appendix, instroduction
This commit is contained in:
elvis
433
document.bib
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document.bib
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}
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}
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|
||||
}
|
||||
|
||||
@Online{rust_2025,
|
||||
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|
||||
author = {The Rust teams},
|
||||
title = {Rust Programming Language},
|
||||
url = {https://rust-lang.org/}
|
||||
@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,
|
||||
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},
|
||||
}
|
||||
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},
|
||||
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{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 = {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},
|
||||
}
|
||||
@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},
|
||||
title = {Graphviz is open source graph visualization
|
||||
software.},
|
||||
author = {Ellson, John},
|
||||
url = {https://graphviz.org/doc/info/lang.html},
|
||||
}
|
||||
@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},
|
||||
title = {GraphML is a comprehensive and easy-to-use file
|
||||
format for graphs.},
|
||||
author = {The GraphML Team},
|
||||
url = {http://graphml.graphdrawing.org/},
|
||||
}
|
||||
@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},
|
||||
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{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},
|
||||
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},
|
||||
}
|
||||
@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},
|
||||
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{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},
|
||||
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},
|
||||
}
|
||||
@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},
|
||||
title = {{layout-rs}: A graph visualization program},
|
||||
url = {https://github.com/nadavrot/layout},
|
||||
date = {2025-04-24},
|
||||
version = {0.1.3},
|
||||
license = {MIT},
|
||||
}
|
||||
@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},
|
||||
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{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},
|
||||
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{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,
|
||||
title = {{binaryen}: a compiler and toolchain infrastructure
|
||||
library for WebAssembly, written in C++.},
|
||||
date = {2025-10-27},
|
||||
url = {https://github.com/WebAssembly/binaryen},
|
||||
}
|
||||
@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,
|
||||
title = {perf(1) — Linux manual page},
|
||||
@manual{manualperf_2025,
|
||||
edition = {6.17-2},
|
||||
month = 11,
|
||||
year = 2025,
|
||||
title = {perf(1) - Linux manual page},
|
||||
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},
|
||||
}
|
||||
@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,
|
||||
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},
|
||||
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,
|
||||
month = 9
|
||||
bdsk-url-1 = {https://doi.org/10.1007/s11047-025-10046-5}
|
||||
}
|
||||
|
||||
@article{Mitrana_Păun_Petre_Prelipcean_2025,
|
||||
title = {Quantitative reaction systems},
|
||||
DOI = {10.1109/iraset64571.2025.11008263},
|
||||
@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)},
|
||||
author = {Mitrana, Victor and Păun, Mihaela and Petre, Ion and
|
||||
Prelipcean, Ana-Maria},
|
||||
year = 2025,
|
||||
month = 5,
|
||||
pages = {1–6}
|
||||
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,
|
||||
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},
|
||||
doi = {10.1007/978-3-031-97274-4_11},
|
||||
journal = {Lecture Notes in Computer Science},
|
||||
pages = {179-193},
|
||||
title = {Multiset Reaction Systems},
|
||||
year = 2025,
|
||||
pages = {179–193}
|
||||
bdsk-url-1 = {https://doi.org/10.1007/978-3-031-97274-4_11}
|
||||
}
|
||||
|
||||
@Misc{ReactionSystemsGit,
|
||||
@misc{ReactionSystemsGit,
|
||||
author = {Rossi, Elvis},
|
||||
title = {ReactionSystems},
|
||||
publisher = {GitHub},
|
||||
journal = {GitHub repository},
|
||||
howpublished = {\url{https://github.com/elvisrossi/ReactionSystems}},
|
||||
year = 2025,
|
||||
journal = {GitHub repository},
|
||||
publisher = {GitHub},
|
||||
title = {ReactionSystems},
|
||||
year = 2025
|
||||
}
|
||||
|
||||
@Misc{ReactionSystemsGUIGit,
|
||||
@misc{ReactionSystemsGUIGit,
|
||||
author = {Rossi, Elvis},
|
||||
title = {ReactionSystems},
|
||||
publisher = {GitHub},
|
||||
journal = {GitHub repository},
|
||||
howpublished =
|
||||
{\url{https://github.com/elvisrossi/ReactionSystemsGUI}},
|
||||
year = 2025,
|
||||
journal = {GitHub repository},
|
||||
publisher = {GitHub},
|
||||
title = {ReactionSystems},
|
||||
year = 2025
|
||||
}
|
||||
|
||||
@Misc{BioResolve2025,
|
||||
@misc{BioResolve2025,
|
||||
howpublished = {\url{https://pages.di.unipi.it/bruni/LTSRS/}},
|
||||
title = {BioResolve web page, a Prolog interpreter for
|
||||
Reaction Systems analysis.},
|
||||
howpublished = {\url{https://pages.di.unipi.it/bruni/LTSRS/}},
|
||||
year = 2025,
|
||||
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},
|
||||
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,
|
||||
month = {6},
|
||||
pages = {509–526}
|
||||
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
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user