In this review we aim to arm the reader not with a comprehensive laundry list of relevant open source projects, but rather with a sense of how far open-source software has come in addressing needs in the bioinformatics arena that range from analysis algorithms and providing interfaces to end users, to toolkit libraries and to standards for interoperability and data dissemination. We select a few projects, primarily toolkit libraries that have had a significant impact on genomics science, to illustrate what open source projects have been able to achieve over the past few years, and what they could help to accomplish in the future. We also highlight the establishment of several standards for data exchange, and the utilization of these standards in research.