biblio.bib

% Encoding: UTF-8

% Chemical-oriented simulation of computational systems with ALCHEMIST
@Article{alchemist2013,
    author      = "Pianini, D.
                    and Montagna, S.
                    and Viroli, M.",
    title       = "Chemical-oriented simulation of computational systems with ALCHEMIST",
    journal     = "Journal of Simulation",
    year        = "2013",
    month       = "Aug",
    day         = "01",
    volume      = "7",
    number      = "3",
    pages       = "202--215",
    abstract    = "In this paper we address the engineering of complex and emerging computational systems featuring situatedness, adaptivity and self-organisation, like pervasive computing applications in which humans and devices, dipped in a very mobile environment, opportunistically interact to provide and exploit information services. We adopt a meta-model in which possibly mobile, interconnected and communicating agents work according to a set of chemical-like laws. According to this view, substantiated by recent research on pervasive computing systems, we present the Alchemist simulation framework, which retains the performance of known Stochastic Simulation Algorithms for (bio)chemistry, though it is tailored to the specific features of complex and situated computational systems.",
    issn        = "1747-7786",
    doi         = "10.1057/jos.2012.27",
    url         = "https://doi.org/10.1057/jos.2012.27"
}

% Protelis: Practical Aggregate Programming
@inproceedings{protelis2015,
    author      = {Pianini, Danilo
                    and Viroli, Mirko
                    and Beal, Jacob},
    title       = {Protelis: Practical Aggregate Programming},
    booktitle   = {Proceedings of the 30th Annual ACM Symposium on Applied Computing},
    series      = {SAC '15},
    year        = {2015},
    isbn        = {9781450331968},
    location    = {Salamanca, Spain},
    pages       = {1846--1853},
    numpages    = {8},
    url         = {http://doi.acm.org/10.1145/2695664.2695913},
    doi         = {10.1145/2695664.2695913},
    acmid       = {2695913},
    publisher   = {ACM},
    address     = {New York, NY, USA},
    keywords    = {aggregate programming,
                    alchemist,
                    computational field,
                    coordination,
                    field calculus},
}

% Revisione e refactoring dell'interfaccia utente del simulatore Alchemist
@phdthesis{casadio,
    author      = {Elisa Casadio},
    title       = {Revisione e refactoring dell'interfaccia utente del simulatore Alchemist},
    keywords    = {Alchemist,
                    Java,
                    JavaFX,
                    interfaccia grafica,
                    simulazione,
                    simulatore},
    abstract    = {Lo scopo di questa tesi {\`e} la revisione e il refactoring dell'interfaccia grafica del simulatore Alchemist, per offrire una migliore esperienza d'uso all'utente. L'interfaccia grafica permette la configurazione completa di una simulazione ed il suo avvio in modalit{\`a} normale o batch. Per il suo sviluppo, {\`e} stata utilizzata la libreria JavaFX, che ha permesso di separare l'aspetto del programma dalla specifica comportamentale, e supporta l'Hi-DPI, che consente al simulatore di essere scalabile anche su schermi ad alta risoluzione. L'ambiente ottenuto {\`e} intuitivo, perch{\'e} offre un'esperienza d'uso simile ad un IDE di sviluppo; ed {\`e} anche consistente rispetto allo stato del file system. Nel testo sono illustrati tutti i requisiti che il progetto deve soddisfare e, inoltre, sono descritte, in modo approfondito, la progettazione e l'implementazione dell'interfaccia realizzata. Il risultato ottenuto {\`e} un ambiente funzionante, che soddisfa buona parte delle specifiche richieste e che potr{\`a} essere ampliato in futuro con nuove funzionalit{\`a}.},
    type        = {Tesi di laurea},
    url         = {http://amslaurea.unibo.it/12310}
}

% Brevetto GUI
@misc{gui,
    title       = {Graphical user interface},
    author      = {O'rourke, Thomas C and O'neill, Brian T and Cook, Rodney C and Taner, Kuntay O and Synder, Steven P and Joyner, Adam R and others},
    year        = {1994},
    month       = sep # "~20",
    publisher   = {Google Patents},
    note        = {US Patent 5,349,658}
}

