metabolicengineeringgroupcbma/ypk-xylose-pathways

Pereira, F., Azevedo, F., Parachin, N. S., Hahn-Hägerdal, B., Gorwa-Grauslund, M. F., & Johansson, B. (2016). Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. ACS Synthetic Biology, 5(5), 386–394.

Pereira et al. 2016

This repository contains Jupyter notebooks describing cloning using Python, Jupyter notebooks and pydna.

The notebooks and other files in this repository accompany the publications:

Pereira, F., Azevedo, F., Parachin, N. S., Hahn-Hägerdal, B., Gorwa-Grauslund, M. F., & Johansson, B. (2016). Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. ACS Synthetic Biology, 5(5), 386–394. PubMed website

and

Romaní, A., Pereira, F., Johansson, B., & Domingues, L. (2015). Metabolic engineering of Saccharomyces cerevisiae ethanol strains PE-2 and CAT-1 for efficient lignocellulosic fermentation. Bioresource Technology, 179, 150–158. PubMed website

The notebooks can be visualized in a number of ways. Each notebook (.ipynb) is accompanied by a HTML file with the same name but with an (.html) extension. These can be opened in a web browser without installing any software.

The notebooks (.ipynb) can be opened in the browser through the nbviewer service here or directly in Github here.

Significant files

Most files have either a .ipynb or .gb extension. The .ipynb files are Jupyter notebooks and .gb files are genbank formatted text files.

index

The index.ipynb notebook is the place to start as it has links to the other notebooks.

Each notebook contain links (usually in the end) to the resulting sequences in Genbank flat file format.

These notebooks are tested on the github action build service.

This means that the notebook outputs are re-executed and compared with saved results once per week to ensure reproducibility.

If the badge below is green, all tests gave the expected results.