Objectives
To familiarize oneself with a single computational framework that will, in parallel, allow us to:
- ensure reproducible access to data and to the associated analysis and modeling tools
- maintain a well-documented record of our progress using GitHub
- demonstrate how to easily:
- write a numerical Markdown notebook (this file) that supports visualizations and quick note-taking
- run a cell-by-cell Jupyter notebook to analyze data and model genome sequences from E. coli strains available in the data folder, starting with the simplest code one can think of. Note that to have access to a folder like data, one needs to add the full url.
- draft notes (like this one) including LaTeX $\rightarrow$ this might later serve as the basis for an article; note, however, that not all symbols are available
- use a GitHub repository to:
- start collaborating
- keep a historical backup of our work
To that end, we will proceed step by step, sometimes in an apparently random order relative to the outline above.