% Discrete event simulation: State of the art
@article{des,
    title       = {Discrete event simulation: State of the art},
    author      = {Babulak, Eduard and Wang, Ming},
    journal     = {International Journal of Online Engineering (iJOE)},
    volume      = {4},
    number      = {2},
    pages       = {60--63},
    year        = {2007},
    url         = {https://doi.org/10.5772/9894},
    doi         = {10.5772/9894},
}

% Principles of discrete event simulation
@book{des2,
    author      = {Fishman, George S.},
    title       = {Principles of Discrete Event Simulation},
    year        = {1978},
    isbn        = {9780471043959},
    publisher   = {John Wiley \& Sons, Inc.},
    address     = {New York, NY, USA},
}

% Discrete-Event System Simulation
@inproceedings{des3,
    author      = {Banks, Jerry
                    and Carson,II, John S.},
    title       = {Introduction to Discrete-event Simulation},
    booktitle   = {Proceedings of the 18th Conference on Winter Simulation},
    series      = {WSC '86},
    year        = {1986},
    isbn        = {9780911801118},
    location    = {Washington, D.C., USA},
    pages       = {17--23},
    numpages    = {7},
    url         = {http://doi.acm.org/10.1145/318242.318253},
    doi         = {10.1145/318242.318253},
    acmid       = {318253},
    publisher   = {ACM},
    address     = {New York, NY, USA},
}

@inproceedings{des4,
    title           = {A Gillespie-based Computational Model for Integrating Event-driven and Multi-Agent Based Simulation},
    author          = {Montagna, Sara
                        and Omicini, Andrea
                        and Pianini, Danilo},
    booktitle       = {Proceedings of the 2015 International Conference on Autonomous Agents and Multiagent Systems},
    pages           = {1763--1764},
    year            = {2015},
    organization    = {International Foundation for Autonomous Agents and Multiagent Systems}
}

% Algoritmo Gillespie 1976
@article{gillespie1976,
    title       = {A general method for numerically simulating the stochastic time evolution of coupled chemical reactions},
    journal     = {Journal of Computational Physics},
    publisher   = {Elsevier},
    volume      = {22},
    number      = {4},
    pages       = {403 - 434},
    year        = {1976},
    issn        = {0021-9991},
    doi         = {https://doi.org/10.1016/0021-9991(76)90041-3},
    url         = {http://www.sciencedirect.com/science/article/pii/0021999176900413},
    author      = {Gillespie, Daniel T.},
    abstract    = {Abstract An exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels. The method is a compact, computer-oriented, Monte Carlo simulation procedure. It should be particularly useful for modeling the transient behavior of well-mixed gas-phase systems in which many molecular species participate in many highly coupled chemical reactions. For “ordinary” chemical systems in which fluctuations and correlations play no significant role, the method stands as an alternative to the traditional procedure of numerically solving the deterministic reaction rate equations. For nonlinear systems near chemical instabilities, where fluctuations and correlations may invalidate the deterministic equations, the method constitutes an efficient way of numerically examining the predictions of the stochastic master equation. Although fully equivalent to the spatially homogeneous master equation, the numerical simulation algorithm presented here is more directly based on a newly defined entity called “the reaction probability density function.” The purpose of this article is to describe the mechanics of the simulation algorithm, and to establish in a rigorous, a priori manner its physical and mathematical validity; numerical applications to specific chemical systems will be presented in subsequent publications.}
}

% Algoritmo Gillespie 1977
@article{gillespie1977,
    author      = {Gillespie, Daniel T.},
    title       = {Exact stochastic simulation of coupled chemical reactions},
    journal     = {The Journal of Physical Chemistry},
    volume      = {81},
    number      = {25},
    pages       = {2340-2361},
    year        = {1977},
    doi         = {10.1021/j100540a008},
    utrl        = {http://dx.doi.org/10.1021/j100540a008},
    eprint      = {http://dx.doi.org/10.1021/j100540a008},
    publisher   = {ACS Publications}
}

