5th International Workshop on Interactions between Computer Science and Biology


Half-day tutorial on Hypernetworks



The 5th edition of the CS2Bio workshop will take place on June 6, 2014 at the Technical University of Berlin as a DisCoTec 2014-affiliated  workshop. This follows the tradition of the previous installements of the workshop, that were organized as satellite events of DisCoTec.

NEW: CS2Bio 2014 also organizes a half-day tutorial on Saturday, June 7, 2014, given by Jeffrey Johnson on “Hypernetworks“.

Invited speakers

Vincent Danos, University of Edinburgh, UK“Formal mean field theories for graph-rewriting


We join ideas from two scientific traditions not seen together often: 1) graph transformation systems (GTS) stemming off of concurrency and formal language theories, and 2) mean field approximations (MFA), a group of techniques used to great effect in statistical physics to obtain simplified descriptions of complex dynamics. When the dynamics of interest is underpinned by a graph transformation system (GTS), we show how to build the associated mean field machinery. Our construction has a number of interesting features. First, it separates clearly the algebraic aspects of MFAs from the difficult questions of their soundness. Second, it completely encapsulates the combinatorics involved in the generation of MFAs. Third, it can be automated so that the order of the approximation is no longer limited to the humanly computable. Last, arguments are couched in terms of axiomatic graph rewriting. And thus, even though we nominally treat only the case of typed directed multi-graphs, the scope of our construction includes a wide range of dynamics on graph-like structures such as hypergraph rewriting.


Marco Pettini, Université D’Aix Marseille, France. “Long-range electrodynamical interactions among biomolecules and prospective applications on biocomputers”


From the physics point of view, the most striking and challenging problem arising from molecular biology stems from the observation that biochemical reactions – which commonly involves a huge number of actors – are coordinated simultaneously to be achieved in due time, thus granting the reality of well organized dynamic systems. The spatial dimensions of these systems are much larger than the “action radii” of chemical reactions, of electrostatic and quasi-electrostatic interactions (which are strongly shielded both by the large static value of water dielectric constant and by freely moving ions), and of van der Waals-London dispersion interactions. Yet the interactions between cognate molecular partners in living matter (eg, nucleic acids and transacting nuclear proteins; cytoskeleton and signaling membrane proteins, etc..) produce a highly specific and efficient spatial-temporal biochemical pattern of encounters, which can hardly be explained by taking into account random diffusion only.

The present talk introduces the problem and discuss how experimentally verify or refute the following working hypothesis: the encounters of distant cognate partners of biomolecular reactions are actively driven by selective (resonant) attractive forces of electrodynamic nature. This will be achieved by means of an interdisciplinary approach involving theoretical and experimental physics, molecular biology, biochemistry, and computer modelling and simulation. The implications of an experimental confirmation of the actual activation of electrodynamic interactions among biomolecules could have a revolutionary impact on our understanding of the functioning of the molecular machinery at work in living matter. This would open new avenues of fundamental research in biophysics and this could be of great prospective on the biomedical side (such as the fight against cancer) and, also, on the fast-growing field of research on biocomputers; “wet computing”; giving a glimpse of possible future scenarios of computer hardware beyond the present silicon-bound reality.


Roberto Barbuti, University of Pisa, Italy. “Using P Systems for Modelling the Dynamics of Hybridogenetic Water Frog Populations”


Some species of European water frogs originated from hybridization between different species. Such hybrid populations have a particular reproduction system called hybridogenesis. In this paper we consider the two species Pelophylax ridibundus and Pelophylax lessonae, and their hybrids Pelophylax esculentus. P. lessonae and P. esculentus form stable complexes (L-E complexes) in which P. esculentus are hemiclonal. In L-E complexes all the transmitted genomes by P. esculentus carry deleterious mutations which are lethal in homozygosity.
We analyze, by means of a P System model, L-E complexes. The results of simulations show that, by eliminating deleterious mutations, L-E complexes collapse. In addition, simulations show that particular female preferences can contribute to the diffusion of deleterious mutations among all P. esculentus frogs. Finally, simulations show how L-E complexes react to the introduction of translocated P. ridibundus.
The model allows us to conclude: (i) deleterious mutations (combined with sexual preferences) strongly contribute to the stability of L-E complexes; (ii) female sexual choice can contribute to the diffusion of deleterious mutations; and (iii) the introduction of P. ridibundus can destabilize L-E complexes.


 9:30 – 10:30 Invited talk

Marco Pettini

Long-range electrodynamical interactions among biomolecules and prospective applications on biocomputers

 10:30 – 11:00 Coffee

11:00 – 11:30 Regular paper

Matej Klement, Tadeas Ded, David Safranek, Jan Cerveny, Stefan Mueller and Ralf Steuer

Biochemical Space: A Framework for Systemic Annotation of Biological Models

 11:30 – 12:30 Invited talk

Vincent Danos

Formal mean field theories for graph-rewriting

 12:30 – 14:00 Lunch

14:00 – 15:30 Regular papers

Thiago Lipinski-Paes and Osmar Norberto de Souza

MASTERS: A general sequence-based MultiAgent System for protein TERtiary Structure prediction

Olga Hrydziuszko, Artur Wrona, Joanna Balbus and Krystian Kubica.

