Overview
Requirements
Data
Support Forum Thanks
Funding
License for Data
Included here are several tutorials in the form of 'Jupyter notebooks'.
The purpose of these tutorials is to help users familiarize themselves with the cloud computing in the specific context of running bioinformatics workflows. Here is a link to a YouTube video that gives you an overview of the tutorials.
These tutorials do this by going step-by-step through specific workflows. These workflows cover the start to finish of basic bioinformatics analysis; starting from downloading raw sequence data, and extending to differential gene expression analysis, and producing common plots in R.
These tutorials were designed to be used on cloud computing platforms, with the aim of requiring nothing but the files within this GitHub repository.
With this in mind, our tutorials use Jupyter Notebook files, which Google Cloud Platform, Amazon Web Service, and Microsoft Azure all provide support for. Therefore, requirements should only require creation of a virtual machine on one of these providers, and the downloading of this github's files to that machine.
For more information on creating a virtual machine and downloading our GitHub repo to that machine, we have a getting started section in each folder in running notebooks in AWS or Google Cloud platform.
These tutorials use example sequence data procured from the Sally Molloy labratory here at University of Maine; which investigates the transcriptome change in prophage infected, versus non-prophage infected M. chelonae bacteria. The respective article can be found here.
Support forum thanks. For almost any programming project, contributions to online databases and support forums are an invaluable resource that are heavily leaned upon. Thank goodness for those people who take the time to answer silly questions.
Funded by the Maine INBRE Program (NIH/NIGMS P20 GM103423).
Text and materials are licensed under a Creative Commons CC-BY-NC-SA license. The license allows you to copy, remix and redistribute any of our publicly available materials, under the condition that you attribute the work (details in the license) and do not make profits from it. More information is available here.
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License