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    "# Index: Tutorials\n",
    "Welcome to the *ssbio* Binder! Here you can interactively launch notebook tutorials or even alter them to run on your own data.\n",
    "\n",
    "## Testing\n",
    "These notebooks make sure the Binder environment has been installed correctly.\n",
    "\n",
    "* [Software Installation Tester](docs/notebooks/Software Installation Tester.ipynb) - This notebook simply tests if external programs have been installed correctly and can run in a Binder environment.\n",
    "* [I-TASSER and TMHMM Install Guide](docs/notebooks/I-TASSER and TMHMM Install Guide.ipynb) - This notebook provides a guide to installing I-TASSER and TMHMM in Binder, since these require you to register with your email and cannot be installed beforehand.\n",
    "\n",
    "## The GEM-PRO Pipeline\n",
    "The GEM-PRO pipeline is focused on annotating genome-scale models with protein structure information, and subsequently making it easier to work with proteins at this scale.\n",
    "\n",
    "* [GEM-PRO - SBML Model (iNJ661)](docs/notebooks/GEM-PRO - SBML Model.ipynb) - This notebook gives an example of how to run the GEM-PRO pipeline with a **SBML model**, in this case *i*NJ661, the metabolic model of *M. tuberculosis*.\n",
    "* [GEM-PRO - Genes & Sequences](docs/notebooks/GEM-PRO - Genes & Sequences.ipynb) - This notebook gives an example of how to run the GEM-PRO pipeline with a **dictionary of gene IDs and their protein sequences**.\n",
    "* [GEM-PRO - List of Gene IDs](docs/notebooks/GEM-PRO - List of Gene IDs.ipynb) - This notebook gives an example of how to run the GEM-PRO pipeline with a **list of gene IDs**.\n",
    "* [GEM-PRO - Calculating Protein Properties](docs/notebooks/GEM-PRO - Calculating Protein Properties.ipynb) - This notebook gives an example of how to **calculate protein properties** for a list of proteins.\n",
    "\n",
    "## The Protein Class\n",
    "* [Protein - Structure Mapping, Alignments, and Visualization](docs/notebooks/Protein - Structure Mapping, Alignments, and Visualization.ipynb) - This notebook gives an example of how to **map a single protein sequence to its structure**, along with conducting sequence alignments and visualizing the mutations.\n",
    "\n",
    "## The StructProp Class\n",
    "* [PDBProp - Working With a Single PDB Structure](docs/notebooks/PDBProp - Working With a Single PDB Structure.ipynb) - This notebook gives a tutorial of the **PDBProp object**, specifically how chains are handled and how to map a sequence to it.\n",
    "\n",
    "## The SeqProp Class\n",
    "* [SeqProp - Protein Sequence Properties](docs/notebooks/SeqProp - Protein Sequence Properties.ipynb) - This notebook gives an overview the available **calculations for properties of a single protein sequence**.\n",
    "\n",
    "## Other tutorials\n",
    "* [SWISS-MODEL - Downloading homology models](docs/notebooks/SWISS-MODEL - Downloading homology models.ipynb) - This notebook gives a tutorial of the **SWISSMODEL object**, which is a simple class to parse and download models from the SWISS-MODEL homology model repository.\n",
    "* [FATCAT - Structure Similarity](docs/notebooks/FATCAT - Structure Similarity.ipynb) - This notebook shows how to run and parse FATCAT, a structural similarity calculator."
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