The advent of new technologies and paradigms is constantly changing the landscape of scientific publications. The use of online journals is rapidly rising and most researchers prefer online materials to print. The Internet has also given rise to open-access, online-only publications. There are several advantages to such journals - most importantly, the articles published can become a starting point for online community-based discourse on the subject. Researchers, given the right web environment, can discuss the articles published online, and such collaboration on the World Wide Web is the hallmark of Web 2.0. Another emergent trend is Web 3.0, in which the web becomes the medium for data, information and knowledge exchange through the use of shared semantics. We have developed the Science Collaboration Framework (SCF), a lightweight software framework that scientific communities can use to create open-access, online, scientific publications. The software uses Web 3.0 technologies (social web, semantic web, text-mining) and thus allows interoperability with other Web 3.0 sites. The software allows communities to publish complex scientific articles, annotate them with controlled vocabularies or ontologies, register research interests of members and conduct discussion forums. The software can integrate with other knowledge repositories and the site knowledge is available as linked data. The software is modular, so different communities can install and enable different features as well as contribute modules back to the main framework; thus creating a software community as well. The first site based on our software, StemBook (, an online open access peer-reviewed collection of invited review chapters covering a range of topics related to stem cell biology, went "live" in September 2008. Several other sites are under development, including a new web community for Parkinson's disease researchers, PD Online, and a re-engineered version of the popular Alzheimer Disease research community Alzforum ( The sites developed on the SCF platform are interoperable with each other and with other sites on the Semantic Web. In this new paradigm, there is a significant reduction in artificial barriers between research disciplines, and a much more dynamic and agile approach to information exchange.