🎤 RAPS: R Aid for P systems

Welcome to the repository behind the RAPS package.

NEWS: Last 21 / 11 / 2022 RAPS 1.0.0 was launched. Have a good time trying it!.

Quickstart

Run the following to install the package locally, directly from GitHub:

devtools::install_github("Xopre/RAPS")

Now you can run every example in the demos' folder. Give the deterministic waiting time algorithm a try!

Main workflow with RAPS:

  graph TD;
    url/path-->path2rap;
    path2rap-->rap;

    load_demo_dataset-->rap;
    
    rap-->choose_rule;
    choose_rule-->apply_rule;
    apply_rule-->new_rap;

    rap-->simulate;
    simulate-->new_rap;

    rap-->alg_gillespie_menv;
    rap-->alg_det_menv;
    alg_det_menv-->new_rap;
    alg_gillespie_menv-->new_rap;

    rap-->get_rule_by_id;
    get_rule_by_id-->show_rule;

    rap-->show_rap;
    new_rap-->show_rap;

Loading

In RAPS we use the rap (Representing A P system) objects, which have the following aspect:

$Configuration

Environment	ID	Label	Objects	SuperM	SubM	Charge	Other_params
1	1	1	[(a, 1)]	0	[2,3]	-1	@immutable
1	2	2	[(b, 2), (c,3)]	1	NULL	+1	NA
1	3	3	[(@filler, 1)]	1	NULL	+1	NA

$Rules

rule_id	dissolves	priority	main_membrane_label	lhs	rhs	propensity
value0	FALSE	-	1	$lhs_1$	$rhs_1$	1974

$Properties

System	PLingua_model	N_membranes	N_environments	N_objects	N_rules
FAS	Stochastic	4	1	53	99

where:

$$lhs_1 = \begin{pmatrix} where & object & multiplicity \\ \hline \\ @here & a & 1 \\ mem_2 & b & 2 \\ @exists & mem_3 & 1 \\ \end{pmatrix}$$

$$rhs_1 = \begin{pmatrix} where & object & multiplicity \\ \hline \\ @here & ap & 2 \\ mem_2 & bp & 3 \\ \end{pmatrix}$$

Main functions

• path2rap(): Create a rap object from a path.
• alg_det_menv(): Run the deterministic algorithm on a rap object.
• alg_gillespie_menv(): Run the Gillespie algorithm on a rap object.
• simulate(): Run a custom simulation algorithm on a rap object.
• show_rap(): Show a rap object.
• apply_rule(): Apply a rule to a rap object.
• choose_rule(): Choose a rule to apply.

Supported rules

Supported rules:

• Evolution: $[u \rightarrow v]_i$
• In-communication: $[\ u \rightarrow v_1 \ [v_2]_j\ ]_i$
• Out-communication: $[\ u_1 \ [u_2]_j \rightarrow v\ ]_i$
• In/Out-communication: $[\ u_1 \ [u_2]_j \rightarrow v_1 \ [v_2]_k\ ]_i$

Will-be-supported rules, by priority:

1. Charge change: $[u]_i^{\alpha} \rightarrow [v]_i^{\beta}$
2. Dissolution: $[u \rightarrow v, \lambda]_i$
3. Membrane generation: $u \rightarrow [\ ]_i$
4. Membrane division: $[a]_i \rightarrow [b]_j [c]_k$

Might be supported but are nonstandard:

• Presence of one or more membranes: $[\ ]_i [\ ]_j \rightarrow a$
• Presence of the residual of an object: $a^0 \rightarrow b$
• Crazy multicommunication: $[u_1]i [u_2]j [u_3]k \rightarrow [v_1]{ip} [v_2]{jp} [v_3]{kp}$

Other stuff

• Check this presentation

General objectives:

• Create README.md

• Complete README.md

  • Workflow diagram
  • Functional demos
  • Simulation of stochastic P systems
    • Monoenvironmental Gillespie algorithm
    • Multienvironmental Gillespie algorithm
      • With control over time
      • Validated with FAS
    • Multienvironmental deterministic waiting time algorithm
      • With control over time
      • Validated with FAS

• Establish the deprecated functions as such

• Prepare RAPS object for monoenvironmental P systems

• Prepare RAPS object for multienvironmental P systems

• Adapt parser to P-Lingua 5 in function path2rap()

• Create one or more simulators for RAPS' objects

Repository contents

• .Rproj.user/: User data.
• demos/: Examples of use of the RAPS package.
• man/: roxygen2-generated documentation.
• R/: The functions included in this package.
• RData/: RData for some demos.
• renv/: Folder for the renv package.
• semantics/: Folder for different semantics.
• utils/: Some auxiliar code. Do not pay much attention.
  • UPDATE.R: Utility for updating the package.
  • RAPS_package.Rmd: The father of UPDATE.R.
• .gitignore: git-ignored files.
• .Rbuildignore: Build ignored files.
• .Rhistory: Ignore this. Should be empty.
• .Rprofile: My profile.
• DESCRIPTION: Description of the package.
• NAMESPACE: roxygen2-generated documentation about exports.
• RAPS.Rproj: The project wherein everything is developed.
• README.md: The document you're reading right now.
• renv.lock: Info for the renv package.

Future work

• Improve the R workflow within GitHub.
• Include the tictoc or the lubridate packages to control time in a convenient way.
• Design custom hexSticker.