Flow chart of methods and data types.

For the ‘grounding’ stage of ASP, with the tool ‘gringo’, we use our rule based representation (logic program), the pathway relations and the appropriately encoded gene expression data sets (facts). Gringo, then produces all possible ground facts, which are then handled by the solver, ‘clasp’, which uses the logic program with the integrity constraints to find consistent ‘answer sets’. Finally, using our own custom made program for path searches, we process the answer sets to identify affected paths in the experiment using each differentially expressed or mutant gene as a starting point and longevity as the end point. These paths are split into primary or secondary effects using the information on the longevity phenotype, acquired by survival assays, complementary to each experiment.