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	Author	Maggioli, F.; Mancini, T.; Tronci, E.
	Title	SBML2Modelica: Integrating biochemical models within open-standard simulation ecosystems			Type	Journal Article
	Year	2019	Publication	Bioinformatics	Abbreviated Journal
	Volume	36	Issue	7	Pages	2165â€“2172
	Keywords
	Abstract	SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g., enable in-silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models.Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems.In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2 -compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate, and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialised SBML simulators.SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-4803	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	MCLab @ davi @ ref10.1093/bioinformatics/btz860			Serial	179
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	Author	Della Penna, Giuseppe; Intrigila, Benedetto; Tronci, Enrico; Venturini Zilli, Marisa
	Title	Synchronized regular expressions			Type	Journal Article
	Year	2003	Publication	Acta Inf.	Abbreviated Journal
	Volume	39	Issue	1	Pages	31-70
	Keywords
	Abstract	Text manipulation is one of the most common tasks for everyone using a computer. The increasing number of textual information in electronic format that every computer user collects everyday also increases the need of more powerful tools to interact with texts. Indeed, much work has been done to provide simple and versatile tools that can be useful for the most common text manipulation tasks. Regular Expressions (RE), introduced by Kleene, are well known in the formal language theory. RE have been extended in various ways, depending on the application of interest. In almost all the implementations of RE search algorithms (e.g. the egrep [15] UNIX command, or the Perl [20] language pattern matching constructs) we find backreferences, i.e. expressions that make reference to the string matched by a previous subexpression. Generally speaking, it seems that all kinds of synchronizations between subexpressions in a RE can be very useful when interacting with texts. In this paper we introduce the Synchronized Regular Expressions (SRE) as an extension of the Regular Expressions. We use SRE to present a formal study of the already known backreferences extension, and of a new extension proposed by us, which we call the synchronized exponents. Moreover, since we are dealing with formalisms that should have a practical utility and be used in real applications, we have the problem of how to present SRE to the final users. Therefore, in this paper we also propose a user-friendly syntax for SRE to be used in implementations of SRE-powered search algorithms.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ actainf03			Serial	39
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	Author	Mancini, T.; Mari, F.; Massini, A.; Melatti, I.; Tronci, E.
	Title	Anytime system level verification via parallel random exhaustive hardware in the loop simulation			Type	Journal Article
	Year	2016	Publication	Microprocessors and Microsystems	Abbreviated Journal
	Volume	41	Issue		Pages	12-28
	Keywords	Model Checking of Hybrid Systems; Model checking driven simulation; Hardware in the loop simulation
	Abstract	Abstract System level verification of cyber-physical systems has the goal of verifying that the whole (i.e., software + hardware) system meets the given specifications. Model checkers for hybrid systems cannot handle system level verification of actual systems. Thus, Hardware In the Loop Simulation (HILS) is currently the main workhorse for system level verification. By using model checking driven exhaustive HILS, System Level Formal Verification (SLFV) can be effectively carried out for actual systems. We present a parallel random exhaustive HILS based model checker for hybrid systems that, by simulating all operational scenarios exactly once in a uniform random order, is able to provide, at any time during the verification process, an upper bound to the probability that the System Under Verification exhibits an error in a yet-to-be-simulated scenario (Omission Probability). We show effectiveness of the proposed approach by presenting experimental results on SLFV of the Inverted Pendulum on a Cart and the Fuel Control System examples in the Simulink distribution. To the best of our knowledge, no previously published model checker can exhaustively verify hybrid systems of such a size and provide at any time an upper bound to the Omission Probability.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0141-9331	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	MCLab @ davi @ Mancini201612			Serial	155
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	Author	Bono, V.; Salvo, I.
	Title	A CuCh Interpretation of an Object-Oriented Language			Type	Journal Article
	Year	2001	Publication	Electronic Notes in Theoretical Computer Science	Abbreviated Journal
	Volume	50	Issue	2	Pages	159-177
	Keywords
	Abstract	CuCh machine extends pure lambdaÃ‚â€“calculus with algebraic data types and provides a the possibility of defining functions over the disjoint sum of algebras. We exploit such natural form of overloading to define a functional interpretation of a simple, but significant fragment of a typical object-oriented language.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	BOTH 2001, BohmÃ¢â‚¬â„¢s theorem: applications to Computer Science Theory (Satellite Workshop of ICALP 2001)			Approved	yes
	Call Number	Sapienza @ mari @ Bono-Salvo:BOTH01			Serial	72
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	Author	Della Penna, Giuseppe; Di Marco, Antinisca; Intrigila, Benedetto; Melatti, Igor; Pierantonio, Alfonso
	Title	Interoperability mapping from XML schemas to ER diagrams			Type	Journal Article
	Year	2006	Publication	Data Knowl. Eng.	Abbreviated Journal
	Volume	59	Issue	1	Pages	166-188
	Keywords
	Abstract	The eXtensible Markup Language (XML) is a de facto standard on the Internet and is now being used to exchange a variety of data structures. This leads to the problem of efficiently storing, querying and retrieving a great amount of data contained in XML documents. Unfortunately, XML data often need to coexist with historical data. At present, the best solution for storing XML into pre-existing data structures is to extract the information from the XML documents and adapt it to the data structuresÃ¢â‚¬â„¢ logical model (e.g., the relational model of a DBMS). In this paper, we introduce a technique called Xere (XML entityÃ‚â€“relationship exchange) to assist the integration of XML data with other data sources. To this aim, we present an algorithm that maps XML schemas into entityÃ‚â€“relationship diagrams, discuss its soundness and completeness and show its implementation in XSLT.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier Science Publishers B. V.	Place of Publication	Amsterdam, The Netherlands, The Netherlands	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0169-023x	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Ddimp06			Serial	77
