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294 results on '"Maggiolo-Schettini, Andrea"'

1. Application of a Semi-automatic Algorithm for Identification of Molecular Components in SBML Models

Author

Maggiolo-Schettini, Andrea, Milazzo, Paolo, and Pardini, Giovanni

Subjects
Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Molecular Networks
Abstract

Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In this paper we show the application of a component identification algorithm to a number of real-world models to experimentally validate the approach. Components identification allows subpathways to be computed to better understand the pathway functioning., Comment: In Proceedings Wivace 2013, arXiv:1309.7122

Published
2013
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2. Towards modular verification of pathways: fairness and assumptions

Author

Drábik, Peter, Maggiolo-Schettini, Andrea, and Milazzo, Paolo

Subjects
Computer Science - Logic in Computer Science
Abstract

Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation that properties of interest often concern a rather small portion of the system. As a consequence, reduced models can be constructed which approximate the overall system behaviour thus allowing more efficient verification. Biochemical pathways can be seen as complex concurrent interactive systems. Consequently, verification of their properties is often computationally very expensive and could take advantage of the modular approach. In this paper we report preliminary results on the development of a modular verification framework for biochemical pathways. We view biochemical pathways as concurrent systems of reactions competing for molecular resources. A modular verification technique could be based on reduced models containing only reactions involving molecular resources of interest. For a proper description of the system behaviour we argue that it is essential to consider a suitable notion of fairness, which is a well-established notion in concurrency theory but novel in the field of pathway modelling. We propose a modelling approach that includes fairness and we identify the assumptions under which verification of properties can be done in a modular way. We prove the correctness of the approach and demonstrate it on the model of the EGF receptor-induced MAP kinase cascade by Schoeberl et al., Comment: In Proceedings MeCBIC 2012, arXiv:1211.3476

Published
2012
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3. A Testing Framework for P Systems

Author

Barbuti, Roberto, Cacciagrano, Diletta Romana, Maggiolo-Schettini, Andrea, Milazzo, Paolo, and Tesei, Luca

Subjects
Computer Science - Logic in Computer Science, Computer Science - Formal Languages and Automata Theory
Abstract

Testing equivalence was originally defined by De Nicola and Hennessy in a process algebraic setting (CCS) with the aim of defining an equivalence relation between processes being less discriminating than bisimulation and with a natural interpretation in the practice of system development. Finite characterizations of the defined preorders and relations led to the possibility of verification by comparing an implementation with a specification in a setting where systems were seen as black boxes with input and output capabilities, thus neglecting internal undetectable behaviours. In this paper, we start defining a porting of the well-established testing theory into membrane computing, in order to investigate possible benefits in terms of inherited analysis/verification techniques and interesting biological applications. P Algebra, a process algebra for describing P Systems, is used as a natural candidate for the porting since it enjoys the desirable property of being compositional and comes with other observational equivalences already defined and studied., Comment: Presented at MeCBIC 2011

Published
2011

4. Aspects of multiscale modelling in a process algebra for biological systems

Author

Barbuti, Roberto, Caravagna, Giulio, Milazzo, Paolo, Maggiolo-Schettini, Andrea, and Tini, Simone

Subjects
Computer Science - Logic in Computer Science, Computer Science - Computational Engineering, Finance, and Science, Computer Science - Formal Languages and Automata Theory
Abstract

We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When different scale levels of biological systems are considered in a single model, one should take into account that actions at a level may take much more time than actions at a lower level. Moreover, it might happen that while a component is involved in one long lasting high level action, it is involved also in several faster lower level actions. Hence, we propose a process algebra with operations and with a semantics aimed at dealing with these aspects of multiscale modelling. We study behavioural equivalences for such an algebra and give some examples., Comment: In Proceedings MeCBIC 2010, arXiv:1011.0051

Published
2010
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5. Modelling the Dynamics of an Aedes albopictus Population

Author

Basuki, Thomas Anung, Cerone, Antonio, Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, and Rossi, Elisabetta

Subjects
Computer Science - Computational Engineering, Finance, and Science, Computer Science - Formal Languages and Automata Theory, Quantitative Biology - Populations and Evolution
Abstract

We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito) and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS) are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls) to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data., Comment: In Proceedings AMCA-POP 2010, arXiv:1008.3147

Published
2010
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6. A Process Calculus for Molecular Interaction Maps

Author

Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Pardini, Giovanni, and Rama, Aureliano

Subjects
Computer Science - Computational Engineering, Finance, and Science, Computer Science - Logic in Computer Science, Quantitative Biology - Molecular Networks, J.3
Abstract

We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks., Comment: 15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC 2009

Published
2009
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7. On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems

Author

Barbuti, Roberto, Caravagna, Giulio, Milazzo, Paolo, and Maggiolo-Schettini, Andrea

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Computational Engineering, Finance, and Science
Abstract

Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differential Equations (DDEs), a kind of differential equations in which the derivative of the unknown function at a certain time is given in terms of the values of the function at previous times. In the literature, delay stochastic simulation algorithms have been proposed. These algorithms follow a "delay as duration" approach, namely they are based on an interpretation of a delay as the elapsing time between the start and the termination of a chemical reaction. This interpretation is not suitable for some classes of biological systems in which species involved in a delayed interaction can be involved at the same time in other interactions. We show on a DDE model of tumor growth that the delay as duration approach for stochastic simulation is not precise, and we propose a simulation algorithm based on a ``purely delayed'' interpretation of delays which provides better results on the considered model.

