12th International Workshop on Constraint-Based Methods for Bioinformatics (WCB'16)

Toulouse, France, September 5 2016
Colocated jointly with CP 2016

Program (Download the proceedings)

View some picture of WCB'16...

B101 - Bosco building
Chair: Simon de Givry
  • Alessandro Dal Palù, Agostino Dovier, Andrea Formisano, Alberto Policriti, Enrico Pontelli.
    Logic Programming Applied to Genome Evolution in Cancer

  • Katinka Becker, Martin Gebser, Torsten Schaub and Alexander Bockmayr.
    Answer Set Programming for Logical Analysis of Data

Cafeteria - Lascrosses building
  • Coffee Break
B101 - Bosco building
Chair: Agostino Dovier
  • Louis Fippo Fitime, Olivier Roux, Carito Guziolowski and Loïc Paulevé.
    Identification of Bifurcations in Biological Regulatory Networks using Answer-Set Programming

  • Jean-Marc Alliot, Martín Diéguez and Luis Farinas del Cerro.
    Metabolic Pathways as Temporal Logic Programs

  • Martin Morterol, Philippe Dague, Sabine Peres and Laurent Simon.
    Minimality of Metabolic Flux Modes under Boolean Regulation Constraints

Cafeteria - Lascrosses building
  • Lunch Break
B101 - Bosco building
Chair: Alessandro Dal Palù
  • Clément Viricel, David Simoncini, Thomas Schiex and Sophie Barbe.
    Guaranteed Weighted Counting for Affinity Computation: beyond Determinism and Structure (CP2016 paper)

  • Maryana Wånggren, Martin Billeter, and Graham Kemp.
    Computational protein modelling based on limited sets of constraints

  • Ludwig Krippahl and Pedro Barahona.
    Improving protein docking with redundancy constraints (CP2016 paper)

Cafeteria - Lascrosses building
  • Coffee Break
B101 - Bosco building
Chair: Matthias Zytnicki
  • Sebastien François, Rumen Andonov, Hristo Djidjev and Dominique Lavenier.
    Global Optimization Methods for Genome Scaffolding

  • Eric Bourreau, Annie Chateau, Clément Dallard and Rodolphe Giroudeau.
    A Graph Constraints Formulation for Contigs Scaffolding

  • WCB16 Concluding Remarks

Workshop Overview

During the last years, Biology has 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. Successful approaches to these problems are likely to have significant applications in several fields of research, such as medicine, agriculture, industry, etc. Several successful applications of the Logic and Constraint Programming paradigms in Bioinformatics have 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 researchers and collecting, if possible, new problems to be faced in the next future by our community.

Paper Submissions

The topic of interest are all those concerning bioinformatics and constraints and related (SAT/ASP/Logic Programming/Integer Linear Programming) techniques, such as:

  • RNA prediction and motif search
  • protein structure and functional prediction
  • genetic linkage analysis and haplotype inference
  • pedigree reconstruction and diagnosis
  • genomic selection design
  • gene regulatory network inference and analysis
  • biochemical network simulation and visualization
  • solvers for problems in biology
  • metabolic pathway analysis
  • DNA sequence assembly
  • contig scaffolding
  • multiple sequence alignment
  • machine learning and big data
  • ontologies in biology
  • constraint databases in bioinformatics
  • logical interfaces to relational biological databases
  • web bioinformatics services

Submitted papers can be:

  • Full papers describing new research results
  • 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 3-15 pages long in the LNCS format. Authors of accepted papers must provide camera-­ready versions in PDF format. Furthermore, at least one author of each accepted paper must attend the conference to present the contribution. All WCB'16 participants have to register for the CP 2016 workshop/conference.

Submissions via EasyChair (closed since July 19, 2016).

Important Dates

  • July 2016
  • Submission

    July 19, 2016

  • Notification of authors

    July 29, 2016

  • August 2016
  • Camera ready version

    August 16, 2016

  • September 2016
  • Constraint-Based Methods for Bioinformatics Workshop

    September 5, 2016

Workshop Organizers

Program Committee


New A CP 2016 Google photo album is available

(since September 12, 2016)

Proceedings & Slides

(since September 6, 2016)

CP 2016 Accepted Papers

(since June 7, 2016)