THREAD: A programming environment for interactive planning-level robotics applications

THREAD programming language, which was developed to meet the needs of researchers in developing robotics applications that perform such tasks as grasp, trajectory design, sensor data analysis, and interfacing with external subsystems in order to perform servo-level control of manipulators and real time sensing is discussed. The philosophy behind THREAD, the issues which entered into its design, and the features of the language are discussed from the viewpoint of researchers who want to develop algorithms in a simulation environment, and from those who want to implement physical robotics systems. The detailed functions of the many complex robotics algorithms and tools which are part of the language are not explained, but an overall impression of their capability is given

Lazy Evaluation and Delimited Control

The call-by-need lambda calculus provides an equational framework for reasoning syntactically about lazy evaluation. This paper examines its operational characteristics. By a series of reasoning steps, we systematically unpack the standard-order reduction relation of the calculus and discover a novel abstract machine definition which, like the calculus, goes "under lambdas." We prove that machine evaluation is equivalent to standard-order evaluation. Unlike traditional abstract machines, delimited control plays a significant role in the machine's behavior. In particular, the machine replaces the manipulation of a heap using store-based effects with disciplined management of the evaluation stack using control-based effects. In short, state is replaced with control. To further articulate this observation, we present a simulation of call-by-need in a call-by-value language using delimited control operations

Toward an Energy Efficient Language and Compiler for (Partially) Reversible Algorithms

We introduce a new programming language for expressing reversibility, Energy-Efficient Language (Eel), geared toward algorithm design and implementation. Eel is the first language to take advantage of a partially reversible computation model, where programs can be composed of both reversible and irreversible operations. In this model, irreversible operations cost energy for every bit of information created or destroyed. To handle programs of varying degrees of reversibility, Eel supports a log stack to automatically trade energy costs for space costs, and introduces many powerful control logic operators including protected conditional, general conditional, protected loops, and general loops. In this paper, we present the design and compiler for the three language levels of Eel along with an interpreter to simulate and annotate incurred energy costs of a program.Comment: 17 pages, 0 additional figures, pre-print to be published in The 8th Conference on Reversible Computing (RC2016

A Rational Deconstruction of Landin's SECD Machine with the J Operator

Landin's SECD machine was the first abstract machine for applicative expressions, i.e., functional programs. Landin's J operator was the first control operator for functional languages, and was specified by an extension of the SECD machine. We present a family of evaluation functions corresponding to this extension of the SECD machine, using a series of elementary transformations (transformation into continu-ation-passing style (CPS) and defunctionalization, chiefly) and their left inverses (transformation into direct style and refunctionalization). To this end, we modernize the SECD machine into a bisimilar one that operates in lockstep with the original one but that (1) does not use a data stack and (2) uses the caller-save rather than the callee-save convention for environments. We also identify that the dump component of the SECD machine is managed in a callee-save way. The caller-save counterpart of the modernized SECD machine precisely corresponds to Thielecke's double-barrelled continuations and to Felleisen's encoding of J in terms of call/cc. We then variously characterize the J operator in terms of CPS and in terms of delimited-control operators in the CPS hierarchy. As a byproduct, we also present several reduction semantics for applicative expressions with the J operator, based on Curien's original calculus of explicit substitutions. These reduction semantics mechanically correspond to the modernized versions of the SECD machine and to the best of our knowledge, they provide the first syntactic theories of applicative expressions with the J operator

Continuation Passing Style for Effect Handlers

We present Continuation Passing Style (CPS) translations for Plotkin and Pretnar's effect handlers with Hillerström and Lindley's row-typed fine-grain call-by-value calculus of effect handlers as the source language. CPS translations of handlers are interesting theoretically, to explain the semantics of handlers, and also offer a practical implementation technique that does not require special support in the target language's runtime. We begin with a first-order CPS translation into untyped lambda calculus which manages a stack of continuations and handlers as a curried sequence of arguments. We then refine the initial CPS translation first by uncurrying it to yield a properly tail-recursive translation and second by making it higher-order in order to contract administrative redexes at translation time. We prove that the higher-order CPS translation simulates effect handler reduction. We have implemented the higher-order CPS translation as a JavaScript backend for the Links programming language

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

Four Lessons in Versatility or How Query Languages Adapt to the Web

Exposing not only human-centered information, but machine-processable data on the Web is one of the commonalities of recent Web trends. It has enabled a new kind of applications and businesses where the data is used in ways not foreseen by the data providers. Yet this exposition has fractured the Web into islands of data, each in different Web formats: Some providers choose XML, others RDF, again others JSON or OWL, for their data, even in similar domains. This fracturing stifles innovation as application builders have to cope not only with one Web stack (e.g., XML technology) but with several ones, each of considerable complexity. With Xcerpt we have developed a rule- and pattern based query language that aims to give shield application builders from much of this complexity: In a single query language XML and RDF data can be accessed, processed, combined, and re-published. Though the need for combined access to XML and RDF data has been recognized in previous work (including the W3C’s GRDDL), our approach differs in four main aspects: (1) We provide a single language (rather than two separate or embedded languages), thus minimizing the conceptual overhead of dealing with disparate data formats. (2) Both the declarative (logic-based) and the operational semantics are unified in that they apply for querying XML and RDF in the same way. (3) We show that the resulting query language can be implemented reusing traditional database technology, if desirable. Nevertheless, we also give a unified evaluation approach based on interval labelings of graphs that is at least as fast as existing approaches for tree-shaped XML data, yet provides linear time and space querying also for many RDF graphs. We believe that Web query languages are the right tool for declarative data access in Web applications and that Xcerpt is a significant step towards a more convenient, yet highly efficient data access in a “Web of Data”

Typechecking protocols with Mungo and StMungo: a session type toolchain for Java

Static typechecking is an important feature of many standard programming languages. However, static typing focuses on data rather than communication, and therefore does not help programmers correctly implement communication protocols in distributed systems. The theory of session types provides a basis for tackling this problem; we use it to develop two tools that support static typechecking of communication protocols in Java. The first tool, Mungo, extends Java with typestate definitions, which allow classes to be associated with state machines defining permitted sequences of method calls: for example, communication methods. The second tool, StMungo, takes a session type describing a communication protocol, and generates a typestate specification of the permitted sequences of messages in the protocol. Protocol implementations can be validated by Mungo against their typestate definitions and then compiled with a standard Java compiler. The result is a toolchain for static typechecking of communication protocols in Java. We formalise and prove soundness of the typestate inference system used by Mungo, and show that our toolchain can be used to typecheck a client for the standard Simple Mail Transfer Protocol (SMTP)