ReactionSystemsThesis/document.bib

@article{Brodo_Bruni_Falaschi_2021,
  title =        {A logical and graphical framework for Reaction
                  Systems},
  volume =       875,
  DOI =          {10.1016/j.tcs.2021.03.024},
  journal =      {Theoretical Computer Science},
  author =       {Brodo, Linda and Bruni, Roberto and Falaschi,
                  Moreno},
  year =         2021,
  month =        7,
  pages =        {1–27}
}

@article{Rozenberg_Engelfriet_1998,
  title =        {Elementary Net Systems},
  DOI =          {10.1007/3-540-65306-6_14},
  journal =      {Lecture Notes in Computer Science},
  author =       {Rozenberg, Grzegorz and Engelfriet, Joost},
  year =         1998,
  pages =        {12–121}
}

@book{Baier_Katoen_Larsen_2016,
  place =        {Cumberland},
  title =        {Principles of model checking},
  publisher =    {MIT Press, The},
  author =       {Baier, Christel and Katoen, Joost-Pieter and Larsen,
                  Kim Guldstrand},
  year =         2016
}

@article{Aceto_Ingolfsdottir_Srba_2011,
  title =        {The algorithmics of Bisimilarity},
  DOI =          {10.1017/cbo9780511792588.004},
  journal =      {Advanced Topics in Bisimulation and Coinduction},
  author =       {Aceto, Luca and Ingolfsdottir, Anna and Srba, Jirí},
  year =         2011,
  month =        9,
  pages =        {100–172}
}

@article{Cleaveland_Sokolsky_2001,
  title =        {Equivalence and preorder checking for finite-state
                  systems},
  DOI =          {10.1016/b978-044482830-9/50024-2},
  journal =      {Handbook of Process Algebra},
  author =       {Cleaveland, Rance and Sokolsky, Oleg},
  year =         2001,
  pages =        {391–424}
}

@article{Paige_Tarjan_1987,
  title =        {Three partition refinement algorithms},
  volume =       16,
  DOI =          {10.1137/0216062},
  number =       6,
  journal =      {SIAM Journal on Computing},
  author =       {Paige, Robert and Tarjan, Robert E.},
  year =         1987,
  month =        12,
  pages =        {973–989}
}

@Online{rust_2025,
  accessed =     {2025-09-14},
  author =       {The Rust teams},
  title =        {Rust Programming Language},
  url =          {https://rust-lang.org/}
}

@report{WebAssemblyCoreSpecification2,
  title =        {{WebAssembly Core Specification}},
  version =      {2.0},
  editor =       {Rossberg, Andreas},
  date =         {2025-09-14},
  institution =  {{W3C}},
  url =          {https://www.w3.org/TR/wasm-core-2/},
  langid =       {english},
}

@software {Burgener2025,
  author =       {Daniel Burgener},
  title =        {{lalrpop}: convenient LR(1) parser generator},
  url =          {https://github.com/lalrpop/lalrpop},
  date =         {2025-05-22},
  version =      {0.22.2},
  license =      {Apache-2.0 OR MIT},
}

@software {Borgna2025,
  author =       {Agustín Borgna},
  title =        {{petgraph}: Graph data structure library. Provides
                  graph types and graph algorithms.},
  url =          {https://github.com/petgraph/petgraph},
  date =         {2025-09-30},
  version =      {0.8.3},
  license =      {MIT OR Apache-2.0},
}

@Online{graphviz_2025,
  accessed =     {2025-09-14},
  title =        {Graphviz is open source graph visualization
                  software.},
  author =       {Ellson, John},
  url =          {https://graphviz.org/doc/info/lang.html},
}

@Online{graphml_2025,
  accessed =     {2025-09-14},
  title =        {GraphML is a comprehensive and easy-to-use file
                  format for graphs.},
  author =       {The GraphML Team},
  url =          {http://graphml.graphdrawing.org/},
}

@software {egui_node_graph22024,
  author =       {trevyn},
  title =        {{egui\_node\_graph2}: A helper library to create
                  interactive node graphs using egui},
  url =          {https://github.com/trevyn/egui_node_graph2},
  date =         {2024-11-03},
  version =      {0.7.0},
  license =      {MIT},
}

@software {Ernerfeldt2025,
  author =       {Emil Ernerfeldt},
  title =        {{egui}: An easy-to-use immediate mode GUI that runs
                  on both web and native},
  url =          {https://github.com/emilk/egui},
  date =         {2025-11-13},
  version =      {0.33.2},
  license =      {MIT OR Apache-2.0},
}

@Online{btree_2025,
  accessed =     {2025-09-14},
  title =        {An ordered set based on a B-Tree.},
  author =       {The Rust teams},
  url =          {https://doc.rust-lang.org/std/collections/struct.BTreeSet.html},
}

