An Open Framework for Extensible Multi-Stage Bioinformatics Software
This addresses the problem of software inflexibility for bioinformatics researchers and developers, though it is incremental as it builds on existing programming paradigms.
The paper tackles the challenge of balancing customizability and performance in bioinformatics software by introducing Friedrich, a framework based on Scala that supports both experimentation and batch processing, demonstrated through a basic genome assembler case study.
In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance. Performance-sensitive tools are often highly monolithic, which can make research difficult. We present a novel set of software development principles and a bioinformatics framework, Friedrich, which is currently in early development. Friedrich applications support both early stage experimentation and late stage batch processing, since they simultaneously allow for good performance and a high degree of flexibility and customisability. These benefits are obtained in large part by basing Friedrich on the multiparadigm programming language Scala. We present a case study in the form of a basic genome assembler and its extension with new functionality. Our architecture has the potential to greatly increase the overall productivity of software developers and researchers in bioinformatics.