Index: Tutorials

Welcome to the ssbio Binder! Here you can interactively launch notebook tutorials or even alter them to run on your own data.

Testing

These notebooks make sure the Binder environment has been installed correctly.

• Software Installation Tester - This notebook simply tests if external programs have been installed correctly and can run in a Binder environment.
• I-TASSER and TMHMM Install Guide - 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.

The GEM-PRO Pipeline

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.

• GEM-PRO - SBML Model (iNJ661) - This notebook gives an example of how to run the GEM-PRO pipeline with a SBML model, in this case iNJ661, the metabolic model of M. tuberculosis.
• GEM-PRO - Genes & Sequences - This notebook gives an example of how to run the GEM-PRO pipeline with a dictionary of gene IDs and their protein sequences.
• GEM-PRO - List of Gene IDs - This notebook gives an example of how to run the GEM-PRO pipeline with a list of gene IDs.
• GEM-PRO - Calculating Protein Properties - This notebook gives an example of how to calculate protein properties for a list of proteins.

The Protein Class

• Protein - Structure Mapping, Alignments, and Visualization - 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.

The StructProp Class

• PDBProp - Working With a Single PDB Structure - This notebook gives a tutorial of the PDBProp object, specifically how chains are handled and how to map a sequence to it.

The SeqProp Class

• SeqProp - Protein Sequence Properties - This notebook gives an overview the available calculations for properties of a single protein sequence.

Other tutorials

• SWISS-MODEL - Downloading homology models - 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.
• FATCAT - Structure Similarity - This notebook shows how to run and parse FATCAT, a structural similarity calculator.