isatools-notebooks

This repository contains notebooks to demonstrate the isatools software package.

Create a simple ISA descriptor.ipynb - Create ISA files using the ISA model objects.

Update Investigation using ISA Model.ipynb - Load an ISA-Tab, update it using ISA model objects, and write back to ISA-Tab.

Study Designer (Sample QC injection).ipynb - Generate ISA-Tab using the sample planning objects with quality control elements.

Study Designer (DNA microarray).ipynb - Generate ISA-Tab using sample and assay planning for DNA microarray.

Study Designer (DNA sequencing).ipynb - Generate ISA-Tab using sample and assay planning for DNA sequencing.

Study Designer (Mass spectrometry).ipynb - Generate ISA-Tab using sample and assay planning for MS.

Study Designer (NMR).ipynb - Generate ISA-Tab using sample and assay planning for NMR.

To run locally:

In the terminal window

Install Python requirements with pip install -r requirements.txt.

In Python

If your using qgrid, either in your Jupyter Notebook or in a Python or iPython console, ensure the following lines are run once to make sure qgrid is fully installed into your Jupyter instance:

import qgrid
qgrid.nbinstall(overwrite=True)

This copies some JavaScript that qgrid needs to render tables in Jupyter. See here for further clarification.

In the terminal window again

Before starting Jupyter (or if you did the previous step inside Jupyter, exit Jupyter first and return to the terminal prompt), please ensure notebook extensions are enabled with jupyter nbextension enable --py widgetsnbextension.

Start Jupyter Notebook with jupyter notebook. This should automatically spawn a browser Window running Jupyter. If it does not, in the terminal window it will give you a link in some text like:

    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://localhost:8888/?token=cf7362977cda558549f13d5a8d40b6929a6c49700a36d56b

*Hint: On MacOS if jupyter notebook does not automatically open the browser for you, try run export BROWSER=open first. You can add this EXPORT line to your ~/.bash_profile.

Alternatively

Or run using the dockerfile: docker build -t isatools . then docker run -it -im -p 8888:888 isatools

If you can't find your local Jupyter running, try docker-machine ls to get the IP instead of using localhost:8888.