Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13), Florence, Italy, 6 June 2013

Abstract

This ENTCS volume contains the post-proceedings of the Fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio’13) held in Florence on the 6th of June 2013. This workshop was organized as an affiliated event of the eighth International Federated Conferences on Distributed Computing Techniques (DisCoTec 2013). For the fourth edition of CS2Bio, the program consisted of two invited lectures by Giuseppe Longo (ENS Paris, France) and Mario Rasetti (ISI Foundation, Italy) complemented by eight technical contributions (five regular papers and three tool presentations), with an accompanying paper in this proceedings, and five short presentations as disseminations of projects results. In line with the theme of the workshop the presentations addressed topics in the area of formal languages and methods for the representation of biological systems and their dynamics, and of analysis and simulation approaches to biological case-studies. Moreover, in this CS2Bio edition, novel computational paradigms for understanding biological com- plex systems where addressed, as Quantum information and life sciences; Geometry, algebraic and computational topology and biomathematics; Information processing and biomedicine; Statistical mechanics and biophysics. In his invited talk Giuseppe Longo spoke about randomness, variability and di- versity in biological dynamics. The dynamic instability of living systems and the superposition of different forms of randomness have been presented as components of the contingently changing, or even increasing, organization of life through onto- genesis or evolution. The lecture of Mario Rasetti focused on Big Data, Topology and Field Theory as main ingredients towards a quantum model of life. He argued that a molecule does not become a message only because of its shape or struc- ture, but in the wider context of the system of physical constraints (a“symmetry”) whereby information plays a dynamical role; living molecules extract information from large sets of data and manipulate it, thus the goal is to understand not molec- ular structures, but the structure of the language molecules mutually communicate with. The four short presentations have been an opportunity to learn interesting projects results. Mara Sangiovanni reported on “A Spin-based Model Checking Approach for Genome-Scale Metabolic Networks Validation and Analysis”, a novel method which integrates Flux Balance Analysis and Model Checking to address the problem of verifying if a metabolic model fulfills the expected biological features. By using a human hepatocyte metabolic network as a case study, it can be proven that presented approach is useful in the validation and analysis of genome-scale metabolic models. It followed a roundup of presentations about the European FET project “TOPDRIM: topology driven methods for complex systems”, sponsor of the CS2BIO 2013. The project has the objective to define an algebraic framework for modeling multilevel complex systems, it aims to exploit theories from topology, combinatorics and statistical mechanics and formal languages whose role is central for building a global vision of big data, the huge amount of information flowing around complex systems. The project aims to contribute to the Big Data Science. Luca Tesei presented preliminary results on a research where the geometrical-based interactions between DNA and a restriction enzyme are modeled to prove the ex- istence of long-range interactions at molecular level. Francesco Vaccarino reported on the study made about the structure of brain functional networks obtained from fMRI data through their homological properties. Matteo Rucco informed about a data-driven approach for modeling clinical predictive rule for Pulmonary Embolism. Finally, Hillary Han discussed the bijective proof for a relation between uni- bi- and tricellular maps of certain topological genus, where the uni-, bi- and tricellular maps corresponds to RNA structures over one, two and three backbones. Result that has immediate consequences for the folding of RNA interaction structures. The workshop in Florence attracted more than 40 participants and the inter- disciplinary atmosphere was productive and pleasant. The organizers express their thanks to all speakers and participants of CS2Bio’13 for their contributions that made this year’s edition a success. In particular, we are grateful to Giuseppe Longo and Mario Rasetti for their interesting talks and inspiring contribution to the in- terdisciplinary discussions. We also acknowledge the efforts of the members of the program committee for the reviewing process. The Program Committee of CS2Bio’13 was composed by: • Luca Cardelli (Microsoft Research Cambridge, UK) • Erik de Vink (Technische Universiteit Eindhoven, the Netherlands) • Jasmin Fisher (Microsoft Research Cambridge, UK) • Paola Giannini (Universit del Piemonte Orientale, Italy) • Radu Grosu (Vienna University of Technology, Austria) • Jean Krivine (CNRS and Universit Paris Diderot, France) • Pietro Lio’ (University of Cambridge, UK) • Daniele Manini (Universit di Torino, Italy) • Emanuela Merelli (Universit di Camerino, Italy) Co-chair • Paolo Milazzo (Università di Pisa, Italy) • Ion Petre (bo Akademi University, Finland) • Marco Pettini (Universit de Marseille, France) • Christian Reidys (University of Southern Denmark, Denmark) • David Safranek (Masaryk University, Czech Republic) • Luca Tesei (Università di Camerino, Italy) • Angelo Troina (Università di Torino, Italy) Co-chair • Verena Wolf (Saarland University, Germany) Emanuela Merelli Angelo Troin