% Next Reaction Method (Gibson and Bruck)
@article{nextReactionMethod,
    author      = {Gibson, Michael A.
                    and Bruck, Jehoshua},
    title       = {Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels},
    journal     = {The Journal of Physical Chemistry A},
    volume      = {104},
    number      = {9},
    pages       = {1876-1889},
    year        = {2000},
    doi         = {10.1021/jp993732q},
    URL         = {http://dx.doi.org/10.1021/jp993732q},
    eprint      = {http://dx.doi.org/10.1021/jp993732q}
}

% Algoritmo di Slepoy in grado di eseguire in tempo costante, 2000
@article{slepoy,
    title       = {A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks},
    author      = {Slepoy, Alexander
                    and Thompson, Aidan P
                    and Plimpton, Steven J},
    journal     = {The journal of chemical physics},
    volume      = {128},
    number      = {20},
    pages       = {05B618},
    year        = {2008},
    publisher   = {AIP}
}

% MVC nel linugaggio Smarttalk-80
@article{mvc,
    title       = {A description of the model-view-controller user interface paradigm in the smalltalk-80 system},
    author      = {Krasner, Glenn E
                    and Pope, Stephen T
                    and others},
    journal     = {Journal of object oriented programming},
    volume      = {1},
    number      = {3},
    pages       = {26--49},
    year        = {1988}
}

% La caffettiera del masochista
@book{norman1988,
    author          = {Norman, Donald A.},
    title           = {The Design of Everyday Things},
    year            = {1988},
    month           = {01},
    isbn            = {9780465067107},
    publisher       = {Basic Books, Inc.},
    address         = {New York, NY, USA},
}

% User Experience
@inproceedings{ux,
    author          = {Hassenzahl, Marc},
    title           = {User Experience (UX): Towards an Experiential Perspective on Product Quality},
    booktitle       = {Proceedings of the 20th Conference on L'Interaction Homme-Machine},
    series          = {IHM '08},
    year            = {2008},
    isbn            = {9781605582856},
    location        = {Metz, France},
    pages           = {11--15},
    numpages        = {5},
    url             = {http://doi.acm.org/10.1145/1512714.1512717},
    doi             = {10.1145/1512714.1512717},
    acmid           = {1512717},
    publisher       = {ACM},
    address         = {New York, NY, USA},
    keywords        = {hedonic quality,
                        user experience (UX),
                        user-centred design,
                        well-being}
}

% UX: ISO 9241-210
@techreport{iso9241,
    type            = {Standard},
    key             = {ISO 9241-210:2010},
    month           = mar,
    year            = {2009},
    title           = {Ergonomics of human system interaction-Part 210: Human-centred design for interactive systems},
    volume          = {1},
    address         = {Geneva, CH},
    howpublished    = {International Organization for Standardization},
    note            = {ISO 9241-210:2010},
    url             = {https://www.iso.org/standard/52075.html}
}

% What Is JavaFX? (Monica Pawlan, 2013)
@misc{pawlan2013javafx,
    title       = {What Is JavaFX?},
    author      = {Pawlan, Monica},
    year        = {2013},
    publisher   = {JavaFX}
}

@article{moritz2008rich,
    title       = {Rich Internet Applications (RIA): A Convergence of User Interface Paradigms of Web and Desktop-Exemplified by JavaFX},
    author      = {Moritz, Florian},
    journal     = {University of AppliedScience Kaiserslautern, Deutschland},
    year        = {2008}
}

@article{friedman1995,
    title           = {Making sense of software: Computer games and interactive textuality},
    author          = {Friedman, Ted},
    journal         = {Cybersociety; Computer-Mediated Communication and Community. Thousand Oaks, Calif.: Sage Publications},
    year            = {1994}
}

