There is a crisis in scholarly publishing. The value of the scholarly information is frequently much less than the cost of providing that information. Consequently, libraries are suffering and scholars do not have access to information that they need. However, certain for-profit publishers and scientific societies are benefiting substantially from the current system. The Internet has demonstrated the potential to change this structure. The Budapest, Berlin and Bethesda initiatives show there is significant worldwide interest to replace the current controlled system with one that allows open access of scholarly information to anyone with Internet access. An examination of the scholarly publishing process is offered using a Tetradic Network Technique (TNT) and a Transaction Cost Economic (TCE) analysis as applied to a traditional subscription-based, print medical journal, Medical Physics, and a Web-based, open access medical journal, the Journal of Applied Clinical Medical Physics. The analysis identifies stakeholders and considers transaction and production costs. TCE analysis is performed between each of the following: Libraries, Scholars, Publishers and Societies, for a total of six transaction exchanges for both the traditional and the open access journal. This analysis allows costs to be compared more easily between the two types of journals, and provides the basis for a model online journal pro forma. Results demonstrate that while production costs remain approximately equivalent for the traditional and open access journal, total transaction costs are reduced by a factor of between 5 and 10 for the open access journal. While the cost of producing an eight-page article in a traditional medical journal is approximately US$2500, the cost of publishing the same article in an open access journal is less than US$500. Recommendations are offered that illustrate how an open access online journal may be produced by a university for approximately the cost of several library print journal subscriptions and physical storage of the printed material. Universities may therefore benefit through greater involvement with the scholarly publishing process. There are several considerations and recommendations that one may draw from this investigation. Universities pay for scholarly research, and then pay again to obtain access to published results. University libraries, always a significant cost center, are now in financial crisis. Scientific societies and large publishers gain under the traditional scholarly publication model. The copyright is essential; the one that holds the copyright holds the power in scholarly publishing. Modern open access initiatives state that scholars should retain copyright and publish online. Universities should require promotion and tenure committees to give equal weight to open access publications. Universities should go into the publishing business with scientific societies and control dissemination of scholarly knowledge for the public good.