Lisp Family Research Articles

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming 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 (DSLs): languages that 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 artificial intelligence research in bioinformatics and computational biology.

XML Applications Development in Scheme

Representation and processing of XML data in Scheme are considered. Scheme is a functional programming language belonging to the LISP family. The SXML specification is discussed, which defines methods for representing XML data in the form of S-expressions in Scheme. Possibilities of extending this specification are considered. Methods of parsing and representing XML data are analyzed, possibilities of applying Scheme to the development of XML applications are discussed, and a survey of the relevant literature is given. Functional methods for processing semistructured data are discussed, and examples of using Scheme for processing SXML data are given. Methods for extracting a schema of semistructured data (DataGuide) and application of those methods are considered, and functional algorithms for the construction of DataGuide are proposed.

The Java syntactic extender (JSE)

The ability to extend a language with new syntactic forms is a powerful tool. A sufficiently flexible macro system allows programmers to build from a common base towards a language designed specifically for their problem domain. However, macro facilities that are integrated, capable, and at the same time simple enough to be widely used have been limited to the Lisp family of languages to date. In this paper we introduce a macro facility, called the Java Syntactic Extender (JSE), with the superior power and ease of use of Lisp macro sytems, but for Java, a language with a more conventional algebraic syntax. The design is based on the Dylan macro system, but exploits Java's compilation model to offer a full procedural macro engine. In other words, syntax expanders may be implemented in, and so use all the facilities of, the full Java language

Programming World Wide Web pages in scheme

In this paper we will argue that pages on the World Wide Web can be made directly as programs in a functional programming language instead of through HTML or an HTML-based authoring tool. We use the Scheme programming language from the Lisp family for WWW page production. It is concluded that a Lisp language is an attractive direct vehicle for authoring of Internet material in the sense that the source of a WWW document becomes a Lisp program. Abstraction from details in the underlying markup language constitutes the main advantage in our approach. This is consistent with the expected advantage of introducing XML as a successor of HTML. In addition we find it useful to have the power of a high quality programming language available for automation of routine tasks during the authoring process.

(algorithms)

I have not been deluged with submissions for this column. I've gotten a few, but not enough to make it easy to put out another issue each quarter. Let me therefore repeat my charter: The (algorithms) department consists of articles that fit into one or more of three broad categories: • Annotated implementations of interesting and relevant algorithms; they should make particularly good or novel use of the unique features of the Lisp family of programming languages (e.g., closures, continuations, code as data, polymorphism), • Annotated implementations of algorithms whose subject matter is the Lisp family of languages (e.g., code analysis tools, iteration facilities, generic arithmetic), and • Discussion of performance issues, bench-marking, or implementation experiences for interesting algorithms written in or about the Lisp family of languages.

(algorithms)

Welcome to the first appearance of this new Lisp Pointers department on Algorithms. It has been noted by some editors that most Lisp hackers would rather write code than articles and I suspect that their reading preferences might run the same way. This department is an attempt to cater to those preferences. The articles you'll see here will tend to fit into one or more of three broad categories: • Annotated implementations of interesting and relevant algorithms that make particularly good or novel use of the unique features of the Lisp family of programming languages (e.g., closures, continuations, code as data, polymorphism). • Annotated implementations of algorithms whose subject matter is the Lisp family of languages (e.g., code analysis tools, iteration facilities, generic arithmetic), and • Discussion of performance issues, benchmarking, or implementation experiences for interesting algorithms written in or about the Lisp family of languages.