Mathematical two-compartment model of human cholesterol transport in application to high blood cholesterol diagnosis and treatment

Matteo Rucco, Jacopo Binchi, Emanuela Merelli, Giovanni Petri and Francesco Vaccarino

jHoles: a tool for understanding biological complex networks via clique weight rank persistent homology

15:30 – 16:00 Project dissemination

Eduardo Hermo Reyes and Joost Joosten

The Selfish Algorithm

Emanuela Merelli

TOPDRIM: Topology Driven Methods for Complex Systems

 16:00 – 16:30 Coffee

16:30 – 17:30 Invited talk

Roberto Barbuti

Using P Systems for Modelling the Dynamics of Hybridogenetic Water Frog Populations


As it was the case for the previous editions of the workshop, the proceedings are planned to be published in Elsevier ENTCS. We plan to make accepted papers available online before the workshop. A special issue of Theoretical Computer Science, based on this workshop, is also planned.

Important dates

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Call for papers

The aim of this workshop is to gather researchers in formal methods that are interested in the convergence of Computer Science, Biology and the Life Sciences. In particular, in this 5th edition, we solicit the contribution of original results, from any research areas, such as Mathematics, Physics, Complex Systems, and Computational Science that address both theoretical aspects of modelling and applied work on the comprehension of biological behaviour. Furthermore, to facilitate the integration of different research areas we encourage the presentation of main objectives and preliminary results of active projects on the CS2Bio topics conducted by interdisciplinary teams.

Papers selected for presentation at CS2Bio should either present the modelling of a specific biological phenomenon using formal techniques, or a modelling, simulation, testing or verification approach in computer science that leads to a novel and promising application to a range of biological or medical systems. In the latter case, some emphasis on the scope and scalability of the approach will be required. The workshop intends to attract researchers interested in models, verification, tools, and programming
primitives concerning the complex interactions encountered. In general, topics of interest include, but are not limited to:

Formal Biological Modelling

  •  Formal methods for the representation of biological systems and their dynamics;
  •  Theoretical links and comparison between different formal models for the modelling of biological processes;
  •  Quantitative (probabilistic, timed, stochastic, etc.) languages and calculi.
  •  Spatial (geometrical, topological) languages and calculi.
  •  Prediction of biological behaviour from incomplete information;
  •  Model checking, abstract interpretation, type systems, etc.

Novel Computational Paradigms for Understanding Biological Complex Systems

  •  Quantum information and life sciences;
  •  Computational topology and biomathematics;
  •  Information processing and biomedicine;
  •  Statistical mechanics and biophysics.
  •  Complex Networks and biomolecular dynamics

Tools and Simulation

  •  Modelling, analysis and simulation tools for systems biology;
  •  Emergence of properties in complex biological and medical systems;
  •  Tools for parallel, distributed, and multi-resolution simulation methods;
  •  Detailed biological case-studies.

Solicited Contributions:
We solicit three kinds of contributions:

  •  Regular papers: must report previously unpublished work and not be submitted concurrently to another conference with refereed proceedings (limited to 14 pages).
  •  Tool presentations: describing new tools or platforms for the modelling of biological systems (limited to 14 pages).
  •  Dissemination of project results: concern recent or ongoing work on topics relevant to CS2Bio and are intended to provide discussion and stimulate feedback during the workshop. The focus of a dissemination should be put on the main objectives and preliminary results of active projects on topics relevant to the workshop. There are no restrictions about previous or future publication of the contents of a dissemination, it could also be based on a recently published paper or on a work which has not yet been submitted (limited to 4 pages).

Selection Procedure:

Each submitted contribution will have at least three anonymous reviewers. The final decision about the received papers will be taken by the PC chairs based on the opinion of the reviewers. Controversial papers will be debated within the PC. Authors should submit their contributions via EasyChair (https://www.easychair.org/conferences/?conf=cs2bio) in the form of a pdf file compiled using the ENTCS style for the workshop proceedings (http://www.entcs.org/files/cs2bio/prentcsmacro.sty). If necessary, detailed proofs or other additional material can be added in an appendix (referees might review it at their discretion).

Programme committee

  • Luca Cardelli, Microsoft Research, UK
  • Erik de Vink, Technische Universiteit Eindhoven, the Netherlands
  • François Fages, INRIA Rocquencourt, France
  • Paola Giannini, Università del Piemonte Orientale, Italy
  • Radu Grosu, Stony Brook University, USA
  • Russ Harmer, CNRS & ENS Lyon, France
  • Jean Krivine, CNRS & Paris Diderot University, France
  • Pietro Lio, University of Cambridge, UK
  • Emanuela Merelli, University of Camerino, Italy (co-chair)
  • Ion Petre, Åbo Akademi University, Finland (co-chair)
  • Ovidiu Radulescu, University of Montpellier 2, France
  • David Safranek, Masaryk University, Czech Republic
  • Angelo Troina, Università di Torino, Italy
  • Verena Wolf, Saarland University, Germany


Emanuela Merelli,University of Camerino, Italy.

Ion Petre, Åbo Akademi University, Finland.


  • Registration fee for participants to CS2Bio only: 100 EURO (early); 120 EURO (late); 140 EURO (onsite)
  • Registration fee for participants to the DisCoTec 2014 conference: 80 EURO (early); 100 (late); 120 EURO (onsite)

Previous editions


Technical University of Berlin , affiliated with DisCoTec 2014.


  • Workshop day today!
    Welcome to 5th International Workshop on Interactions between Computer Science and Biology! We have a highly interesting day of talks today, followed by a tutorial tomorrow.


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  • Emanuela Merelli, University of Camerino, Italy, emanuela.merelli 'at' unicam.it.
  • Ion Petre, Åbo Akademi University, Finland, ipetre 'at' abo.fi.


Topology Driven Methods
for Complex Systems