Integrating a universal query mechanism into java

This thesis discusses design, architecture, and application of a universal query language embedded in Java. Utilizing various design patterns and Java\u27s polymorphism, the current result is a preprocessor that will convert an embedded language into compilable Java. The resulting Java utilizes a back{end developed for the queried data structure, capable of querying that structures internal data

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

Structure and Interpretation of Computer Programs

Structure and Interpretation of Computer Programs has had a dramatic impact on computer science curricula over the past decade. This long-awaited revision contains changes throughout the text. There are new implementations of most of the major programming systems in the book, including the interpreters and compilers, and the authors have incorporated many small changes that reflect their experience teaching the course at MIT since the first edition was published. A new theme has been introduced that emphasizes the central role played by different approaches to dealing with time in computational models: objects with state, concurrent programming, functional programming and lazy evaluation, and nondeterministic programming. There are new example sections on higher-order procedures in graphics and on applications of stream processing in numerical programming, and many new exercises. In addition, all the programs have been reworked to run in any Scheme implementation that adheres to the IEEE standard

Foundations of Programming Languages

This clearly written textbook provides an accessible introduction to the three programming paradigms of object-oriented/imperative, functional, and logic programming. Highly interactive in style, the text encourages learning through practice, offering test exercises for each topic covered. Review questions and programming projects are also presented, to help reinforce the concepts outside of the classroom. This updated and revised new edition features new material on the Java implementation of the JCoCo virtual machine

An Analytical Approach to Programs as Data Objects

This essay accompanies a selection of 32 articles (referred to in bold face in the text and marginally marked in the bibliographic references) submitted to Aarhus University towards a Doctor Scientiarum degree in Computer Science.The author's previous academic degree, beyond a doctoral degree in June 1986, is an "Habilitation à diriger les recherches" from the Université Pierre et Marie Curie (Paris VI) in France; the corresponding material was submitted in September 1992 and the degree was obtained in January 1993.The present 32 articles have all been written since 1993 and while at DAIMI.Except for one other PhD student, all co-authors are or have been the author's students here in Aarhus

Simple optimizing JIT compilation of higher-order dynamic programming languages

Implémenter efficacement les langages de programmation dynamiques demande beaucoup d’effort de développement. Les compilateurs ne cessent de devenir de plus en plus complexes. Aujourd’hui, ils incluent souvent une phase d’interprétation, plusieurs phases de compilation, plusieurs représentations intermédiaires et des analyses de code. Toutes ces techniques permettent d’implémenter efficacement un langage de programmation dynamique, mais leur mise en oeuvre est difficile dans un contexte où les ressources de développement sont limitées. Nous proposons une nouvelle approche et de nouvelles techniques dynamiques permettant de développer des compilateurs performants pour les langages dynamiques avec de relativement bonnes performances et un faible effort de développement. Nous présentons une approche simple de compilation à la volée qui permet d’implémenter un langage en une seule phase de compilation, sans transformation vers des représentations intermédiaires. Nous expliquons comment le versionnement de blocs de base, une technique de compilation existante, peut être étendue, sans effort de développement significatif, pour fonctionner interprocéduralement avec les langages de programmation d’ordre supérieur, permettant d’appliquer des optimisations interprocédurales sur ces langages. Nous expliquons également comment le versionnement de blocs de base permet de supprimer certaines opérations utilisées pour implémenter les langages dynamiques et qui impactent les performances comme les vérifications de type. Nous expliquons aussi comment les compilateurs peuvent exploiter les représentations dynamiques des valeurs par Tagging et NaN-boxing pour optimiser le code généré avec peu d’effort de développement. Nous présentons également notre expérience de développement d’un compilateur à la volée pour le langage de programmation Scheme, pour montrer que ces techniques permettent effectivement de construire un compilateur avec un effort moins important que les compilateurs actuels et qu’elles permettent de générer du code efficace, qui rivalise avec les meilleures implémentations du langage Scheme.Efficiently implementing dynamic programming languages requires a significant development effort. Over the years, compilers have become more complex. Today, they typically include an interpretation phase, several compilation phases, several intermediate representations and code analyses. These techniques allow efficiently implementing these programming languages but are difficult to implement in contexts in which development resources are limited. We propose a new approach and new techniques to build optimizing just-in-time compilers for dynamic languages with relatively good performance and low development effort. We present a simple just-in-time compilation approach to implement a language with a single compilation phase, without the need to use code transformations to intermediate representations. We explain how basic block versioning, an existing compilation technique, can be extended without significant development effort, to work interprocedurally with higherorder programming languages allowing interprocedural optimizations on these languages. We also explain how basic block versioning allows removing operations used to implement dynamic languages that degrade performance, such as type checks, and how compilers can use Tagging and NaN-boxing to optimize the generated code with low development effort. We present our experience of building a JIT compiler using these techniques for the Scheme programming language to show that they indeed allow building compilers with less development effort than other implementations and that they allow generating efficient code that competes with current mature implementations of the Scheme language

