This paper describes our experience using the HERMIT toolkit to apply well-known transformations to the internal core language of the Glasgow Haskell Compiler. HERMIT provides several mechanisms to support writing general-purpose transformations: a domain-specific language for strategic programming specialized to GHC’s core language, a library of primitive rewrites, and a shell-style–based scri...

UNLABELLED The Sun Grid Engine (SGE) high-performance computing batch queueing system is commonly used in bioinformatics analysis. Creating re-usable scripts for the SGE is a common challenge. The qsubsec template language and interpreter described here allow researchers to easily create generic template definitions that encapsulate a particular computational job, effectively separating the pro...

UNLABELLED There is a large amount of tools for interactive display of phylogenetic trees. However, there is a shortage of tools for the automation of tree rendering. Scripting phylogenetic graphics would enable the saving of graphical analyses involving numerous and complex tree handling operations and would allow the automation of repetitive tasks. ScripTree is a tool intended to fill this ga...

This paper presents Gamera, a new toolkit for the creation of domain-specific structured document recognition applications by domain experts with limited programming experience. The goal of the Gamera system is to leverage the user’s knowledge of the target documents to create custom applications rather than attempting to meet the needs of diverse users with a monolithic application. The system...

Ganga is a frontend for job definition and management in a distributed environment. It is being developed in the context of two high-energy physics experiments, ATLAS and LHCb, but is a component-based system that can readily be extended to meet the needs of other user communities. Ganga allows the user to specify the software to run, which may include user code, to set values for any configura...

SUMMARY simuPOP is a forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run ...

This paper describes our experience using the HERMIT toolkit to apply well-known transformations to the internal core language of the Glasgow Haskell Compiler. HERMIT provides several mechanisms to support writing general-purpose transformations: a domain-specific language for strategic programming specialized to GHC’s core language, a library of primitive rewrites, and a shell-style–based scri...

In this paper we describe JCLEC, a Java software system for the development of evolutionary computation applications. This system has been designed as a framework, applying design patterns to maximize its reusability and adaptability to new paradigms with a minimum of programming effort. JCLEC architecture comprises three main modules: the core contains all abstract type definitions and their i...

The jLab environment extends the potential of Java for scientific computing. It provides a Matlab/Scilab like scripting language that is executed by an interpreter implemented in the Java language. The scripting language supports the basic programming constructs with Matlab like matrix manipulation operators. The jLab "core" provides the general purpose functionality with an extensive set of bu...