Bringing LTL Model Checking to Biologists

  • Zara Ahmed ,
  • David Benque ,
  • Sergey Berezin ,
  • Jasmin Fisher ,
  • Anna Caroline E. Dahl ,
  • Benjamin A. Hall ,
  • Samin Ishtiaq ,
  • Jay Nanavati ,
  • Nir Piterman ,
  • Maik Riechert ,
  • Nikita Skoblov

Verification, Model Checking and Abstract Interpretation (VMCAI) |

Published by Springer

The BioModelAnalyzer (BMA) is a web based tool for the development of discrete models of biological systems. Through a graphicaluser interface, it allows rapid development of complex models of gene and protein interaction networks and stability analysis without requiring users to be proficient computer programmers. Whilst stability is a useful specification for testing many systems, testing temporal specifications in BMA presently requires the user to perform simulations. Here we describe the LTL module, which includes a graphical and natural language interfaces to testing LTL queries. The graphical interface allows for graphical construction of the queries and presents results visually in keeping with the current style of BMA. The Natural language interface complements the graphical interface by allowing a gentler introduction to formal logic and exposing educational resources.