. In this dissertation, statistical methods are used to describe historical programming language trends and predict the evolution of the future trends. Several statistics models are constructed to describe the relationships among these factors. Canonical correlation is used to do the factor analysis. Multivariate multiple regression method has been used to construct the statistics models for programming language trends. After statistics models are constructed to describe the historical programming language trends, they are extended to do tentative prediction for future trends. The models are validated by comparing the predictive data and the actual data