Programming Paradigms & Object-Oriented
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Bioconductor: Open Software Development for Computational Biology and Bioinformatics Robert C
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Collection Of Biostatistics Research Archive Bioconductor Project Bioconductor Project Working Papers Year 2004 Paper 1 Bioconductor: Open software development for computational biology and bioinformatics Robert C. Gentleman, Department of Biostatistical Sciences, Dana Farber Can- cer Institute Vincent J. Carey, Channing Laboratory, Brigham and Women’s Hospital Douglas J. Bates, Department of Statistics, University of Wisconsin, Madison Benjamin M. Bolstad, Division of Biostatistics, University of California, Berkeley Marcel Dettling, Seminar for Statistics, ETH, Zurich, CH Sandrine Dudoit, Division of Biostatistics, University of California, Berkeley Byron Ellis, Department of Statistics, Harvard University Laurent Gautier, Center for Biological Sequence Analysis, Technical University of Denmark, DK Yongchao Ge, Department of Biomathematical Sciences, Mount Sinai School of Medicine Jeff Gentry, Department of Biostatistical Sciences, Dana Farber Cancer Institute Kurt Hornik, Computational Statistics Group, Department of Statistics and Math- ematics, Wirtschaftsuniversitat¨ Wien, AT Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universitat Erlangen-Nurnberg, DE Wolfgang Huber, Department for Molecular Genome Analysis (B050), German Cancer Research Center, Heidelberg, DE Stefano Iacus, Department of Economics, University of Milan, IT Rafael Irizarry, Department of Biostatistics, Johns Hopkins University Friedrich Leisch, Institut fur¨ Statistik und Wahrscheinlichkeitstheorie, Technische Universitat¨ Wien, AT Cheng Li, Department of Biostatistical Sciences, Dana Farber Cancer Institute Martin Maechler, Seminar for Statistics, ETH, Zurich, CH Anthony J. Rossini, Department of Medical Education and Biomedical Informat- ics, University of Washington Guenther Sawitzki, Statistisches Labor, Institut fuer Angewandte Mathematik, DE Colin Smith, Department of Molecular Biology, The Scripps Research Institute, San Diego Gordon K. -
A Feature Model of Actor, Agent, Functional, Object, and Procedural Programming Languages
Accepted Manuscript A feature model of actor, agent, functional, object, and procedural programming languages H.R. Jordan, G. Botterweck, J.H. Noll, A. Butterfield, R.W. Collier PII: S0167-6423(14)00050-1 DOI: 10.1016/j.scico.2014.02.009 Reference: SCICO 1711 To appear in: Science of Computer Programming Received date: 9 March 2013 Revised date: 31 January 2014 Accepted date: 5 February 2014 Please cite this article in press as: H.R. Jordan et al., A feature model of actor, agent, functional, object, and procedural programming languages, Science of Computer Programming (2014), http://dx.doi.org/10.1016/j.scico.2014.02.009 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Highlights • A survey of existing programming language comparisons and comparison techniques. • Definitions of actor, agent, functional, object, and procedural programming concepts. • A feature model of general-purpose programming languages. • Mappings from five languages (C, Erlang, Haskell, Jason, and Java) to this model. A Feature Model of Actor, Agent, Functional, Object, and Procedural Programming Languages H.R. Jordana,∗, G. Botterwecka, J.H. Nolla, A. Butterfieldb, R.W. Collierc aLero, University of Limerick, Ireland bTrinity College Dublin, Dublin 2, Ireland cUniversity College Dublin, Belfield, Dublin 4, Ireland Abstract The number of programming languages is large [1] and steadily increasing [2]. -
Paradigms of Computer Programming
Paradigms of computer programming l This course aims to teach programming as a unified discipline that covers all programming languages l We cover the essential concepts and techniques in a uniform framework l Second-year university level: requires some programming experience and mathematics (sets, lists, functions) l The course covers four important themes: l Programming paradigms l Mathematical semantics of programming l Data abstraction l Concurrency l Let’s see how this works in practice Hundreds of programming languages are in use... So many, how can we understand them all? l Key insight: languages are based on paradigms, and there are many fewer paradigms than languages l We can understand many languages by learning few paradigms! What is a paradigm? l A programming paradigm is an approach to programming a computer based on a coherent set of principles or a mathematical theory l A program is written to solve problems l Any realistic program needs to solve different kinds of problems l Each kind of problem needs its own paradigm l So we need multiple paradigms and we need to combine them in the same program How can we study multiple paradigms? l How can we study multiple paradigms without studying multiple languages (since most languages only support one, or sometimes two paradigms)? l Each language has its own syntax, its own semantics, its own system, and its own quirks l We could pick three languages, like Java, Erlang, and Haskell, and structure our course around them l This would make the course complicated for no good reason -
