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Add Colab badges and install cells to notebooks
Added 'Open in Colab' badges and initial %pip install cells to Basic.ipynb and KineticModelling.ipynb for easier setup and execution in Google Colab.
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examples/Basic.ipynb

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"source": [
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"# Basic PyEnzyme usage\n",
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"\n",
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"<a target=\"_blank\" href=\"https://colab.research.google.com/github/EnzymeML/PyEnzyme/blob/main/examples/Basic.ipynb\">\n",
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" <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
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"</a>\n",
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"\n",
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"This notebook demonstrates the basic usage of PyEnzyme:\n",
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"\n",
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"* Creating an EnzymeML document from scratch\n",
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"* Converting to SBML and PeTab"
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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": "90fe9fe1",
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"metadata": {},
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"outputs": [],
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"source": [
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"%pip install pyenzyme"
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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,

examples/KineticModelling.ipynb

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"source": [
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"# Kinetic Modelling with PySCeS\n",
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"\n",
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"<a target=\"_blank\" href=\"https://colab.research.google.com/github/EnzymeML/PyEnzyme/blob/main/examples/KineticModelling.ipynb\">\n",
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" <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n",
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"</a>\n",
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"\n",
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"This notebook demonstrates how to utilize the [PySCeS](https://pysces.sourceforge.io/) library to model kinetic data.\n",
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"\n",
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"We will use the [abts_reaction.json](./data/abts_reaction.json) EnzymeML document as an example, which describes the oxidation of [ABTS](https://en.wikipedia.org/wiki/ABTS) catalyzed by a [Small Laccase](https://pmc.ncbi.nlm.nih.gov/articles/PMC2280001/).\n",
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"Lets explore the PySCeS thin layer in more detail!"
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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": "5debd1d7",
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"metadata": {},
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"outputs": [],
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"source": [
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"%pip install pyenzyme pysces lmfit"
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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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