@book{aPatternLanguage,
    abstract        = {The second of three books published by the Center for Environmental Structure
                        to provide a "working alternative to our present ideas about architecture,
                        building, and planning," {\_A} Pattern Language\_ offers a practical language for
                        building and planning based on natural considerations. The reader is given an
                        overview of some 250 patterns that are the units of this language, each
                        consisting of a design problem, discussion, illustration, and solution. By
                        understanding recurrent design problems in our environment, readers can
                        identify extant patterns in their own design projects and use these patterns
                        to create a language of their own. Extraordinarily thorough, coherent, and
                        accessible, this book has become a bible for homebuilders, contractors, and
                        developers who care about creating healthy, high-level design.},
    author          = {Alexander, Christopher
                        and Ishikawa, Sara
                        and Silverstein, Murray
                        and Jacobson, Max
                        and Fiksdahl-King, Ingrid
                        and Angel, Shlomo},
    day             = {17},
    edition         = {Later printing},
    howpublished    = {Hardcover},
    isbn            = {9780195019193},
    keywords        = {architecture,
                        dictionary,
                        model,
                        pattern,
                        reference,
                        theory},
    month           = aug,
    posted-at       = {2006-05-11 04:08:13},
    priority        = {2},
    publisher       = {Oxford University Press},
    title           = {A Pattern Language: Towns, Buildings, Construction (Center for Environmental Structure)},
    year            = {1977}
}

% Intervista di Wired a Will Wright
@article{wiredWright,
    title           = {Will Wright: The Mayor of SimCity},
    author          = {Kelly, Kevin},
    year            = {1994},
    publisher       = {Wired},
    url             = {https://www.wired.com/1994/01/wright/}
}

@article{unisandTechradar,
    title           = {How one man created his own universe - How Dan Dixon fashioned a whole universe out of mere bytes},
    author          = {Alex Cox},
    year            = {2008},
    publisher       = {PC Plus, Issue 274 and techradar.com},
    url             = {http://www.techradar.com/news/software/computing/how-one-man-created-his-own-universe-470870}
}

@article{2058-7058-25-05-40,
    author={Roger Bridgman},
    title={When Creativity met Necessity},
    journal={Physics World},
    volume={25},
    number={05},
    pages={44},
    url={http://stacks.iop.org/2058-7058/25/i=05/a=40},
    year={2012},
    abstract={Necessity, they say, is the mother of invention. A metaphorical DNA test, however, suggests that its father is probably that old reprobate, Creativity. The simple fact is that for many inventors, a pressing need is not essential: scientists often create something new just because they can.}
}

@misc{multipanedmodel,
    title={Multi-pane navigation model for graphical user interfaces},
    author={Clark, B. and Feliberti, V.},
    url={https://www.google.com/patents/US20060101353},
    year={2006},
    month=may # "~11",
    publisher={Google Patents},
    note={US Patent App. 11/333,164}
}

% JSON
@techreport{json,
    abstract      = {JavaScript Object Notation (JSON) is a lightweight, text-based, language-independent data interchange format. It was derived from the ECMAScript Programming Language Standard. JSON defines a small set of formatting rules for the portable representation of structured data.},
    added-at      = {2011-02-21T16:50:26.000+0100},
    author        = {Crockford, Douglas},
    url           = {https://www.ietf.org/rfc/rfc4627.txt},
    howpublished  = {IETF},
    interhash     = {9b4bd5b999b2787008a18856f4ab33fa},
    intrahash     = {1960e0b98f196064c932c85508eec33d},
    keywords      = {RFC
                    RFC4627
                    json},
    month         = {7},
    number        = 4627,
    timestamp     = {2013-01-06T13:19:18.000+0100},
    title         = {The application/json Media Type for JavaScript Object Notation (JSON)},
    type          = {RFC},
    year          = 2006
}

% Effective Java - 1st Edition
@book{Bloch:2001:EJP:380153,
    author = {Bloch, Joshua},
    title = {Effective Java Programming Language Guide},
    year = {2001},
    isbn = {9780201310054},
    publisher = {Sun Microsystems, Inc.},
    address = {Mountain View, CA, USA},
}

% Effective Java - 2nd Edition
@book{Bloch:2008:EJ:1377533,
    author = {Bloch, Joshua},
    title = {Effective Java (2nd Edition) (The Java Series)},
    year = {2008},
    isbn = {9780321356680},
    edition = {2},
    publisher = {Prentice Hall PTR},
    address = {Upper Saddle River, NJ, USA},
}

