ReactionSystemsThesis/document.bib

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

@article{Rozenberg_Engelfriet_1998,
  author =       {Rozenberg, Grzegorz and Engelfriet, Joost},
  doi =          {10.1007/3-540-65306-6_14},
  journal =      {Lecture Notes in Computer Science},
  pages =        {12-121},
  title =        {Elementary Net Systems},
  year =         1998,
  bdsk-url-1 =   {https://doi.org/10.1007/3-540-65306-6_14}
}

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

@article{Aceto_Ingolfsdottir_Srba_2011,
  author =       {Aceto, Luca and Ingolfsdottir, Anna and Srba,
                  Jir{\'\i}},
  doi =          {10.1017/cbo9780511792588.004},
  journal =      {Advanced Topics in Bisimulation and Coinduction},
  month =        9,
  pages =        {100-172},
  title =        {The algorithmics of Bisimilarity},
  year =         2011,
  bdsk-url-1 =   {https://doi.org/10.1017/cbo9780511792588.004}
}

@article{Cleaveland_Sokolsky_2001,
  author =       {Cleaveland, Rance and Sokolsky, Oleg},
  doi =          {10.1016/b978-044482830-9/50024-2},
  journal =      {Handbook of Process Algebra},
  pages =        {391-424},
  title =        {Equivalence and preorder checking for finite-state
                  systems},
  year =         2001,
  bdsk-url-1 =   {https://doi.org/10.1016/b978-044482830-9/50024-2}
}

@article{Paige_Tarjan_1987,
  author =       {Paige, Robert and Tarjan, Robert E.},
  doi =          {10.1137/0216062},
  journal =      {SIAM Journal on Computing},
  month =        12,
  number =       6,
  pages =        {973-989},
  title =        {Three partition refinement algorithms},
  volume =       16,
  year =         1987,
  bdsk-url-1 =   {https://doi.org/10.1137/0216062}
}

@online{rust_2025,
  accessed = {2025-09-14},
  author = {The Rust teams},
  title = {Rust Programming Language},
  url = {https://rust-lang.org/},
  bdsk-url-1 = {https://rust-lang.org/}
}

@report{WebAssemblyCoreSpecification2,
	date = {2025-09-14},
	editor = {Rossberg, Andreas},
	institution = {{W3C}},
	langid = {english},
	title = {{WebAssembly Core Specification}},
	url = {https://www.w3.org/TR/wasm-core-2/},
	version = {2.0},
	bdsk-url-1 = {https://www.w3.org/TR/wasm-core-2/}}

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

@software{Borgna2025,
	author = {Agust{\'\i}n Borgna},
	date = {2025-09-30},
	license = {MIT OR Apache-2.0},
	title = {{petgraph}: Graph data structure library. Provides graph types and graph algorithms.},
	url = {https://github.com/petgraph/petgraph},
	version = {0.8.3},
	bdsk-url-1 = {https://github.com/petgraph/petgraph}}

@online{graphviz_2025,
	accessed = {2025-09-14},
	author = {Ellson, John},
	title = {Graphviz is open source graph visualization software.},
	url = {https://graphviz.org/doc/info/lang.html},
	bdsk-url-1 = {https://graphviz.org/doc/info/lang.html}}

@online{graphml_2025,
	accessed = {2025-09-14},
	author = {The GraphML Team},
	title = {GraphML is a comprehensive and easy-to-use file format for graphs.},
	url = {http://graphml.graphdrawing.org/},
	bdsk-url-1 = {http://graphml.graphdrawing.org/}}

@software{egui_node_graph22024,
	author = {trevyn},
	date = {2024-11-03},
	license = {MIT},
	title = {{egui\_node\_graph2}: A helper library to create interactive node graphs using egui},
	url = {https://github.com/trevyn/egui_node_graph2},
	version = {0.7.0},
	bdsk-url-1 = {https://github.com/trevyn/egui_node_graph2}}

@software{Ernerfeldt2025,
	author = {Emil Ernerfeldt},
	date = {2025-11-13},
	license = {MIT OR Apache-2.0},
	title = {{egui}: An easy-to-use immediate mode GUI that runs on both web and native},
	url = {https://github.com/emilk/egui},
	version = {0.33.2},
	bdsk-url-1 = {https://github.com/emilk/egui}}

@online{btree_2025,
	accessed = {2025-09-14},
	author = {The Rust teams},
	title = {An ordered set based on a B-Tree.},
	url = {https://doc.rust-lang.org/std/collections/struct.BTreeSet.html},
	bdsk-url-1 = {https://doc.rust-lang.org/std/collections/struct.BTreeSet.html}}

@online{arc_2025,
	accessed = {2025-09-14},
	author = {The Rust teams},
	title = {A thread-safe reference-counting pointer. `Arc' stands for `Atomically Reference Counted'.},
	url = {https://doc.rust-lang.org/std/sync/struct.Arc.html},
	bdsk-url-1 = {https://doc.rust-lang.org/std/sync/struct.Arc.html}}

@software{Rotem2025,
	author = {Nadav Rotem},
	date = {2025-04-24},
	license = {MIT},
	title = {{layout-rs}: A graph visualization program},
	url = {https://github.com/nadavrot/layout},
	version = {0.1.3},
	bdsk-url-1 = {https://github.com/nadavrot/layout}}

@software{Stampfl2025,
	author = {Laurenz Stampfl},
	date = {2025-04-17},
	license = {Apache-2.0 OR MIT},
	title = {{resvg}: An SVG rendering library.},
	url = {https://github.com/linebender/resvg},
	version = {0.45.1},
	bdsk-url-1 = {https://github.com/linebender/resvg}}

