Collection of random .ipynb tutorials and experiments.

I mount this directory into ~/work in a jupyterlab docker container running locally. Pushing up to GH to explore ways of collaboratively playing with a common notebook with friends & fam.

Dockerfile is included w/ deps for conda-forge, pydna (BjornFJohansson), biopython, numpy, pydna, mpldatacursor, pint. Have added a few more python packages and notebook kernels to my local image but haven't kept them in sync w/ the dockerfile.

It'd be nice to have an easy, repeatable way of provisioning/tearing-down an on-demand cloud-based dockerized jupyter environment for myself and some friends. Looks like a configuration rabbit-hole for now, though. Maaaaybe someone already has a nice ansible script for google cloud platform etc? yencarnacion/GCP-jupyter-notebook

Simple alternatives to setting up a dockerized jupyterlab cloud instance:

1. mybinder.org - github repo -> transient dockerized jupyter notebook cloud hosting service.
   • Some dependancies can be accommodated but not all.
2. ngrok.com freemium service that sets up transient http tunnel from your local machine to an ngrok.com hosted endpoint. If it works, it could be the fastest way to share jupyterlab docker environment with friends w/o having to be rigorous in dockerfile etc about unlisted dependancies & packages.
3. mozilla/jupyter-notebook-gist - "Create, list, and load GitHub Gists from Jupyter notebooks". sounds intriguing. haven't checked it out yet. maybe a scriptable tool that glues together local jupyter project w/ temporary binder instance via gist? update: seems to work fine ngrok w/ jupyterlab. setup took approx 30 seconds and it's free.

~/dev/jupyterlab
❯ docker run jupyterlab

~/dev/jupyterlab
❯ ./ngrok http 8888
ngrok by @inconshreveable                                                                                                                                (Ctrl+C to quit)

Session Status                online
Account                       100ideas (Plan: Free)
Version                       2.2.8
Region                        United States (us)
Web Interface                 http://127.0.0.1:4040
Forwarding                    http://5b4aadf.ngrok.io -> localhost:8888
Forwarding                    https://5b4aadf.ngrok.io -> localhost:8888

• https://www.datacamp.com/community/blog/jupyter-notebook-r
• https://5b4aadf6.ngrok.io/lab/tree/work%2Fpydna%2Fgel_inline_ex.ipynb

function jupyterlab
  docker run -it --rm -p 8888:8888 \
    -v (pwd):/home/jovyan/work \
    jupyter/scipy-notebook start.sh jupyter lab --NotebookApp.token=''
end

docker run -it --rm -p 8888:8888 \
    -v (pwd):/home/jovyan/work \
    jupyter/scipy-notebook start.sh jupyter lab --NotebookApp.token=''

Google Groups

A dynamic and interactive Javascript component for pydna: This project aims at writing javascript for rich representations in Jupyter notebooks for the Assembly and Contig classes. These objects are so complex that it would be nice to have an image to click on in order to see which sequences recombined and in which order. I was inspired by the AngularPlasmid component.

Automatic restriction strategy strategy finder for Synthetic Biology Constructs: Here the idea is to suggest optimal restriction digest strategies in order to differentiate a number of > sequences. Input would be a list of sequences and at least a smallest desirable restriction fragment. Possibly also a > list of available restriction enzymes. This could be useful for analyzing recombination products from random or > combinatorial assembly.

Look out for these functionalities in the coming months. Questions and comments are welcome.

cheers, Bjorn

pydna gel-module example in jupyter: pydna/gel_inline_ex.ipynb at py3dev · BjornFJohansson/pydna · GitHub

jupyterlab/packages/services at master · jupyterlab/jupyterlab · GitHub

"official" example repo + dockerfile: GitHub - BjornFJohansson/pydna-examples: Jupyter notebooks and data files that demonstrates how pydna can be used to simulate and document cloning

my dockerfile:

FROM jupyter/scipy-notebook
RUN conda config --append channels conda-forge && \
    conda config --append channels BjornFJohansson && \
    # conda install opencv pydna && \
    conda install numpy pydna mpldatacursor pint && \
    conda clean -tipsy && \
    fix-permissions $CONDA_DIR

#### build
# docker build -t jupyterlab-pydna .

#### run:
# docker run -it --rm -p 8888:8888 \
#   -v (pwd):/home/jovyan/work \
#   jupyter/scipy-notebook start.sh jupyter lab --NotebookApp.token=''

#### preinstalled python packages:
# pandas, matplotlib, scipy, seaborn, scikit-learn, scikit-image, sympy, cython, patsy, statsmodel, cloudpickle, dill, numba, bokeh, vincent, beautifulsoup, xlrd pre-installed

#### lots of great conda packages!
# https://conda-forge.org/feedstocks/