The 19th International Conference on
Principles and Practice of
Constraint Programming
Uppsala, Sweden
September 16-20, 2013

WCB 2013 - Workshop on Constraint-Based-Methods for Bioinformatics

During the last years, Biology become a source of challenging problems for the entire field of Computer Science in general, and for the areas of computational logic and constraint programming in particular. A successful approach for any of these problems is expected to have significant applications in several fields of research, such as medicine, agriculture, industry, etc. Several successful applications of Constraint Programming in Bioinformatics has been carried out in the last years, in the area of phylogenetic tree reconstruction, in haplotype inference, in proteins structure prediction, in RNA secondary structure prediction, and in system biology, just to cite a few. The workshop aims at exchanging ideas between researcher and collecting, if possible, new problems to be faced in the next future by our community.

WCB'13 is the 9-th of a series of consecutive Workshop on Constraint Based Methods for Bioinformatics. Previous editions of WCB were co-located with various important international conferences, as reported below:

  • WCB'05: co-located with ICLP-CP 2005 in Sitges;
  • WCB'06: co-located with CP 2006 in Nantes;
  • WCB'07: co-located with ICLP 2007 in Porto;
  • WCB'08: co-located with CPAIOR 2008 in Paris;
  • WCB'09: co-located with CP 2009 in Lisbon;
  • WCB'10: co-located with FLOC 2010 in Edinburgh.
  • WCB'11: co-located with CP 2011 in Perugia.
  • WCB'12: co-located with ICLP 2012 in Budapest.

Details about WCB'12 can be found at
From this site one can easily reach the web sites of previous editions of the workshop. Moreover, two preliminary editions with slightly different names were organized at CP 1997, and CP 1998, and the topic was one of the selected arguments of the CP summer school in 2012 in Wroclaw.



  • 9:00-10:00 INVITED TALK

    Peter Stuckey: "What is the minimal dictionary of protein substructures of which all known proteins are made?"
    (joint work with Arun Konagurthu, Arthur M. Lesk, David Abramson, and Lloyd Allison)

  • 10:00-10:30. SESSION 1

    Laszlo David and Alexander Bockmayr :
    Constrained Flux Coupling Analysis
  • 10.30-11.00 Coffee Break

  • 11.00-12.30 SESSION 2

    Akihiro Kishimoto and Radu Marinescu:
    Recursive Best-First AND/OR Search with Overestimation for Genetic Linkage Analysis

    Jean-Michel Elsen, Simon de Givry, Felicien Shumbusho and
    George Katsirelos:
    Optimizing the reference population in a genomic selection design

    Ferdinando Fioretto and Enrico Pontelli:
    Community-based Gene Regulatory Network Inference with Constraint Programming

  • 12.30-14.00 Lunch Break

  • 14.00-15.30 SESSION 3

    Steven Gay, Fran├žois Fages, Francesco Santini and Sylvain Soliman:
    Solving Subgraph Epimorphism Problems using CLP and SAT

    Sylvain Soliman, Fran├žois Fages and Ovidiu Radulescu
    A Constraint Solving Approach to Tropical Equilibration and Model Reduction

    David Lesaint, Deepak Mehta and Barry O'Sullivan:
    Soft Pattern Discovery in Pre-Classified Protein Families

  • 15.30-16-00 Coffee Break

  • 16.00-17.00 SESSION 4

    Alexander Bau, Johannes Waldmann and Sebastian Will:
    RNA Design by Program Inversion via SAT Solving

    Martin Mann and Bernhard Thiel:
    Kelkule structure enumeration yields unique SMILES

  • 17.00 - 18.00 Panel (What are we doing in our groups?
    And about projects?) 5/10 minutes x participant


The topic of interest are all those concerning bioinformatics and constraints and related techniques. Submitted papers can be:

  • Extended Abstracts concerning original (unpublished) results.
  • Abstracts describing ongoing work.
  • System descriptions (with demos at the workshop).
  • Summaries of already accepted or recently published papers/results.
  • Well-motivated proposals of bioinformatics problems for constraint based methods.

Submitted papers should be 6-8 pages papers in LNCS format. For each contribution we plan to have (at least) 3 reviews.

Important dates

  • Submission Deadline: June 15th
  • Notification to Authors: July 30th
  • Final version: September 1st
  • Workshop: September 16th

Submissions are managed through EasyChair

After past editions of WCB, selections of (improved versions of) the contributions were included (after a further reviewing process) in a special issues of Constraint (13, 2008), and as special track in Algorithms for Molecular Biology journal, 2012.

PC members

  • Nicos Angelopoulos
  • Rolf Backofen
  • Pedro Barahona
  • Alexander Bockmayr
  • Alessandro Dal Palu' (co-chair)
  • Simon De Givry
  • Agostino Dovier (co-chair)
  • Francois Fages
  • Ines Lynce
  • Enrico Pontelli
  • Thomas Schiex
  • Sven Thiele
  • Pascal van Hentenryck
  • Sebastian Will