title: CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.
abstract: BACKGROUND
  Qualitative reasoning frameworks, such as the Sign Consistency Model (SCM), enable modelling regulatory networks to check whether observed behaviour can be explained or if unobserved behaviour can be predicted. The BioASP software collection offers ideal tools for such analyses. Additionally, the Cytoscape platform can offer extensive functionality and visualisation capabilities. However, specialist programming knowledge is required to use BioASP and no methods exist to integrate both of these software platforms effectively.
  
  
  RESULTS
  We report the implementation of CytoASP, an app that allows the use of BioASP for influence graph consistency checking, prediction and repair operations through Cytoscape. While offering inherent benefits over traditional approaches using BioASP, it provides additional advantages such as customised visualisation of predictions and repairs, as well as the ability to analyse multiple networks in parallel, exploiting multi-core architecture. We demonstrate its usage in a case study of a yeast genetic network, and highlight its capabilities in reasoning over regulatory networks.
  
  
  CONCLUSIONS
  We have presented a user-friendly Cytoscape app for the analysis of regulatory networks using BioASP. It allows easy integration of qualitative modelling, combining the functionality of BioASP with the visualisation and processing capability in Cytoscape, and thereby greatly simplifying qualitative network modelling, promoting its use in relevant projects.
authors.affiliation: Department of Informatics, King's College London, Strand, London, WC2R 2LS, UK. akittas@gmail.com.
authors.forename: Aristotelis
authors.initials: A
authors.lastname: Kittas
authors.affiliation: Department of Informatics, King's College London, Strand, London, WC2R 2LS, UK. abarozet@gmail.com.
authors.forename: Amélie
authors.initials: A
authors.lastname: Barozet
authors.affiliation: Department of Medical Oncology, NCT, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany. jekaterina.sirjajeva@gmx.de.
authors.forename: Jekaterina
authors.initials: J
authors.lastname: Sereshti
authors.affiliation: Department of Medical Oncology, NCT, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany. niels.grabe@bioquant.uni-heidelberg.de.
authors.forename: Niels
authors.initials: N
authors.lastname: Grabe
authors.affiliation: Department of Informatics, King's College London, Strand, London, WC2R 2LS, UK. sophia.tsoka@kcl.ac.uk.
authors.forename: Sophia
authors.initials: S
authors.lastname: Tsoka
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D053263:Gene Regulatory Networks; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software