The Machine That Builds Itself: How the Strengths of Lisp Family
Khomtchouk et al. OPINION NOTE The Machine that Builds Itself: How the Strengths of Lisp Family Languages Facilitate Building Complex and Flexible Bioinformatic Models Bohdan B. Khomtchouk1*, Edmund Weitz2 and Claes Wahlestedt1 *Correspondence: [email protected] Abstract 1Center for Therapeutic Innovation and Department of We address the need for expanding the presence of the Lisp family of Psychiatry and Behavioral programming languages in bioinformatics and computational biology research. Sciences, University of Miami Languages of this family, like Common Lisp, Scheme, or Clojure, facilitate the Miller School of Medicine, 1120 NW 14th ST, Miami, FL, USA creation of powerful and flexible software models that are required for complex 33136 and rapidly evolving domains like biology. We will point out several important key Full list of author information is features that distinguish languages of the Lisp family from other programming available at the end of the article languages and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSL): languages which are specialized to a particular area and thus not only facilitate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the “programmable programming language.” We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and AI research in bioinformatics and computational biology. -
15-150 Lectures 27 and 28: Imperative Programming
15-150 Lectures 27 and 28: Imperative Programming Lectures by Dan Licata April 24 and 26, 2012 In these lectures, we will show that imperative programming is a special case of functional programming. We will also investigate the relationship between imperative programming and par- allelism, and think about what happens when the two are combined. 1 Mutable Cells Functional programming is all about transforming data into new data. Imperative programming is all about updating and changing data. To get started with imperative programming, ML provides a type 'a ref representing mutable memory cells. This type is equipped with: • A constructor ref : 'a -> 'a ref. Evaluating ref v creates and returns a new memory cell containing the value v. Pattern-matching a cell with the pattern ref p gets the contents. • An operation := : 'a ref * 'a -> unit that updates the contents of a cell. For example: val account = ref 100 val (ref cur) = account val () = account := 400 val (ref cur) = account 1. In the first line, evaluating ref 100 creates a new memory cell containing the value 100, which we will write as a box: 100 and binds the variable account to this cell. 2. The next line pattern-matches account as ref cur, which binds cur to the value currently in the box, in this case 100. 3. The next line updates the box to contain the value 400. 4. The final line reads the current value in the box, in this case 400. 1 It's important to note that, with mutation, the same program can have different results if it is evaluated multiple times. -
Scripting: Higher- Level Programming for the 21St Century
. John K. Ousterhout Sun Microsystems Laboratories Scripting: Higher- Cybersquare Level Programming for the 21st Century Increases in computer speed and changes in the application mix are making scripting languages more and more important for the applications of the future. Scripting languages differ from system programming languages in that they are designed for “gluing” applications together. They use typeless approaches to achieve a higher level of programming and more rapid application development than system programming languages. or the past 15 years, a fundamental change has been ated with system programming languages and glued Foccurring in the way people write computer programs. together with scripting languages. However, several The change is a transition from system programming recent trends, such as faster machines, better script- languages such as C or C++ to scripting languages such ing languages, the increasing importance of graphical as Perl or Tcl. Although many people are participat- user interfaces (GUIs) and component architectures, ing in the change, few realize that the change is occur- and the growth of the Internet, have greatly expanded ring and even fewer know why it is happening. This the applicability of scripting languages. These trends article explains why scripting languages will handle will continue over the next decade, with more and many of the programming tasks in the next century more new applications written entirely in scripting better than system programming languages. languages and system programming -
Functional and Imperative Object-Oriented Programming in Theory and Practice
