| Records |
| 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 |
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Volume  |
36 |
Issue |
7 |
Pages |
2165–2172 |
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| 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 |
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| ISSN |
1367-4803 |
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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 |
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| Volume |
39 |
Issue |
1 |
Pages |
31-70 |
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| 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. |
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yes |
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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 |
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| Volume |
41 |
Issue |
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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. |
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0141-9331 |
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no |
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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 |
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| Volume |
50 |
Issue |
2 |
Pages |
159-177 |
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| Abstract |
CuCh machine extends pure lambda–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. |
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Elsevier |
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BOTH 2001, Bohm’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 |
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59 |
Issue |
1 |
Pages |
166-188 |
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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 structures’ logical model (e.g., the relational model of a DBMS). In this paper, we introduce a technique called Xere (XML entity–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 entity–relationship diagrams, discuss its soundness and completeness and show its implementation in XSLT. |
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Elsevier Science Publishers B. V. |
Place of Publication |
Amsterdam, The Netherlands, The Netherlands |
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0169-023x |
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Approved |
yes |
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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 |
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| Volume |
62 |
Issue |
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Pages |
195-210 |
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| 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 well–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 user–friendly syntax for SRE to be used in implementations of SRE–powered search algorithms. |
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TOSCA 2001, Theory of Concurrency, Higher Order Languages and Types |
Approved |
yes |
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Sapienza @ mari @ entcs02 |
Serial |
46 |
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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 |
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| Volume |
62 |
Issue |
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Pages |
229-243 |
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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. |
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TOSCA 2001, Theory of Concurrency, Higher Order Languages and Types |
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yes |
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Sapienza @ mari @ entcs02a |
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47 |
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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 |
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62 |
Issue |
10 |
Pages |
5357-5364 |
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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. |
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0018-9286 |
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no |
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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 |
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Journal Article |
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2002 |
Publication |
Electronic Notes in Theoretical Computer Science |
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62 |
Issue |
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Pages |
83-101 |
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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. |
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Elsevier |
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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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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. |
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78 |
Issue |
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We present an ambient-like calculus in which the open capability is dropped, and a new form of “lightweight  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 “minimal  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. |
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yes |
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Sapienza @ mari @ Coppo-Dezani-Giovannetti-Salvo:03 |
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74 |
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