This repository is a GitHub template intended to make it easier for undergraduate and postgraduate bioinformatics project students to get started with their own git and GitHub repositories.
Most of the advice in this repository and template is based on that in the ten great papers on this page, though they contain much more information and advice than can be included here.
This template was written specifically with the following kinds of users in mind:
- people working on their first (or an early) bioinformatics or computational biology project
- anyone who would like some guidance setting up a computational project structure in line with good practice to keep files, code and data in order
If you are already very familiar with building your own project repositories with git and GitHub, or you have experience with good practice in this kind of project structure, this template may not be of as much use to you. But it might save some time if it aligns well with your preferred way of working.
This repository is a template. It does not contain any project information itself, but it does lay out a directory structure with a minimal skeleton of explanatory README.md files explaining the motivation behind each directory in the project structure.
These files can - and should - be modified for your own project. For example, this README.md file is a landing page for the project, explaining what it is, why it exists, and how to use it. Your project repository should replace this README.md file with information that performs the same task for your project.
The same applies to README.md files in the subdirectories under this project root folder
There are several ways to get this template onto your machine, so you can use it. You should use the method that suits the way you work
- The easiest method is to download this template as a
.zipfile and uncompress it on your computer. Using this approach, you do not need to usegit(which can be intimidating)-
If you do not use
gitto manage your project files, you will not benefit from the advantages it gives in terms of version control and replicability. - To download the template, use this link or click on the
Codebutton, then theDownload ZIPlink at the GitHub page (see image below)
-
- To use
gitwith your project, and this template, you will need to do these things- Create a GitHub account (if you do not already have one)
- Create a new repository from this template in your GitHub account
- Clone your new repository to your local machine
-
Use of
gitis beyond the scope of thisREADME.mdbut some links are provided in theUseful Resourcessection, below. -
A short guide to creating a new repository and cloning it to your own machine is given in the sections below.
To create a new repository from this template at GitHub:
- Log in to GitHub at
https://github.com - Use your browser to navigate to the GitHub page for this repository: https://github.com/sipbs-compbiol/template_bioinformatics_project
- Click on the
Use This Templatebutton
- Click on the
Ownerdrop-down menu, and select the account you would like to own the new repository (this will most likely be your own account) - Type the name of the repository you want to create into the
Repository Namefield. - Add a short description of your repository (or your project) in the
Descriptionfield. - Choose whether your repository should be
Public(anyone can see or clone it),Private(only you and those you authorise can see or clone it), orInternal(this is probably not relevant to you, and can be ignored) - Click
Create Repository from Template
This will create a new repository in your GitHub account, which should be visible from your account page. You can then clone this repository to your machine, or work with it in the browser.
The official guidance for creating a new repository can be found on GitHub at the link below.
This repository follows the guidance in Noble, 2009 as a starting point. There are a few small changes with respect to that manuscript's example, but you are free to modify the folders and the files they contain, to suit your own purposes.
If there is a part of this repository you think could be improved, or you think there is something missing that could be included, please do make a suggestion on our Issues page.
If you would like to make a direct contribution to improve this repository, please do submit a pull request. For guidance in submitting pull requests, please see the wiki page associated with this repository.
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Ten great papers for biologists starting out in computational biology
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Noble, W. S. (2009). A quick guide to organizing computational biology projects. PLoS Computational Biology, 5(7), e1000424. http://doi.org/10.1371/journal.pcbi.1000424
This repository is licensed under the Creative Commons Attribution-Sharealike 4.0 licence. Please see the LICENSE file in this repository for further detail.