Published
2009
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8. Modelling Population Dynamics Using Grid Systems

Author

Barbuti, Roberto, Cerone, Antonio, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Setiawan, Suryana, Cerone, Antonio, editor, Persico, Donatella, editor, Fernandes, Sara, editor, Garcia-Perez, Alexeis, editor, Katsaros, Panagiotis, editor, Shaikh, Siraj Ahmed, editor, and Stamelos, Ioannis, editor

Published
2014
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9. Systolic Automata and P Systems

Author

Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Pardini, Giovanni, Tini, Simone, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Calude, Cristian S., editor, Freivalds, Rūsiņš, editor, and Kazuo, Iwama, editor

Published
2014
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11. A Compositional Semantics of Reaction Systems with Restriction

Author

Pardini, Giovanni, Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Tini, Simone, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bonizzoni, Paola, editor, Brattka, Vasco, editor, and Löwe, Benedikt, editor

Published
2013
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13. Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach

Author

Barbuti, Roberto, Caravagna, Giulio, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Priami, Corrado, editor, Back, Ralph-Johan, editor, Petre, Ion, editor, and de Vink, Erik, editor

Published
2011
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14. Membrane Systems Working in Generating and Accepting Modes: Expressiveness and Encodings

Author

Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Tini, Simone, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Gheorghe, Marian, editor, Hinze, Thomas, editor, Păun, Gheorghe, editor, Rozenberg, Grzegorz, editor, and Salomaa, Arto, editor

Published
2011
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15. Simulation of Kohn’s Molecular Interaction Maps through Translation into Stochastic CLS+

Author

Barbuti, Roberto, Lepri, Daniela, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Pardini, Giovanni, Rama, Aureliano, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Pnueli, Amir, editor, Virbitskaite, Irina, editor, and Voronkov, Andrei, editor

Published
2010
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18. The Calculus of Looping Sequences

Author

Barbuti, Roberto, Caravagna, Giulio, Maggiolo–Schettini, Andrea, Milazzo, Paolo, Pardini, Giovanni, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bernardo, Marco, editor, Degano, Pierpaolo, editor, and Zavattaro, Gianluigi, editor

Published
2008
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21. The Calculus of Looping Sequences for Modeling Biological Membranes

Author

Barbuti, Roberto, Maggiolo–Schettini, Andrea, Milazzo, Paolo, Troina, Angelo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Eleftherakis, George, editor, Kefalas, Petros, editor, Păun, Gheorghe, editor, Rozenberg, Grzegorz, editor, and Salomaa, Arto, editor

Published
2007
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22. Bisimulation Congruences in the Calculus of Looping Sequences

Author

Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Troina, Angelo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Barkaoui, Kamel, editor, Cavalcanti, Ana, editor, and Cerone, Antonio, editor

Published
2006
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23. Modeling Long–Running Transactions with Communicating Hierarchical Timed Automata

Author

Lanotte, Ruggero, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Troina, Angelo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Gorrieri, Roberto, editor, and Wehrheim, Heike, editor

Published
2006
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25. Automatic Covert Channel Analysis of a Multilevel Secure Component

Author

Lanotte, Ruggero, Maggiolo-Schettini, Andrea, Tini, Simone, Troina, Angelo, Tronci, Enrico, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Lopez, Javier, editor, Qing, Sihan, editor, and Okamoto, Eiji, editor

Published
2004
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26. Structural Model Checking for Communicating Hierarchical Machines

Author

Lanotte, Ruggero, Maggiolo-Schettini, Andrea, Peron, Adriano, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Fiala, Jiří, editor, Koubek, Václav, editor, and Kratochvíl, Jan, editor

Published
2004
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27. Concurrency in Timed Automata

Author

Lanotte, Ruggero, Maggiolo-Schettini, Andrea, Tini, Simone, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, and Freivalds, Rūsiņš, editor

Published
2001
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31. Priorities in Statecharts

Author

Maggiolo-Schettini, Andrea, Merro, Massimo, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, and Dam, Mads, editor

Published
1997
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32. Retiming techniques for Statecharts

Author

Maggiolo-Schettini, Andrea, Peron, Adriano, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Jonsson, Bengt, editor, and Parrow, Joachim, editor

Published
1996
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33. Equivalences of Statecharts

Author

Maggiolo-Schettini, Andrea, Peron, Adriano, Tini, Simone, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Montanari, Ugo, editor, and Sassone, Vladimiro, editor

Published
1996
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34. Dynamic graphs

Author

Maggiolo-Schettini, Andrea, Winkowski, Józef, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Penczek, Wojciech, editor, and Szałas, Andrzej, editor

Published
1996
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47. Systolic Automata and P Systems

Author

Barbuti, Roberto, primary, Maggiolo-Schettini, Andrea, additional, Milazzo, Paolo, additional, Pardini, Giovanni, additional, and Tini, Simone, additional

Published
2014
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48. Spatial P systems

Author

Barbuti, Roberto, Maggiolo-Schettini, Andrea, Milazzo, Paolo, Pardini, Giovanni, and Tesei, Luca

Published
2011
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