% Gang of Four: Design Pattern
@book{designPattern,
    author     = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John},
    title      = {Design Patterns: Elements of Reusable Object-oriented Software},
    year       = {1995},
    isbn       = {9780201633610},
    publisher  = {Addison-Wesley Longman Publishing Co., Inc.},
    address    = {Boston, MA, USA},
}

% Pattern Observer
@Inbook{observer,
    author="McDonough, James E.",
    title="Observer Design Pattern",
    bookTitle="Object-Oriented Design with ABAP: A Practical Approach",
    year="2017",
    publisher="Apress",
    address="Berkeley, CA",
    pages="155--171",
    abstract="The next stop on your voyage through the Design Patterns galaxy takes you to the Observer design pattern, another of the design patterns found in the GoF catalog. You will find this design pattern useful in situations where one class needs to be kept aware of changes occurring in another class.",
    isbn="9781484228388",
    doi="10.1007/978-1-4842-2838-8_13",
    url="https://doi.org/10.1007/978-1-4842-2838-8_13"
}

% Pattern Template Method
@Inbook{templateMethod,
    author="McDonough, James E.",
    title="Template Method Design Pattern",
    bookTitle="Object-Oriented Design with ABAP: A Practical Approach",
    year="2017",
    publisher="Apress",
    address="Berkeley, CA",
    pages="247--254",
    abstract="The next stop on your voyage through the Design Patterns galaxy takes you to the Template Method design pattern, another of the design patterns found in the GoF catalog. You will find this design pattern useful when you need to establish a fixed sequence of steps while allowing for some flexibility in their implementation.",
    isbn="9781484228388",
    doi="10.1007/978-1-4842-2838-8_19",
    url="https://doi.org/10.1007/978-1-4842-2838-8_19"
}

% Pattern Iterable
@Inbook{iterator,
    author="McDonough, James E.",
    title="Iterator Design Pattern",
    bookTitle="Object-Oriented Design with ABAP: A Practical Approach",
    year="2017",
    publisher="Apress",
    address="Berkeley, CA",
    pages="239--246",
    abstract="The next stop on your voyage through the Design Patterns galaxy takes you to the Iterator design pattern, another of the design patterns found in the GoF catalog. You will find this design pattern useful when you need to access the elements of a structure sequentially without having to know the representation of those elements.",
    isbn="9781484228388",
    doi="10.1007/978-1-4842-2838-8_18",
    url="https://doi.org/10.1007/978-1-4842-2838-8_18"
}

% Algoritmo di Rabin–Karp utilizzato da PMD
@article{RabinKarp,
    author      = {Richard M. Karp and Michael O. Rabin},
    journal     = {{IBM} Journal of Research and Development},
    title       = {Efficient randomized pattern-matching algorithms},
    year        = {1987},
    month       = {mar},
    publisher   = {{IBM}},
    volume      = {31},
    number      = {2},
    pages       = {249-260},
    abstract    = {We present randomized algorithms to solve the following string-matching problem and some of its generalizations: Given a string X of length n (the pattern) and a string Y (the text), find the first occurrence of X as a consecutive block within Y. The algorithms represent strings of length n by much shorter strings called fingerprints, and achieve their efficiency by manipulating fingerprints instead of longer strings. The algorithms require a constant number of storage locations, and essentially run in real time. They are conceptually simple and easy to implement. The method readily generalizes to higher-dimensional pattern-matching problems.},
    doi         = {10.1147/rd.312.0249},
    url         = {https://doi.org/10.1147/rd.312.0249},
    ISSN        = {0018-8646}
}

% Ergonomia cognitiva
@book{cognitiveErgonomics,
    editor = {Long, John and Whitefield, A.},
    title = {Cognitive Ergonomics and Human Computer Interaction},
    year = {1989},
    isbn = {9780521371797},
    publisher = {Cambridge University Press},
    address = {New York, NY, USA},
}