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A Tutorial on Specifying Data Structures in Maude

Narciso Martí-Oliet, Miguel Palomino, Alberto Verdejo
2005 Electronical Notes in Theoretical Computer Science  
This tutorial describes the equational specification of a series of typical data structures in Maude. We start with the well-known stacks, queues, and lists, to continue with binary and search trees.  ...  The operator attributes available in Maude allow the specification of data based on constructors that satisfy some equational properties, like concatenation of lists which is associative and has the empty  ...  Acknowledgement We warmly thank Ricardo Peña for our discussions on functional implementations of data structures, Manuel Clavel for his work on the ITP and his help in understanding its idiosyncrasies  ... 
doi:10.1016/j.entcs.2005.01.041 fatcat:llijkamjdjgz7bcghyrfhgavmi

Maude-NPA: Cryptographic Protocol Analysis Modulo Equational Properties [chapter]

Santiago Escobar, Catherine Meadows, José Meseguer
2009 Lecture Notes in Computer Science  
In this tutorial, we give an overview of the Maude-NRL Protocol Analyzer (Maude-NPA), a tool for the analysis of cryptographic protocols using functions that obey dierent equational theories.  ...  A tool is said to use the bounded session model if the user must specify the maximum number of sessions that can be generated in a search.  ...  in this tutorial, and a graphical user interface [44] that allows a user to examine a Maude-NPA search tree in detail.  ... 
doi:10.1007/978-3-642-03829-7_1 fatcat:l4ptn4q3erhrrdnpctq6eofxy4

Analysis of Automated External Defibrillator Device Failures Reported to the Food and Drug Administration

Lawrence A. DeLuca, Allan Simpson, Dan Beskind, Kristi Grall, Lisa Stoneking, Uwe Stolz, Daniel W. Spaite, Ashish R. Panchal, Kurt R. Denninghoff
2012 Annals of Emergency Medicine  
This analysis was also validated by comparing the results with those of a preliminary analysis performed by 2 of the reviewers on a subset of the MAUDE data. 19 RESULTS MAUDE data was uploaded from  ...  Other cause (specify) 178 (15.5)* N/A Table 3 . 3 Interrater agreement for data abstraction instrument.  ... 
doi:10.1016/j.annemergmed.2011.07.022 pmid:21872969 fatcat:slmd4axwevaufbx3jlkbbwgjfu

Rewriting Logic and Maude: A Wide-Spectrum Semantic Framework for Object-Based Distributed Systems [chapter]

José Meseguer
2000 IFIP Advances in Information and Communication Technology  
Using Maude and its associated tools, such executable specifications can then be formally analyzed in a variety of ways.  ...  As a wide-spectrum semantic framework, rewriting logic can span the gap between high-level properties and architectural designs on the one hand, and distributed or mobile system implementations on the  ...  The work on rewriting logic and Maude is ajoint research effort with all my colleagues in the Maude team, with Carolyn Talcott at Stanford University, and with other colleagues and research teams in the  ... 
doi:10.1007/978-0-387-35520-7_5 fatcat:7oy4kfnjxnadxmojkv7jv34t3q

Symbolic Modeling of Signal Transduction in Pathway Logic

Carolyn Talcott
2006 Proceedings of the 2006 Winter Simulation Conference  
Pathway Logic is a step towards a vision of symbolic systems biology. It is an approach to modeling cellular processes based on formal methods.  ...  In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a  ...  This work was supported in part by NIH/NIGMS grant GM68146 and by a Public Health Service Grant CA112970 from the National Cancer Institute.  ... 
doi:10.1109/wsc.2006.322940 dblp:conf/wsc/Talcott06 fatcat:5ljrdo7rnbeivpozcvrdnqreym

Twenty years of rewriting logic

José Meseguer
2012 The Journal of Logic and Algebraic Programming  
This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations  ...  Rewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality.  ...  This work has been supported in part by NSF Grants CNS 07-16638, CNS 08-34709, CNS 08-31064, CNS 09-04749, and CCF 09-05584, AFOSR Grant FA8750-11-2-0084, and the "Programa de Apoyo a la Investigación  ... 
doi:10.1016/j.jlap.2012.06.003 fatcat:5tx4a5uxlvapfpf5fajozkbboi

Twenty Years of Rewriting Logic [chapter]

José Meseguer
2010 Lecture Notes in Computer Science  
This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations  ...  Rewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality.  ...  This work has been supported in part by NSF Grants CNS 07-16638, CNS 08-34709, CNS 08-31064, CNS 09-04749, and CCF 09-05584, AFOSR Grant FA8750-11-2-0084, and the "Programa de Apoyo a la Investigación  ... 
doi:10.1007/978-3-642-16310-4_2 fatcat:ho7s76r67nc63bndpoptbh5k4e

Contents and abstracts of the electronic notes in theoretical computer science vol. 4

