title: The Cyni framework for network inference in Cytoscape.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store http://apps.cytoscape.org/apps/cynitoolbox
  
  
  BACKGROUND
  benno.schwikowski@pasteur.fr.
authors.affiliation: Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Oriol
authors.initials: O
authors.lastname: Guitart-Pla
authors.affiliation: Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Manjunath
authors.initials: M
authors.lastname: Kustagi
authors.affiliation: Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Frank
authors.initials: F
authors.lastname: Rügheimer
authors.affiliation: Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Califano
authors.affiliation: Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Benno
authors.initials: B
authors.lastname: Schwikowski
mesh_terms: D000465:Algorithms; D053263:Gene Regulatory Networks; D012984:Software