Compiler of a Language with User-Defined Syntax for New Constructs

Tato práce si klade za cíl navrhnout a implementovat experimentální programovací jazyk s podporou uživatelsky definovaných syntaktických konstrukcí. Nový jazyk je kompilován do nativní binární podoby a vyžaduje statickou typovou disciplínu v době překladu. Jazyk se skládá ze dvou hlavních komponent. První z nich je minimalistické jádro založené na principech zásobníkově orientovaných jazyků. Druhou částí je mechanismus pro definici nových syntaktických konstrukcí uživatelem. Poté jsou shrnuty poznatky nabyté při návrhu a experimentování s prototypem překladače tohoto jazyka.This project aims to design and implement an experimental programming language. The main feature of the language shall be the ability of the user to define new syntactic constructs. The language shall be statically typed and compiled to a native binary form. The language consists of two parts. The first part is a minimalistic core based on the principles of stack-oriented languages. The second part is a mechanism that lets users define new syntactic constructs. Then we elaborate on findings that have risen from design and experiments performed with the prototype implementation of the language.

GNU epsilon - an extensible programming language

Reductionism is a viable strategy for designing and implementing practical programming languages, leading to solutions which are easier to extend, experiment with and formally analyze. We formally specify and implement an extensible programming language, based on a minimalistic first-order imperative core language plus strong abstraction mechanisms, reflection and self-modification features. The language can be extended to very high levels: by using Lisp-style macros and code-to-code transforms which automatically rewrite high-level expressions into core forms, we define closures and first-class continuations on top of the core. Non-self-modifying programs can be analyzed and formally reasoned upon, thanks to the language simple semantics. We formally develop a static analysis and prove a soundness property with respect to the dynamic semantics. We develop a parallel garbage collector suitable to multi-core machines to permit efficient execution of parallel programs.Comment: 172 pages, PhD thesi

A Tracing JIT Compiler for Erlang using LLVM

We have modified the Erlang runtime to add support for a tracing just-in-time (JIT) compiler, similar to Mozilla’s TraceMonkey. Tracing is a technique to augment an existing interpreter with a JIT simply by recording the instructions executed during a loop iteration, and then generate optimized native code from this. Tracing compilers are particularly suited to optimize number crunching tight loops, an area where Erlang traditionally has been lacking. We make use of the LLVM compiler library to optimize and emit native code. In micro benchmarks we show some major improvements, reducing execution time by up to 75%. However, from an engineering point of view, we conclude that the effort of an industrial strength implementation would be substantial – essentially reimplementing large parts of Erlang’s interpreter – and discuss a potential solution based on recent research in the area.Nästan alla moderna programspråk använder en interpretator – en flexibel och praktisk om än långsam lösning. Vi prövar ett enkelt sätt att kraftigt öka prestandan på Erlangs interpretator

Liveness-Based Garbage Collection for Lazy Languages

We consider the problem of reducing the memory required to run lazy first-order functional programs. Our approach is to analyze programs for liveness of heap-allocated data. The result of the analysis is used to preserve only live data---a subset of reachable data---during garbage collection. The result is an increase in the garbage reclaimed and a reduction in the peak memory requirement of programs. While this technique has already been shown to yield benefits for eager first-order languages, the lack of a statically determinable execution order and the presence of closures pose new challenges for lazy languages. These require changes both in the liveness analysis itself and in the design of the garbage collector. To show the effectiveness of our method, we implemented a copying collector that uses the results of the liveness analysis to preserve live objects, both evaluated (i.e., in WHNF) and closures. Our experiments confirm that for programs running with a liveness-based garbage collector, there is a significant decrease in peak memory requirements. In addition, a sizable reduction in the number of collections ensures that in spite of using a more complex garbage collector, the execution times of programs running with liveness and reachability-based collectors remain comparable