The number of web services, applications, data sources and scripts available to biomedical researchers increases day by day. Complex analysis, annotation, and data integration could potentially be orchestrated from these services, if only they could be seamlessly connected. Biomedical researchers often do not have the time or expertise required to download, install, and adapt these tools, nor would the input and output formats required make this adoption easy. In this short paper, we provide a preview of the challenges that biomedical applications present to the use of web services, and explore existing workflow definition frameworks for web service orchestration. We conclude that the current offering of support software for this task is not at the level to be desired to provide a viable answer to the challenges of orchestrating complex service-based biomedical applications, but the benefits to be gained from such support invites further systematic research in this area.