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Merge pull request #62 from BrainAnnex/dev
Dev Beta31
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‎LICENSE.txt‎

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MIT License
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Copyright (c) 2022 Julian West
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Copyright (c) 2022-2024 Julian West
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎README.md‎

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### BETA 30.1 (v0.30.1)
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# Life123
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Dynamical Modeling of Biological Systems in 1, 2 and 3D (as well as single-compartment reactions)
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‎VERSION_NUMBER.txt‎

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version 1.0.0-beta.31

‎experiments/1D/diffusion/diffusion_1.ipynb‎

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‎experiments/1D/reaction/down_regulation_1.ipynb‎

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‎experiments/1D/reaction/down_regulation_1.log.htm‎

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<meta charset="UTF-8">
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<title>Log</title>
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<link type="text/css" rel="stylesheet" href="https://life123.science/libraries/vue_components/vue_cytoscape_1.css">
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<link type="text/css" rel="stylesheet" href="https://life123.science/libraries/vue_components/vue_cytoscape_2.css">
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<script src="https://life123.science/libraries/vue_2.6.12.js"></script>
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<script src="https://d3js.org/d3.v7.min.js"></script>
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</head>
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<body>
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<h3>List of reactions:</h3><span style='padding-left:4ch'>&nbsp;</span>0: A + 2 B <-> Y<br>
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<div id="vue-root-1"> <!-- DIV container for the VUE COMPONENTS below : Vue ROOT element -->
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<vue_cytoscape_1
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v-bind:graph="graph_json"
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v-bind:color_mapping="color_mapping_json"
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v-bind:component_id="component_id_json"
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>
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</vue_cytoscape_1>
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<vue_cytoscape_2 v-bind:graph_data="graph_data_json">
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</vue_cytoscape_2>
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</div> <!-- ~~~~~~~~~~~~~~~~~~~~~ END of Vue root element ~~~~~~~~~~~~~~~~~ -->
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<!--
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Vue components (and other JS). This must appear AFTER the Vue-containing elements
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-->
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<script src="https://life123.science/libraries/vue_components/vue_cytoscape_1.js"></script>
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<script src="https://life123.science/libraries/vue_components/vue_cytoscape_2.js"></script>
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<script>
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// Instantiation of the Vue ROOT component
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new Vue({
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el: '#vue-root-1',
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data: {
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graph_json: [{"id": 3, "label": "Reaction", "name": "RXN", "kF": "8", "kR": "2", "delta_G": "-3,436.56", "K": "4"}, {"id": 2, "label": "Chemical", "name": "Y", "diff_rate": null, "stoich": 1, "rxn_order": 1}, {"id": 4, "source": 3, "target": 2, "name": "produces"}, {"id": 0, "label": "Chemical", "name": "A", "diff_rate": null, "stoich": 1, "rxn_order": 1}, {"id": 5, "source": 0, "target": 3, "name": "reacts"}, {"id": 1, "label": "Chemical", "name": "B", "diff_rate": null, "stoich": 2, "rxn_order": 1}, {"id": 6, "source": 1, "target": 3, "name": "reacts"}],
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color_mapping_json: {"Chemical": "neo4j_green", "Reaction": "neo4j_lightbrown"},
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component_id_json: 1
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graph_data_json: {"structure": [{"name": "RXN", "kF": "8", "kR": "2", "delta_G": "-3,436.56", "K": "4", "id": "R-0", "labels": ["Reaction"]}, {"name": "Y", "diff_rate": null, "id": "C-2", "labels": ["Chemical"]}, {"name": "produces", "source": "R-0", "target": "C-2", "id": "edge-1", "stoich": 1, "rxn_order": 1}, {"name": "A", "diff_rate": null, "id": "C-0", "labels": ["Chemical"]}, {"name": "reacts", "source": "C-0", "target": "R-0", "id": "edge-2", "stoich": 1, "rxn_order": 1}, {"name": "B", "diff_rate": null, "id": "C-1", "labels": ["Chemical"]}, {"name": "reacts", "source": "C-1", "target": "R-0", "id": "edge-3", "stoich": 2, "rxn_order": 1}], "color_mapping": {"Chemical": "#8DCC92", "Reaction": "#D9C8AD"}, "caption_mapping": {"Chemical": "name", "Reaction": "name"}, "component_id": 1}
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}
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});

