The research environment of scholars is increasingly web-based. This makes it urgent to study the effects of moving to the Web on research practices, scholarly output and innovation. We propose a theoretical framework and a methodology to study these effects. In a pilot study, we apply theory and method on an online community in biodiversity research, to demonstrate the feasibility of the approach. We also indicate the practical relevance of this kind of analysis for improving the quality of virtual research environments. In the last section, directions for further research are suggested. © Daphne Duin, Peter van den Besselaar.