MOTIVATION: Research on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. Here, we present Cyni, an open-source 'fill-in-the-algorithm' framework that provides common network inference functionality and user interface elements. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app. AVAILABILITY AND IMPLEMENTATION: Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store http://apps.cytoscape.org/apps/cynitoolbox CONTACT: [email protected].

A significant number of scientific and economic problems is characterised by a large number of interrelated variables. But with larger variable number, the domain under consideration may grow fast, so that analyses and reasoning become increasingly difficult. Graphical models allow to represent the combined distributions compactly and are suitable for dealing with uncertain and incomplete information. We describe their application to a problem of industrial planning. We also demonstrate how the iterative planning process can be supported by allowing the users to adapt the model using revision and updating operators. Moreover we discuss the problem of inconsistent inputs.