Uppsala universitet Inst. för informatik och media Functional and Imperative Object-Oriented Programming in Theory and Practice A Study of Online Discussions in the Programming Community Per Jernlund & Martin Stenberg Kurs: Examensarbete Nivå: C Termin: VT-19 Datum: 14-06-2019 Abstract Functional programming (FP) has progressively become more prevalent and techniques from the FP paradigm has been implemented in many different Imperative object-oriented programming (OOP) languages. However, there is no indication that OOP is going out of style. Nevertheless the increased popularity in FP has sparked new discussions across the Internet between the FP and OOP communities regarding a multitude of related aspects. These discussions could provide insights into the questions and challenges faced by programmers today. This thesis investigates these online discussions in a small and contemporary scale in order to identify the most discussed aspect of FP and OOP. Once identified the statements and claims made by various discussion participants were selected and compared to literature relating to the aspects and the theory behind the paradigms in order to determine whether there was any discrepancies between practitioners and theory. It was done in order to investigate whether the practitioners had different ideas in the form of best practices that could influence theories. The most discussed aspect within FP and OOP was immutability and state relating primarily to the aspects of concurrency and performance. This thesis presents a selection of representative quotes that illustrate the different points of view held by groups in the community and then addresses those claims by investigating what is said in literature. -
Functional and Logic Programming - Wolfgang Schreiner
COMPUTER SCIENCE AND ENGINEERING - Functional and Logic Programming - Wolfgang Schreiner FUNCTIONAL AND LOGIC PROGRAMMING Wolfgang Schreiner Research Institute for Symbolic Computation (RISC-Linz), Johannes Kepler University, A-4040 Linz, Austria, [email protected]. Keywords: declarative programming, mathematical functions, Haskell, ML, referential transparency, term reduction, strict evaluation, lazy evaluation, higher-order functions, program skeletons, program transformation, reasoning, polymorphism, functors, generic programming, parallel execution, logic formulas, Horn clauses, automated theorem proving, Prolog, SLD-resolution, unification, AND/OR tree, constraint solving, constraint logic programming, functional logic programming, natural language processing, databases, expert systems, computer algebra. Contents 1. Introduction 2. Functional Programming 2.1 Mathematical Foundations 2.2 Programming Model 2.3 Evaluation Strategies 2.4 Higher Order Functions 2.5 Parallel Execution 2.6 Type Systems 2.7 Implementation Issues 3. Logic Programming 3.1 Logical Foundations 3.2. Programming Model 3.3 Inference Strategy 3.4 Extra-Logical Features 3.5 Parallel Execution 4. Refinement and Convergence 4.1 Constraint Logic Programming 4.2 Functional Logic Programming 5. Impacts on Computer Science Glossary BibliographyUNESCO – EOLSS Summary SAMPLE CHAPTERS Most programming languages are models of the underlying machine, which has the advantage of a rather direct translation of a program statement to a sequence of machine instructions. Some languages, however, are based on models that are derived from mathematical theories, which has the advantages of a more concise description of a program and of a more natural form of reasoning and transformation. In functional languages, this basis is the concept of a mathematical function which maps a given argument values to some result value. -
Programming Language
Programming language A programming language is a formal language, which comprises a set of instructions that produce various kinds of output. Programming languages are used in computer programming to implement algorithms. Most programming languages consist of instructions for computers. There are programmable machines that use a set of specific instructions, rather than general programming languages. Early ones preceded the invention of the digital computer, the first probably being the automatic flute player described in the 9th century by the brothers Musa in Baghdad, during the Islamic Golden Age.[1] Since the early 1800s, programs have been used to direct the behavior of machines such as Jacquard looms, music boxes and player pianos.[2] The programs for these The source code for a simple computer program written in theC machines (such as a player piano's scrolls) did not programming language. When compiled and run, it will give the output "Hello, world!". produce different behavior in response to different inputs or conditions. Thousands of different programming languages have been created, and more are being created every year. Many programming languages are written in an imperative form (i.e., as a sequence of operations to perform) while other languages use the declarative form (i.e. the desired result is specified, not how to achieve it). The description of a programming language is usually split into the two components ofsyntax (form) and semantics (meaning). Some languages are defined by a specification document (for example, theC programming language is specified by an ISO Standard) while other languages (such as Perl) have a dominant implementation that is treated as a reference. -
Logic Programming Logic Department of Informatics Informatics of Department Based on INF 3110 – 2016 2