@software{wasm-bindgen2025,
	author = {daxpedda},
	date = {2025-10-27},
	license = {MIT OR Apache-2.0},
	title = {{wasm-bindgen}: Easy support for interacting between JS and Rust.},
	url = {https://github.com/wasm-bindgen/wasm-bindgen},
	version = {0.2.105},
	bdsk-url-1 = {https://github.com/wasm-bindgen/wasm-bindgen}}

@software{binaryen_2025,
	date = {2025-10-27},
	title = {{binaryen}: a compiler and toolchain infrastructure library for WebAssembly, written in C++.},
	url = {https://github.com/WebAssembly/binaryen},
	bdsk-url-1 = {https://github.com/WebAssembly/binaryen}}

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

@software{Ochtman2025,
	author = {Dirkjan Ochtman},
	date = {2025-11-07},
	license = {MIT OR Apache-2.0},
	title = {{flamegraph}: A simple cargo subcommand for generating flamegraphs, using inferno under the hood},
	url = {https://github.com/flamegraph-rs/flamegraph},
	version = {0.6.10},
	bdsk-url-1 = {https://github.com/flamegraph-rs/flamegraph}}

@article{Brodo_Bruni_Falaschi_Gori_Milazzo_2025,
  author =       {Brodo, Linda and Bruni, Roberto and Falaschi, Moreno
                  and Gori, Roberta and Milazzo, Paolo},
  doi =          {10.1007/s11047-025-10046-5},
  journal =      {Natural Computing},
  month =        9,
  title =        {Slicing analyses for negative dependencies in
                  Reaction Systems Modeling Gene Regulatory Networks},
  year =         2025,
  bdsk-url-1 =   {https://doi.org/10.1007/s11047-025-10046-5}
}

@article{Mitrana_Paun_Petre_Prelipcean_2025,
  author =       {Mitrana, Victor and P{\u a}un, Mihaela and Petre,
                  Ion and Prelipcean, Ana-Maria},
  doi =          {10.1109/iraset64571.2025.11008263},
  journal =      {2025 5th International Conference on Innovative
                  Research in Applied Science, Engineering and
                  Technology (IRASET)},
  month =        5,
  pages =        {1-6},
  title =        {Quantitative reaction systems},
  year =         2025,
  bdsk-url-1 =   {https://doi.org/10.1109/iraset64571.2025.11008263}
}

@article{Bottoni_Mitrana_Petre_2025,
  author =       {Bottoni, Paolo and Mitrana, Victor and Petre, Ion},
  doi =          {10.1007/978-3-031-97274-4_11},
  journal =      {Lecture Notes in Computer Science},
  pages =        {179-193},
  title =        {Multiset Reaction Systems},
  year =         2025,
  bdsk-url-1 =   {https://doi.org/10.1007/978-3-031-97274-4_11}
}

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

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

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

@article{Brodo_Bruni_Falaschi_Gori_Milazzo_Montagna_Pulieri_2024,
  author =       {Brodo, Linda and Bruni, Roberto and Falaschi, Moreno
                  and Gori, Roberta and Milazzo, Paolo and Montagna,
                  Valeria and Pulieri, Pasquale},
  doi =          {10.1007/s10009-024-00757-y},
  journal =      {International Journal on Software Tools for
                  Technology Transfer},
  month =        6,
  number =       4,
  pages =        {509-526},
  title =        {Causal analysis of positive reaction systems},
  volume =       26,
  year =         2024,
  bdsk-url-1 =   {https://doi.org/10.1007/s10009-024-00757-y}
}

@inbook{Ehrenfeucht_Rozenberg_2004,
  place =        {Auckland, New Zealand},
  title =        {Basic Notions of Reaction Systems},
  volume =       {8th International Conference},
  booktitle =    {Developments in Language Theory},
  publisher =    {Springer},
  author =       {A. Ehrenfeucht and G. Rozenberg},
  year =         2004,
  pages =        {27-29}
}

@article{Ehrenfeucht_Rozenberg_2007,
  author =       {Ehrenfeucht, A. and Rozenberg, G.},
  title =        {Reaction Systems},
  year =         2007,
  issue_date =   {January 2007},
  publisher =    {IOS Press},
  address =      {NLD},
  volume =       75,
  number =       {1-4},
  issn =         {0169-2968},
  abstract =     {Interactions between biochemical reactions lie at
                  the heart of functioning of a living cell. In order
                  to formalize these interactions we introduce
                  reaction systems. We motivate them by explicitely
                  stating a number of assumptions/axioms that (we
                  believe) hold for a great number of biochemical
                  reactions - we point out that these assumptions are
                  very different from the ones underlying traditional
                  models of computation. The paper provides the basic
                  definitions, illustrates them by biology and
                  computer science oriented examples, relates reaction
                  systems to some traditional models of computation,
                  and proves some basic properties of reaction
                  systems.},
  journal =      {Fundam. Inf.},
  month =        jan,
  pages =        {263-280},
  numpages =     18
}

@inbook{Clark_Pazdernik_McGehee_2018,
  edition =      {3rd},
  title =        {Regulation of Transcription in Prokaryotes},
  booktitle =    {Molecular Biology},
  publisher =    {Academic Press},
  author =       {Clark, David P. and Pazdernik, Nanette J. and
                  McGehee, Michelle R.},
  year =         2018,
  pages =        {532-542}
}

@Misc{git,
  key =          {https://git-scm.com/},
  author =       {Junio Hamano and others},
  title =        {Git},
  year =         2025
}

@Misc{rustup,
  key =          {https://rustup.rs/},
  author =       {The Rust Project},
  title =        {Rustup: the Rust toolchain installer},
  year =         2025
}