super-Charging Object-Oriented Programming Through Precise Typing of Open Recursion

We present a new variation of object-oriented programming built around three simple and orthogonal constructs: classes for storing object state, interfaces for expressing object types, and mixins for reusing and overriding implementations. We show that the latter can be made uniquely expressive by leveraging a novel feature that we call precisely-typed open recursion. This features uses "this" and "super" annotations to express the requirements of any given partial method implementation on the types of respectively the current object and the inherited definitions. Crucially, the fact that mixins do not introduce types nor subtyping relationships means they can be composed even when the overriding and overridden methods have incomparable types. Together with advanced type inference and structural typing support provided by the MLscript programming language, we show that this enables an elegant and powerful solution to the Expression Problem

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

Tydi-lang: A Language for Typed Streaming Hardware

Transferring composite data structures with variable-length fields often requires designing non-trivial protocols that are not compatible between hardware designs. When each project designs its own data format and protocols the ability to collaborate between hardware developers is diminished, which is an issue especially in the open-source community. Because the high-level meaning of a protocol is often lost in translation to low-level languages when a custom protocol needs to be designed, extra documentation is required, the interpretation of which introduces new opportunities for errors. The Tydi specification (Tydi-spec) was proposed to address the above issues by codifying the composite and variable-length data structures in a type and providing a standard protocol to transfer typed data among hardware components. The Tydi intermediate representation (Tydi-IR) extends the Tydi-spec by defining typed interfaces, typed components, and connections among typed components. In this paper, we propose Tydi-lang, a high-level hardware description language (HDL) for streaming designs. The language incorporates Tydi-spec to describe typed streams and provides templates to describe abstract reusable components. We also implement an open-source compiler from Tydi-lang to Tydi-IR. We leverage a Tydi-IR to VHDL compiler, and also present a simulator blueprint to identify streaming bottlenecks. We show several Tydi-lang examples to translate high-level SQL to VHDL to demonstrate that Tydi-lang can efficiently raise the level of abstraction and reduce design effort.Comment: 8 pages and 1 page of reference, 4 figures, 4 table