Logic Programming INF 3110 3110 INF Volker Stolz – 2016 [email protected] Department of Informatics – University of Oslo Based on slides by G. Schneider, A. Torjusen and Martin Giese, UiO. 1 Outline ◆ A bit of history ◆ Brief overview of the logical paradigm 3110 INF – ◆ Facts, rules, queries and unification 2016 ◆ Lists in Prolog ◆ Different views of a Prolog program 2 History of Logic Programming ◆ Origin in automated theorem proving ◆ Based on the syntax of first-order logic ◆ 1930s: “Computation as deduction” paradigm – K. Gödel 3110 INF & J. Herbrand – ◆ 1965: “A Machine-Oriented Logic Based on the Resolution 2016 Principle” – Robinson: Resolution, unification and a unification algorithm. • Possible to prove theorems of first-order logic ◆ Early seventies: Logic programs with a restricted form of resolution introduced by R. Kowalski • The proof process results in a satisfying substitution. • Certain logical formulas can be interpreted as programs 3 History of Logic Programming (cont.) ◆ Programming languages for natural language processing - A. Colmerauer & colleagues ◆ 1971–1973: Prolog - Kowalski and Colmerauer teams 3110 INF working together ◆ First implementation in Algol-W – Philippe Roussel – 2016 ◆ 1983: WAM, Warren Abstract Machine ◆ Influences of the paradigm: • Deductive databases (70’s) • Japanese Fifth Generation Project (1982-1991) • Constraint Logic Programming • Parts of Semantic Web reasoning • Inductive Logic Programming (machine learning) 4 Paradigms: Overview ◆ Procedural/imperative Programming • A program execution is regarded as a sequence of operations manipulating a set of registers (programmable calculator) 3110 INF ◆ Functional Programming • A program is regarded as a mathematical function – 2016 ◆ Object-Oriented Programming • A program execution is regarded as a physical model simulating a real or imaginary part of the world ◆ Constraint-Oriented/Declarative (Logic) Programming • A program is regarded as a set of equations ◆ Aspect-Oriented, Intensional, .. -
Multi-Paradigm Declarative Languages*
c Springer-Verlag In Proc. of the International Conference on Logic Programming, ICLP 2007. Springer LNCS 4670, pp. 45-75, 2007 Multi-paradigm Declarative Languages⋆ Michael Hanus Institut f¨ur Informatik, CAU Kiel, D-24098 Kiel, Germany. [email protected] Abstract. Declarative programming languages advocate a program- ming style expressing the properties of problems and their solutions rather than how to compute individual solutions. Depending on the un- derlying formalism to express such properties, one can distinguish differ- ent classes of declarative languages, like functional, logic, or constraint programming languages. This paper surveys approaches to combine these different classes into a single programming language. 1 Introduction Compared to traditional imperative languages, declarative programming lan- guages provide a higher and more abstract level of programming that leads to reliable and maintainable programs. This is mainly due to the fact that, in con- trast to imperative programming, one does not describe how to obtain a solution to a problem by performing a sequence of steps but what are the properties of the problem and the expected solutions. In order to define a concrete declarative language, one has to fix a base formalism that has a clear mathematical founda- tion as well as a reasonable execution model (since we consider a programming language rather than a specification language). Depending on such formalisms, the following important classes of declarative languages can be distinguished: – Functional languages: They are based on the lambda calculus and term rewriting. Programs consist of functions defined by equations that are used from left to right to evaluate expressions. -
Unit 2 — Imperative and Object-Oriented Paradigm
Programming Paradigms Unit 2 — Imperative and Object-oriented Paradigm J. Gamper Free University of Bozen-Bolzano Faculty of Computer Science IDSE PP 2018/19 Unit 2 – Imperative and Object-oriented Paradigm 1/38 Outline 1 Imperative Programming Paradigm 2 Abstract Data Types 3 Object-oriented Approach PP 2018/19 Unit 2 – Imperative and Object-oriented Paradigm 2/38 Imperative Programming Paradigm Outline 1 Imperative Programming Paradigm 2 Abstract Data Types 3 Object-oriented Approach PP 2018/19 Unit 2 – Imperative and Object-oriented Paradigm 3/38 Imperative Programming Paradigm Imperative Paradigm/1 The imperative paradigm is the oldest and most popular paradigm Based on the von Neumann architecture of computers Imperative programs define sequences of commands/statements for the computer that change a program state (i.e., set of variables) Commands are stored in memory and executed in the order found Commands retrieve data, perform a computation, and assign the result to a memory location Data ←→ Memory CPU (Data and Address Program) ←→ The hardware implementation of almost all Machine code computers is imperative 8B542408 83FA0077 06B80000 Machine code, which is native to the C9010000 008D0419 83FA0376 computer, and written in the imperative style B84AEBF1 5BC3 PP 2018/19 Unit 2 – Imperative and Object-oriented Paradigm 4/38 Imperative Programming Paradigm Imperative Paradigm/2 Central elements of imperative paradigm: Assigment statement: assigns values to memory locations and changes the current state of a program Variables refer