Modeling Bioinformatics with Logic Programming.

Enrico Pontelli (NMSU) and Agostino Dovier (UNIUD)


In this lectures we provide a broad overview of how logic programming, and more specifically Answer Set Programming, can be used to model and solve some popular and challenging classes of problems in the general domain of bioinformatics. In particular, the chapter explores the use of ASP in Genomics studies, such as Haplotype inference and Phylogenetic inference, in Structural studies, such as RNA secondary structure prediction and Protein structure prediction, and in Systems Biology.

The course offers a brief introduction to logic programming as well as to biology and bioinformatics and provides working ASP code fragments for the various problems investigated.

Program and material

  1. 06/11/2015. 2 hours. Introduction to AI, KR, LP and to the use of Benchmarks in the AI community. LUCIDI
  2. 13/11/2015. 2 hours. Syntax and (a bit of) semantics of Logic Programming. LUCIDI
  3. 20/11/2015. 2 hours. Herbrand Models. Minimimum, minimal, and stable models. The language ASP. Syntactic extensions. LUCIDI
  4. 04/12/2015. 2 hours. Modeling with ASP. N-Queens, Magic Square, ``capra e cavolo'', the 3 barrels. LUCIDI
  5. 11/12/2015. 2 hours. Modeling with ASP. Hanoi's tower, Sam Lloyd's puzzle, Hamming codes, Sudoku, Scheduling (a fussball tournament) LUCIDI
  6. 21/12/2015. 10:00-12:30. Introduction to Bioinformatics. Modeling: Haplotype Inference Philogenetics trees
  7. 21/12/2015. 14:00-16:30. Modeling: RNA Secondary structure prediction Protein Structure Prediction Structure Some simple systems Biology modelings.
  8. 22/12/2015. 10:00-12:30. A complete (logic programming) system for Phylogenetics
  9. 22/12/2015. 14:00-16:30. A tour on parallelism and Logic Programming
For other material and software related questions, see also HERE.