José Meseguer
1998 Theoretical Computer Science  
discussions on specific topics, and by scheduling a tutorial at the beginning of the workshop.  ...  Besides work on models and on concurrency aspects, there are several papers describing the different rewriting logic languages developed so far in Europe and the US, as well as a paper on semantic foundations  ...  the p-calculus to a specification in Maude.  ... 
doi:10.1016/s0304-3975(97)00247-8 fatcat:3cfgzbipsrenxoh5vxznnvaxl4

Maude: specification and programming in rewriting logic

M. Clavel, F. Durán, S. Eker, P. Lincoln, N. Martı́-Oliet, J. Meseguer, J.F. Quesada
2002 Theoretical Computer Science  
We conclude with some remarks about applications, work on a formal environment for Maude, and a mobile language extension of Maude.  ...  Maude is a high-level language and a high-performance system supporting executable speciÿcation and declarative programming in rewriting logic.  ...  some more specialized data types such as Diophantine equations and Tarjan's union-ÿnd data structure.  ... 
doi:10.1016/s0304-3975(01)00359-0 fatcat:qx6ctc4thbgghje2mqarzxjxdy

Modelling Adaptable Distributed Object Oriented Systems Using the HATS Approach: A Fredhopper Case Study [chapter]

Peter Y. H. Wong, Nikolay Diakov, Ina Schaefer
2012 Lecture Notes in Computer Science  
Such systems also have high demands on their dependability and trustworthiness.  ...  The HATS approach allows precisely specifying and analyzing the abstract behaviour of distributed software systems and their variability.  ...  Maude/Java back ends The current version of the ABS tool suite comes with a back end for Maude and Java: The Maude back end takes the type checked AST of an ABS model and outputs the corresponding Maude  ... 
doi:10.1007/978-3-642-31762-0_5 fatcat:gnfs7ctumzdxdb6zrhsewwmrea

Two Decades of Maude [chapter]

Manuel Clavel, Francisco Durán, Steven Eker, Santiago Escobar, Patrick Lincoln, Narciso Martí-Oliet, Carolyn Talcott
2015 Lecture Notes in Computer Science  
This paper is a tribute to José Meseguer, from the rest of us in the Maude team, reviewing the past, the present, and the future of the language and system with which we have been working for around two  ...  This paper is not an introduction to Maude, and some familiarity with it and with rewriting logic are indeed assumed.  ...  Maude 1 was presented in RTA 1999 [18] , in FASE 2000 [21] , in an ETAPS 2000 tutorial [19] , and in a journal paper published in 2002 [22] .  ... 
doi:10.1007/978-3-319-23165-5_11 fatcat:cre7i55r4reg3indrng3w5fgqa

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data

Delphine Naquin, Yves d'Aubenton-Carafa, Claude Thermes, Maud Silvain
2014 BMC Bioinformatics  
Results: We implemented an R package called CIRCUS to analyze genomic structural variations. It generates both data and configuration files necessary for Circos, to produce graphs.  ...  Circos (Genome Res, 19:1639-1645), a Perl script, is a powerful visualization software that requires setting up numerous configuration files with a large number of parameters to handle.  ...  Acknowledgements The authors thank Mireille Ansaldi for providing the data used for the figures.  ... 
doi:10.1186/1471-2105-15-198 pmid:24938393 pmcid:PMC4071023 fatcat:jn2c47hm3nc3rayfmdxsf75obm

Formal Executable Models of Cell Signaling Primitives

Carolyn Talcott
2006 Second International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (isola 2006)  
It also allows the knowledge base to be queried as data base, for example finding all rules that involve a given protein (in any or a specified state or location).  ...  Static analysis allows one to examine the structure of the model and to understand how the elements are related and organized (the sort structure).  ... 
doi:10.1109/isola.2006.66 dblp:conf/isola/Talcott06 fatcat:app6qyvmpzd2beqiqku67nw4y4

nosoi: a stochastic agent-based transmission chain simulation framework in R [article]

Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
2020 biorxiv/medrxiv   pre-print
epidemic modeling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic  ...  or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can - for example - be used to validate a wide range of reconstruction methods, including  ...  The tutorials also provide guidelines on how to set up simulations in various combinations of settings currently available.  ... 
doi:10.1101/2020.03.03.973107 fatcat:ddk7kzqd3jf7rgg6zyd2dpkzyu

A Systematic Approach to Uncover Security Flaws in GUI Logic

Shuo Chen, Jose Meseguer, Ralf Sasse, Helen J. Wang, Yi-Min Wang
2007 2007 IEEE Symposium on Security and Privacy (SP '07)  
Specifically, based on an in-depth study of key subsets of Internet Explorer (IE) browser source code, we have developed a formal model for the browser GUI logic and have applied formal reasoning to uncover  ...  GUI logic flaws are a category of software vulnerabilities that result from logic bugs in GUI design/implementation.  ...  We give a brief tutorial here.  ... 
doi:10.1109/sp.2007.6 dblp:conf/sp/MeseguerSWW07 fatcat:pcrsvg3atjfy3gnmxrdkjaxyiu
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