101,201 research outputs found
Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications
We describe Slisp (pronounced âEss-Lispâ), a hybrid LispâC programming toolkit for the development of scriptable and distributed applications. Computationally expensive operations implemented as separate C-coded modules are selectively compiled into a small Xlisp interpreter, then called as Lisp functions in a Lisp-coded program. The resulting hybrid program may run in several modes: as a stand-alone executable, embedded in a different C program, as a networked server accessed from another Slisp client, or as a
networked server accessed from a C-coded client. Five years of experience with Slisp, as well experience with other scripting languages such as Tcl and Perl, are summarized. These experiences suggest that Slisp will be most useful for mid-sized applications in which the kinds of scripting and embeddability features provided by Tcl and Perl can be extended in an efïŹcient manner to larger applications, while maintaining a
well-deïŹned standard (Common Lisp) for these extensions. In addition, the generality of Lisp makes Lisp a good candidate for an application-level communication language in distributed environments
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
Pattern Reification as the Basis for Description-Driven Systems
One of the main factors driving object-oriented software development for
information systems is the requirement for systems to be tolerant to change. To
address this issue in designing systems, this paper proposes a pattern-based,
object-oriented, description-driven system (DDS) architecture as an extension
to the standard UML four-layer meta-model. A DDS architecture is proposed in
which aspects of both static and dynamic systems behavior can be captured via
descriptive models and meta-models. The proposed architecture embodies four
main elements - firstly, the adoption of a multi-layered meta-modeling
architecture and reflective meta-level architecture, secondly the
identification of four data modeling relationships that can be made explicit
such that they can be modified dynamically, thirdly the identification of five
design patterns which have emerged from practice and have proved essential in
providing reusable building blocks for data management, and fourthly the
encoding of the structural properties of the five design patterns by means of
one fundamental pattern, the Graph pattern. A practical example of this
philosophy, the CRISTAL project, is used to demonstrate the use of
description-driven data objects to handle system evolution.Comment: 20 pages, 10 figure
Open Programming Language Interpreters
Context: This paper presents the concept of open programming language
interpreters and the implementation of a framework-level metaobject protocol
(MOP) to support them. Inquiry: We address the problem of dynamic interpreter
adaptation to tailor the interpreter's behavior on the task to be solved and to
introduce new features to fulfill unforeseen requirements. Many languages
provide a MOP that to some degree supports reflection. However, MOPs are
typically language-specific, their reflective functionality is often
restricted, and the adaptation and application logic are often mixed which
hardens the understanding and maintenance of the source code. Our system
overcomes these limitations. Approach: We designed and implemented a system to
support open programming language interpreters. The prototype implementation is
integrated in the Neverlang framework. The system exposes the structure,
behavior and the runtime state of any Neverlang-based interpreter with the
ability to modify it. Knowledge: Our system provides a complete control over
interpreter's structure, behavior and its runtime state. The approach is
applicable to every Neverlang-based interpreter. Adaptation code can
potentially be reused across different language implementations. Grounding:
Having a prototype implementation we focused on feasibility evaluation. The
paper shows that our approach well addresses problems commonly found in the
research literature. We have a demonstrative video and examples that illustrate
our approach on dynamic software adaptation, aspect-oriented programming,
debugging and context-aware interpreters. Importance: To our knowledge, our
paper presents the first reflective approach targeting a general framework for
language development. Our system provides full reflective support for free to
any Neverlang-based interpreter. We are not aware of any prior application of
open implementations to programming language interpreters in the sense defined
in this paper. Rather than substituting other approaches, we believe our system
can be used as a complementary technique in situations where other approaches
present serious limitations
Recommended from our members
Reusability in software engineering
This paper surveys recent work concerning reusability in software engineering. The current directions in software reusability are discussed, and the two major approaches of reusable building blocks and reusable patterns studied. An extensive bibliography, parts of which are annotated, is included
Abstract State Machines 1988-1998: Commented ASM Bibliography
An annotated bibliography of papers which deal with or use Abstract State
Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm
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