Published: 27th August 2013|
|Preface Thao Dang and Carla Piazza||1|
|On the Robustness of Temporal Properties for Stochastic Models Ezio Bartocci, Luca Bortolussi, Laura Nenzi and Guido Sanguinetti||3|
|Robustness Analysis for Value-Freezing Signal Temporal Logic L. Brim, T. Vejpustek, D. Šafránek and J. Fabriková||20|
|The impact of high density receptor clusters on VEGF signaling Ye Chen, Christopher Short, Ádám M. Halász and Jeremy S. Edwards||37|
|Falsifying Oscillation Properties of Parametric Biological Models Thao Dang and Tommaso Dreossi||53|
|A hybrid mammalian cell cycle model Vincent Noël, Sergey Vakulenko and Ovidiu Radulescu||68|
|Exploring the Dynamics of Mass Action Systems Oded Maler, Ádám M. Halász, Olivier Lebeltel and Ouri Maler||84|
|Producing a Set of Models for the Iron Homeostasis Network Nicolas Mobilia, Alexandre Donzé, Jean Marc Moulis and Éric Fanchon||92|
|A Hybrid Model of a Genetic Regulatory Network in Mammalian Sclera Qin Shu, Diana Catalina Ardila, Ricardo G. Sanfelice and Jonathan P. Vande Geest||99|
Systems biology aims at providing a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. Due to the intrinsic multi-scale nature of these systems in space, in organization levels and in time, it is extremely difficult to model them in a uniform way, e.g., by means of differential equations or discrete stochastic processes. Furthermore, such models are often not easily amenable to formal analysis, and their simulations at the organ or even at the cell levels are frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale well for both simulation and formal analysis of biological processes. Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in such a context, and they have been successfully applied to capture the behavior of many biological complex systems, ranging from genetic networks, biochemical reactions, signaling pathways, cardiac tissues electro-physiology, and tumor genesis. This workshop aims at bringing together researchers in computer science, mathematics, and life sciences, interested in the opportunities and the challenges of hybrid modeling applied to systems biology.
The workshop programme included the keynote presentation of Alessandro Astolfi (Imperial College of London, UK) on Immune response enhancement via hybrid control. Furthermore, 5 full papers and 3 short papers were selected out of 13 submissions by the Program Committee of HSB 2013. The papers in this volume address the hybrid modeling of a number important biological processes (iron homeostasis network, mammalian cell cycle, vascular endothelial growth factor (VEGF), genetic regulatory network in mammalian sclera) and, the formalisms and techniques for specifying and validating properties of biological systems (such as, robustness, oscillations). The Program Committee of HSB 2013 involved:
We would like to thank the ECAL organisers, all the authors, the invited speaker, the Programme Committee and the external referees for their valuable contributions. Special thanks go to the organizers of HSB 2012, Ezio Bartocci and Luca Bortolussi, who helped us during all the organizaion steps, and to GNCS (Gruppo Nazionale per il Calcolo Scientifico) at INdAM for financially supporting our workshop.
|August, 2013|| Thao Dang