A Scientific Software Product Line for the Bioinformatics domain

Area of Science:

• Bioinformatics
• Computational Biology
• Software Engineering

Background:

• Specialized users like scientists often lack software development expertise.
• Software Product Lines (SPL) facilitate software development through artifact reuse.
• Developing collections of related bioinformatics applications can benefit from an SPL approach.

Purpose of the Study:

• Introduce the PL-Science approach, integrating SPL and ontologies for scientific experiments and bioinformatics workflows.
• Utilize ontologies to enable SPL application within biological domains.
• Assist scientists in defining experiments and specifying associated bioinformatics workflows.

Main Methods:

• Scientific Software Product Line (SSPL) utilizes an abstract scientific workflow model tailored to specific domains.
• This abstract model allows for the instantiation of scientific applications and algorithms.
• Ontologies serve as knowledge representation models for domain restrictions and semantic enrichment.

Main Results:

• Ontologies facilitate the selection and organization of bioinformatics workflows within an SSPL.
• Ontologies enable the expression and inference of formal restrictions crucial for scientific domains.
• The PL-Science approach provides a structured methodology and infrastructure for developing scientific software.

Conclusions:

• The PL-Science approach, combining SPL and ontologies, offers a robust framework for bioinformatics application development.
• Case studies in bioinformatics conducted at Brazilian research institutions demonstrate the approach's evaluation.
• This approach enhances the ability of scientists to manage and develop complex bioinformatics workflows.