@Online{arc_2025,
  accessed =     {2025-09-14},
  title =        {A thread-safe reference-counting pointer. ‘Arc’
                  stands for ‘Atomically Reference Counted’.},
  author =       {The Rust teams},
  url =          {https://doc.rust-lang.org/std/sync/struct.Arc.html},
}

@software {Rotem2025,
  author =       {Nadav Rotem},
  title =        {{layout-rs}: A graph visualization program},
  url =          {https://github.com/nadavrot/layout},
  date =         {2025-04-24},
  version =      {0.1.3},
  license =      {MIT},
}

@software {Stampfl2025,
  author =       {Laurenz Stampfl},
  title =        {{resvg}: An SVG rendering library.},
  url =          {https://github.com/linebender/resvg},
  date =         {2025-04-17},
  version =      {0.45.1},
  license =      {Apache-2.0 OR MIT},
}

@software {wasm-bindgen2025,
  author =       {daxpedda},
  title =        {{wasm-bindgen}: Easy support for interacting between
                  JS and Rust.},
  url =          {https://github.com/wasm-bindgen/wasm-bindgen},
  date =         {2025-10-27},
  version =      {0.2.105},
  license =      {MIT OR Apache-2.0},
}

@Software{binaryen_2025,
  title =        {{binaryen}: a compiler and toolchain infrastructure
                  library for WebAssembly, written in C++.},
  date =         {2025-10-27},
  url =          {https://github.com/WebAssembly/binaryen},
}

@Manual{manualperf_2025,
  title =        {perf(1) — Linux manual page},
  edition =      {6.17-2},
  month =        11,
  year =         2025,
}

@software {Ochtman2025,
    author = {Dirkjan Ochtman},
    title = {{flamegraph}: A simple cargo subcommand for generating flamegraphs, using inferno under the hood},
    url = {https://github.com/flamegraph-rs/flamegraph},
    date = {2025-11-07},
    version = {0.6.10},
    license = {MIT OR Apache-2.0},
}

@article{Brodo_Bruni_Falaschi_Gori_Milazzo_2025,
  title =        {Slicing analyses for negative dependencies in
                  Reaction Systems Modeling Gene Regulatory Networks},
  DOI =          {10.1007/s11047-025-10046-5},
  journal =      {Natural Computing},
  author =       {Brodo, Linda and Bruni, Roberto and Falaschi, Moreno
                  and Gori, Roberta and Milazzo, Paolo},
  year =         2025,
  month =        9
}

@article{Mitrana_Păun_Petre_Prelipcean_2025,
  title =        {Quantitative reaction systems},
  DOI =          {10.1109/iraset64571.2025.11008263},
  journal =      {2025 5th International Conference on Innovative
                  Research in Applied Science, Engineering and
                  Technology (IRASET)},
  author =       {Mitrana, Victor and Păun, Mihaela and Petre, Ion and
                  Prelipcean, Ana-Maria},
  year =         2025,
  month =        5,
  pages =        {1–6}
}

@article{Bottoni_Mitrana_Petre_2025,
  title =        {Multiset Reaction Systems},
  DOI =          {10.1007/978-3-031-97274-4_11},
  journal =      {Lecture Notes in Computer Science},
  author =       {Bottoni, Paolo and Mitrana, Victor and Petre, Ion},
  year =         2025,
  pages =        {179–193}
}

@Misc{ReactionSystemsGit,
  author =       {Rossi, Elvis},
  title =        {ReactionSystems},
  publisher =    {GitHub},
  journal =      {GitHub repository},
  howpublished = {\url{https://github.com/elvisrossi/ReactionSystems}},
  year =         2025,
}

@Misc{ReactionSystemsGUIGit,
  author =       {Rossi, Elvis},
  title =        {ReactionSystems},
  publisher =    {GitHub},
  journal =      {GitHub repository},
  howpublished =
                  {\url{https://github.com/elvisrossi/ReactionSystemsGUI}},
  year =         2025,
}

@Misc{BioResolve2025,
  title =        {BioResolve web page, a Prolog interpreter for
                  Reaction Systems analysis.},
  howpublished = {\url{https://pages.di.unipi.it/bruni/LTSRS/}},
  year =         2025,
}

@article{Brodo_Bruni_Falaschi_Gori_Milazzo_Montagna_Pulieri_2024,
  title =        {Causal analysis of positive reaction systems},
  volume =       26,
  DOI =          {10.1007/s10009-024-00757-y},
  number =       4,
  journal =      {International Journal on Software Tools for
                  Technology Transfer},
  author =       {Brodo, Linda and Bruni, Roberto and Falaschi, Moreno
                  and Gori, Roberta and Milazzo, Paolo and Montagna,
                  Valeria and Pulieri, Pasquale},
  year =         2024,
  month =        {6},
  pages =        {509–526}
}