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	Author	Della Penna, Giuseppe; Intrigila, Benedetto; Tronci, Enrico; Venturini Zilli, Marisa
	Title	Synchronized Regular Expressions			Type	Journal Article
	Year	2002	Publication	Electr. Notes Theor. Comput. Sci.	Abbreviated Journal
	Volume	62	Issue		Pages	195-210
	Keywords
	Abstract	Text manipulation is one of the most common tasks for everyone using a computer. The increasing number of textual information in electronic format that every computer user collects everyday stresses the need of more powerful tools to interact with texts. Indeed, much work has been done to provide nonprogramming tools that can be useful for the most common text manipulation issues. Regular Expressions (RE), introduced by Kleene, are wellÃ‚â€“known in the formal language theory. RE received several extensions, depending on the application of interest. In almost all the implementations of RE search algorithms (e.g. the egrep [A] UNIX command, or the Perl [17] language pattern matching constructs) we find backreferences (as defind in [1]), i.e. expressions that make reference to the string matched by a previous subexpression. Generally speaking, it seems that all the kinds of synchronizations between subexpressions in a RE can be very useful when interacting with texts. Therefore, we introduce the Synchronized Regular Expressions (SRE) as a derivation of the Regular Expressions. We use SRE to present a formal study of the already known backreferences extension, and of a new extension proposed by us, which we call the synchronized exponents. Moreover, since we are talking about formalisms that should have a practical utility and can be used in the real world, we have the problem of how to present SRE to the final users. Therefore, in this paper we also propose a userÃ‚â€“friendly syntax for SRE to be used in implementations of SREÃ‚â€“powered search algorithms.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	TOSCA 2001, Theory of Concurrency, Higher Order Languages and Types			Approved	yes
	Call Number	Sapienza @ mari @ entcs02			Serial	46
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	Author	Focardi, Riccardo; Gorrieri, Roberto; Lanotte, Ruggero; Maggiolo-Schettini, Andrea; Martinelli, Fabio; Tini, Simone; Tronci, Enrico
	Title	Formal Models of Timing Attacks on Web Privacy			Type	Journal Article
	Year	2002	Publication	Electronic Notes in Theoretical Computer Science	Abbreviated Journal
	Volume	62	Issue		Pages	229-243
	Keywords
	Abstract	We model a timing attack on web privacy proposed by Felten and Schneider by using three different approaches: HL-Timed Automata, SMV model checker, and tSPA Process Algebra. Some comparative analysis on the three approaches is derived.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	TOSCA 2001, Theory of Concurrency, Higher Order Languages and Types			Approved	yes
	Call Number	Sapienza @ mari @ entcs02a			Serial	47
Permanent link to this record



	Author	Alimguzhin, V.; Mari, F.; Melatti, I.; Salvo, I.; Tronci, E.
	Title	Linearising Discrete Time Hybrid Systems			Type	Journal Article
	Year	2017	Publication	IEEE Transactions on Automatic Control	Abbreviated Journal
	Volume	62	Issue	10	Pages	5357-5364
	Keywords
	Abstract	Model Based Design approaches for embedded systems aim at generating correct-by-construction control software, guaranteeing that the closed loop system (controller and plant) meets given system level formal specifications. This technical note addresses control synthesis for safety and reachability properties of possibly non-linear discrete time hybrid systems. By means of syntactical transformations that require non-linear terms to be Lipschitz continuous functions, we over-approximate non-linear dynamics with a linear system whose controllers are guaranteed to be controllers of the original system. We evaluate performance of our approach on meaningful control synthesis benchmarks, also comparing it to a state-of-the-art tool.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0018-9286	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	Sapienza @ mari @ ref7902199			Serial	164
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	Author	Barbanera, Franco; Dezani-Ciancaglini, Mariangiola; Salvo, Ivano; Sassone, Vladimiro
	Title	A Type Inference Algorithm for Secure Ambients			Type	Journal Article
	Year	2002	Publication	Electronic Notes in Theoretical Computer Science	Abbreviated Journal
	Volume	62	Issue		Pages	83-101
	Keywords
	Abstract	We consider a type discipline for the Ambient Calculus that associates ambients with security levels and constrains them to be traversed by or opened in ambients of higher security clearance only. We present a bottom-up algorithm that, given an untyped process P, computes a minimal set of constraints on security levels such that all actions during runs of P are performed without violating the security level priorities. Such an algorithm appears to be a prerequisite to use type systems to ensure security properties in the web scenario.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	TOSCA 2001, Theory of Concurrency, Higher Order Languages and Types			Approved	yes
	Call Number	Sapienza @ mari @ Barbanera-Dezani-Salvo-Sassone:01			Serial	73
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	Author	Coppo, Mario; Dezani-Ciancaglini, Mariangiola; Giovannetti, Elio; Salvo, Ivano
	Title	Mobility Types for Mobile Processes in Mobile Ambients			Type	Journal Article
	Year	2003	Publication	Electr. Notes Theor. Comput. Sci.	Abbreviated Journal
	Volume	78	Issue		Pages
	Keywords
	Abstract	We present an ambient-like calculus in which the open capability is dropped, and a new form of Ã¢â‚¬Å“lightweightÃ¢â‚¬Â process mobility is introduced. The calculus comes equipped with a type system that allows the kind of values exchanged in communications and the access and mobility properties of processes to be controlled. A type inference procedure determines the Ã¢â‚¬Å“minimalÃ¢â‚¬Â requirements to accept a system or a component as well typed. This gives a kind of principal typing. As an expressiveness test, we show that some well known calculi of concurrency and mobility can be encoded in our calculus in a natural way.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Coppo-Dezani-Giovannetti-Salvo:03			Serial	74
Permanent link to this record