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fabriciocravofabriciocravo
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Added final notebooks requested by reviwers
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‎docs/example_models/tutorial_notebooks/.ipynb_checkpoints/10_Reaction_Rates-checkpoint.ipynb

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‎docs/example_models/tutorial_notebooks/.ipynb_checkpoints/18_Reversible_Reactions-checkpoint.ipynb

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{
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"cells": [],
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"metadata": {},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎docs/example_models/tutorial_notebooks/.ipynb_checkpoints/19_Plot_Configuration-checkpoint.ipynb

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{
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"cells": [],
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"metadata": {},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎docs/example_models/tutorial_notebooks/10_Reaction_Rates.ipynb

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"S = Simulation(A_Count | A_Con | P)\n",
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"print(S.compile())"
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]
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},
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{
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"cell_type": "markdown",
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"id": "9e2f8527-25ef-42f3-b0da-7add0cc2e225",
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"metadata": {},
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"source": [
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"## Strings for Rates\n",
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"\n",
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"MobsPy allows rates to be supplied as string types. If a string is supplied as a rate, it will be taken as it is without any modifications. Therefore, string versions of numbers will not have mass-action kinetics applied to them and expressions will not be checked for correctness. "
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "venv",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.7"
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"version": "3.13.1"
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}
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},
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"nbformat": 4,

‎docs/example_models/tutorial_notebooks/18_Reversible_Reactions.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "86fb738a-7e02-4130-a660-1bfa90110cb3",
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"metadata": {},
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"source": [
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"## Reversible Reactions \n",
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"\n",
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"MobsPy has two available syntaxes for reversible reactions. Firstly, if a meta-reaction is defined with two rates instead of one, two meta-reactions will be defined. The direct sense with the first rate and the backwards sense with the second rate. \n",
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"\n",
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"Here is an example:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "408db175-d6e8-4fe1-9b47-32b2634fe85b",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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"Species\n",
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"A,0\n",
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"\n",
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"Mappings\n",
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"A :\n",
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"A\n",
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"\n",
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"Parameters\n",
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"volume,1\n",
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"\n",
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"Reactions\n",
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"reaction_0,{'re': [(1, 'A')], 'pr': [], 'kin': '((2*(100-A))*A)'}\n",
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"reaction_1,{'re': [], 'pr': [(1, 'A')], 'kin': '1 * volume'}\n",
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"\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Compiling model\n"
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]
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}
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],
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"source": [
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"from mobspy import *\n",
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"\n",
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"A = BaseSpecies()\n",
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"\n",
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"A >> Zero [lambda r: 2*(100 - r)*r, 1]\n",
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"\n",
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"S = Simulation(A)\n",
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"print(S.compile())"
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]
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},
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{
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"cell_type": "markdown",
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"id": "55c92ce6-985a-463c-a4e7-18b62c8b5de6",
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"metadata": {},
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"source": [
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"The other reversible reaction notation uses the Rev operator and an example follows bellow "
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "a2f2bf5d-64c9-49e2-af7b-47849e25fd6e",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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"Species\n",
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"A,0\n",
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"\n",
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"Mappings\n",
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"A :\n",
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"A\n",
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"\n",
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"Parameters\n",
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"volume,1\n",
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"\n",
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"Reactions\n",
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"reaction_0,{'re': [(1, 'A')], 'pr': [], 'kin': '((2*(100-A))*A)'}\n",
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"reaction_1,{'re': [], 'pr': [(1, 'A')], 'kin': '1 * volume'}\n",
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"\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Compiling model\n"
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]
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}
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],
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"source": [
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"from mobspy import *\n",
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"\n",
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"A = BaseSpecies()\n",
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"\n",
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"Rev[A >> Zero][lambda r: 2*(100 - r)*r, 1]\n",
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"\n",
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"S = Simulation(A)\n",
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"print(S.compile())"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4d097916-bf4c-4d26-8d2c-464ca7bb12ce",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎docs/example_models/tutorial_notebooks/19_Plot_Configuration.ipynb

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‎for_local_use.py

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if __name__ == '__main__':
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pass
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