This paper introduces eResearch workflow tools as a model for the research community studying free and open source software and its development. The paper first introduces eResearch as increasingly practiced in fields such as astrophysics and biology, then contrasts the practice of research on free and open source software. After outlining suitable research data sets the paper introduces a class of tools known as scientific workflow frameworks, focusing on one "Taverna" and introducing its features. To further explain the tool a complete workflow used for original research on FLOSS is described. Finally the paper considers the trade-offs inherent in these tools.