Peripheral Constraint Versus On-line Programming in Rapid Aimed Sequestial Movements

The purpose of this investigation was to examine how the programming and control of a rapid aiming sequence shifts with increased complexity. One objective was to determine if a preprogramming/peripheral constraint explanation is adequate to characterize control of an increasingly complex rapid aiming sequence, and if not, at what point on-line programming better accounts for the data. A second objective was to examine when on-line programming occurs. Three experiments were conducted in which complexity was manipulated by increasing the number of targets from 1 to 11. Initiation- and execution-timing patterns, probe reaction time, and movement kinematics were measured. Results supported the peripheral constraint/pre-programming explanation for sequences up to 7 targets if they were executed in a blocked fashion. For sequences executed in a random fashion (one length followed by a different length), preprogramming did not increase with complexity, and on-line programming occurred without time cost. Across all sequences there was evidence that the later targets created a peripheral constraint on movements to previous targets. We suggest that programming is influenced by two factors: the overall spatial trajectory, which is consistent with Sidaway’s subtended angle hypothesis (1991), and average velocity, with the latter established based on the number of targets in the sequence. As the number of targets increases, average velocity decreases, which controls variability of error in the extent of each movement segment. Overall the data support a continuous model of processing, one in which programming and execution co-occur, and can do so without time cost

Programming an interpreter using molecular dynamics

PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.Comment: 27 page

Cis-regulatory module detection using constraint programming

We propose a method for finding CRMs in a set of co-regulated genes. Each CRM consists of a set of binding sites of transcription factors. We wish to find CRMs involving the same transcription factors in multiple sequences. Finding such a combination of transcription factors is inherently a combinatorial problem. We solve this problem by combining the principles of itemset mining and constraint programming. The constraints involve the putative binding sites of transcription factors, the number of sequences in which they co-occur and the proximity of the binding sites. Genomic background sequences are used to assess the significance of the modules. We experimentally validate our approach and compare it with state-of-the-art techniques

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks.

Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended and paired end strings to a reference remains computationally demanding. Further tailoring Bioinformatics tools to each new task or scanner remains highly skilled and labour intensive. With this in mind, we recently demonstrated a genetic programming based automated technique which generated a version of the state-of-the-art alignment tool Bowtie2 which was considerably faster on short sequences produced by a scanner at the Broad Institute and released as part of The Thousand Genome Project

Sustaining interaction in a mathematical community of practice

This paper focuses on an activity in which students explore sequences through a game, using ToonTalk programming and a web-based collaboration system. Our analytical framework combines theory of communities of practice with domain epistemology. We note three factors which influence the length and quality of interactions: facilitation, reciprocation and audience-awareness

Modular session types for objects

Session types allow communication protocols to be specified type-theoretically so that protocol implementations can be verified by static type checking. We extend previous work on session types for distributed object-oriented languages in three ways. (1) We attach a session type to a class definition, to specify the possible sequences of method calls. (2) We allow a session type (protocol) implementation to be modularized, i.e. partitioned into separately-callable methods. (3) We treat session-typed communication channels as objects, integrating their session types with the session types of classes. The result is an elegant unification of communication channels and their session types, distributed object-oriented programming, and a form of typestate supporting non-uniform objects, i.e. objects that dynamically change the set of available methods. We define syntax, operational se-mantics, a sound type system, and a sound and complete type checking algorithm for a small distributed class-based object-oriented language with structural subtyping. Static typing guarantees that both sequences of messages on channels, and sequences of method calls on objects, conform to type-theoretic specifications, thus ensuring type-safety. The language includes expected features of session types, such as delegation, and expected features of object-oriented programming, such as encapsulation of local state.Comment: Logical Methods in Computer Science (LMCS), International Federation for Computational Logic, 201