‎experiments/1D/reaction/down_regulation_1.py‎

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#
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# Based on experiment `reactions_single_compartment/down_regulate_2`
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#
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# LAST REVISED: Dec. 6, 2023
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# LAST REVISED: May 6, 2024
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# %%
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import set_path # Importing this module will add the project's home directory to sys.path
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# Set up the use of some specified graphic (Vue) components
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GraphicLog.config(filename=log_file,
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components=["vue_cytoscape_1"],
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components=["vue_cytoscape_2"],
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extra_js="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.21.2/cytoscape.umd.js")
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# %%
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chem_data.describe_reactions()
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# Send the plot of the reaction network to the HTML log file
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graph_data = chem_data.prepare_graph_network()
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GraphicLog.export_plot(graph_data, "vue_cytoscape_1")
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chem_data.plot_reaction_network("vue_cytoscape_2")
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# %%
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bio = BioSim1D(n_bins=1, chem_data=chem_data)

‎experiments/1D/reaction/reaction_1.ipynb‎

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‎experiments/1D/reaction/reaction_1.log.htm‎

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<meta charset="UTF-8">
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<title>Log</title>
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<link type="text/css" rel="stylesheet" href="https://life123.science/libraries/vue_components/vue_cytoscape_1.css">
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<link type="text/css" rel="stylesheet" href="https://life123.science/libraries/vue_components/vue_cytoscape_2.css">
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<script src="https://life123.science/libraries/vue_2.6.12.js"></script>
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<script src="https://d3js.org/d3.v7.min.js"></script>
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</head>
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<body>
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<h3>List of reactions:</h3><span style='padding-left:4ch'>&nbsp;</span>0: A <-> B<br>
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<div id="vue-root-1"> <!-- DIV container for the VUE COMPONENTS below : Vue ROOT element -->
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<vue_cytoscape_1
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v-bind:graph="graph_json"
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v-bind:color_mapping="color_mapping_json"
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v-bind:component_id="component_id_json"
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>
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</vue_cytoscape_1>
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<vue_cytoscape_2 v-bind:graph_data="graph_data_json">
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</vue_cytoscape_2>
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</div> <!-- ~~~~~~~~~~~~~~~~~~~~~ END of Vue root element ~~~~~~~~~~~~~~~~~ -->
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<!--
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Vue components (and other JS). This must appear AFTER the Vue-containing elements
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-->
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<script src="https://life123.science/libraries/vue_components/vue_cytoscape_1.js"></script>
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<script src="https://life123.science/libraries/vue_components/vue_cytoscape_2.js"></script>
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<script>
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// Instantiation of the Vue ROOT component
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new Vue({
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el: '#vue-root-1',
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data: {
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graph_json: [{"id": 2, "label": "Reaction", "name": "RXN", "kF": "3", "kR": "2", "Delta_G": "-1,005.13", "K": "1.5"}, {"id": 1, "label": "Chemical", "name": "B", "diff_rate": null, "stoich": 1, "rxn_order": 1}, {"id": 3, "source": 2, "target": 1, "name": "produces"}, {"id": 0, "label": "Chemical", "name": "A", "diff_rate": null, "stoich": 1, "rxn_order": 1}, {"id": 4, "source": 0, "target": 2, "name": "reacts"}],
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color_mapping_json: {"Chemical": "neo4j_green", "Reaction": "neo4j_lightbrown"},
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component_id_json: 1
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graph_data_json: {"structure": [{"name": "RXN", "kF": "3", "kR": "2", "delta_G": "-1,005.13", "K": "1.5", "id": "R-0", "labels": ["Reaction"]}, {"name": "B", "diff_rate": null, "id": "C-1", "labels": ["Chemical"]}, {"name": "produces", "source": "R-0", "target": "C-1", "id": "edge-1", "stoich": 1, "rxn_order": 1}, {"name": "A", "diff_rate": null, "id": "C-0", "labels": ["Chemical"]}, {"name": "reacts", "source": "C-0", "target": "R-0", "id": "edge-2", "stoich": 1, "rxn_order": 1}], "color_mapping": {"Chemical": "#8DCC92", "Reaction": "#D9C8AD"}, "caption_mapping": {"Chemical": "name", "Reaction": "name"}, "component_id": 1}
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}
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});

‎experiments/1D/reaction/reaction_1.py‎

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#
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# See also the experiment _"reactions_single_compartment/react_1"_
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#
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# LAST REVISED: July 14, 2023
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# LAST REVISED: May 6, 2024
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# %%
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import set_path # Importing this module will add the project's home directory to sys.path
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# Set up the use of some specified graphic (Vue) components
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GraphicLog.config(filename=log_file,
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components=["vue_cytoscape_1"],
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components=["vue_cytoscape_2"],
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extra_js="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.21.2/cytoscape.umd.js")
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# %% [markdown]
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# %%
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# Send a plot of the network of reactions to the HTML log file
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graph_data = chem_data.prepare_graph_network()
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GraphicLog.export_plot(graph_data, "vue_cytoscape_1")
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chem_data.plot_reaction_network("vue_cytoscape_2")
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# %% [markdown] tags=[]
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# ### <a name="sec_1"></a>First step

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