The Machine that Builds Itself: How the Strengths of Lisp Family Languages Facilitate Building Complex and Flexible Bioinformatic Models

TL;DR

This paper advocates for the use of Lisp family languages in bioinformatics, highlighting their features that enable the development of complex, flexible models and domain-specific languages to advance AI and machine learning in biology.

Contribution

It demonstrates how Lisp languages facilitate building sophisticated bioinformatics models and domain-specific languages, enhancing research productivity and standards in the field.

Findings

Lisp languages support the creation of flexible bioinformatics models.

Lisp enables development of domain-specific languages for biology.

Lisp's features improve AI and machine learning applications in bioinformatics.

Abstract

We address the need for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Languages of this family, like Common Lisp, Scheme, or Clojure, facilitate the creation of powerful and flexible software models that are 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 (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.