{ "cells": [ { "cell_type": "markdown", "id": "eaa3d3d4-8573-469e-80e6-ec2aaaab39da", "metadata": { "tags": [] }, "source": [ "
\n", " \"icon_proposal.svg\"\n", "
\n", "\n", "# Gempipe documentation\n", "\n", "Gempipe is a tool for drafting, curating and analyzing pan and multi-strain genome-scale metabolic models (GSMMs or GEMs)." ] }, { "cell_type": "markdown", "id": "74ec63a7-1781-4316-8c6d-431c32deb3d1", "metadata": { "jp-MarkdownHeadingCollapsed": true, "tags": [] }, "source": [ "```{toctree}\n", ":maxdepth: 1\n", "\n", "introduction.ipynb\n", "```" ] }, { "cell_type": "markdown", "id": "90fe0138-5778-4f8e-892c-171d289b20f8", "metadata": {}, "source": [ "```{toctree}\n", ":maxdepth: 1\n", "\n", "how_to_install.ipynb\n", "```" ] }, { "cell_type": "markdown", "id": "90c7d512-ebc4-41d9-a386-8f79b6b7450a", "metadata": { "jp-MarkdownHeadingCollapsed": true, "tags": [] }, "source": [ "```{toctree}\n", ":maxdepth: 2\n", "\n", "part_1_gempipe_recon.ipynb\n", "part_2_manual_curation.ipynb\n", "part_3_gempipe_derive.ipynb\n", "part_4_multi_strain_analysis.ipynb\n", "gempipe_autopilot.ipynb\n", "```" ] }, { "cell_type": "markdown", "id": "73747378-5d02-4c73-bd6a-172818d070db", "metadata": {}, "source": [ "```{toctree}\n", ":maxdepth: 1\n", "\n", "how_to_cite.ipynb\n", "```" ] }, { "cell_type": "markdown", "id": "78dda056-88e6-480a-888e-a24f3f15246d", "metadata": {}, "source": [ "```{toctree}\n", ":maxdepth: 1\n", ":caption: API\n", ":hidden:\n", "\n", "autoapi/gempipe/interface/index\n", "tutorial_sanity_check.ipynb\n", "tutorial_gapfilling.ipynb\n", "tutorial_clustering.ipynb\n", "```" ] }, { "cell_type": "markdown", "id": "1b004b37-a9f1-4833-938a-309e04624f40", "metadata": {}, "source": [ "\n", "" ] }, { "cell_type": "code", "execution_count": null, "id": "07df7917-5d17-495d-be48-f59738b934e8", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.15" } }, "nbformat": 4, "nbformat_minor": 5 }