ABPL

Abstract

Computer analysis of biological systems, using approaches such as metabolic control analysis is common. A typical example is a language like Herbert Sauro's SCAMP (Sauro & Fell, 1991), which allows simulations of enzyme systems, and calculation of control coefficients and elasticities. However such systems are motivated by the underlying biochemical theory and often have limitations as programming languages which mean that they can only be applied to particular classes of problems.

ABPL (a biochemical programming language) extends these ideas by adding all the facilities of a fully-fledged programming language, together with some of the capabilities of a modern computer algebra system. Syntactically it derives from the programming language LISP, while the underlying functionality is that of iMAP, the successor to SCAMP.

This provides us with a computer system capable of performing most of the tasks undertaken by existing packages, but more importantly, a system which can be easily extended into new areas.

Key features of the work are:

• - Ability to use the language both interactively and as a batch programming language

• - Ability to work both symbolically and numerically

• - Ability to handle matrices and vectors

• - Ability to define and manipulate reaction schemes

• - Common techniques are built in to the language

• - Ability to add new operations to the language

The implementation is in ANSI standard C for portability.