University of Maryland, College Park bioinformatics and computational biology interest group.
For more information about the club and upcoming meetings, check out the BYOB website and Google Group.
If you are planning to give a presentation at BYOB, and have related materials that you are able to share, the below steps will describe how they can be added to this repository.
Ideally, everything needed to reproduce the results of the presentation, along with the presentation itself should be included. "Presentation" is used loosely here are may refer to any number of different formats such as a powerpoint presentation, a well-commented script or code example, a Knitr source file, IPython notebook, Markdown notes, etc.
In cases where datasets have been used as part of the analysis, special care must be taken. First, when possible, try and make use of datasets that are publically available and do not require any special access. In cases where the datasets are very small (less than ~500Kb) then you can simply include them in the repository directly. When larger datasets are used in the analysis, instructions should be included on how to find and download the dataset, ideally from a permanent location. In both cases be sure to provide information about the source of the dataset.
- README.md - A Brief description of the presentation including the title and author, along with descriptions of the material included, and how to use them.
- Presentation - Powerpoint slides, Markdown, IPython notebooks, etc.
- Code - Code examples, or shell script of commands used in presentation.
- Data - Any datasets used in tutorial (see above for notes on how to handle).
- Output - If output is generated as part of the tutorial, and the resulting files are not too large, they may be included directly in the repo. Otherwise, the output should be described as best as possible so that users can judge whether they obtained the correct output.
- Other - As long as you have the rights, and the filesizes are small, any additional files that are relevant to the presenation, and do not fit well in any of the above categories may be included.
When in doubt, look at examples of other presentations that have been uploaded in the past to get an idea for what to include.
If you used Knitr/RMarkdown to generate all or part of your presntation, it may be more convenient to rename the generated .md file README.md and use it as your prensentation overview file described above. If you do this, please be sure to include your name and presentation title in the output as well.
If this is your first time using Git or Github, it is advisable to first take a little bit of time familiarising yourself with the basics of these tools. Some tutorials have been included at the bottom of the page to help get you started. Once you feel more comfortable with these tools, continue reading below.
The first step is to create a fork of the byob repo.
Once you have done this, clone your fork
Enter the 'presentations' directory, and then the directory for the current year. Create a new directory with the format:
mmdd-short_presentation_title
All of your materials will go inside this directory.
Begin adding your materials here. Feel free to make multiple commits as you are working on your materials.
Create a README.md as described above.
If you have not already commited all of your changes, do so now. E.g.:
git add .
git commit -am "Adding presentation xxx"
git push
The last command will push the changes to your fork of the BYOB repository.
Once your materials are finished and ready to be added to the main BYOB repo, submit a pull request with your changes:
From the github page for your fork, click on the "pull requests" button on the right of the page, and then click "new pull request".
Follow the instructions to enter a description of the changes and submit your request.
All done! Once your changes have been reviewed to make sure they look okay they will be added to the main repo.
At this point you are finished. If you wish to make additional changes later on, however, the same steps above may be followed to submit additional pull requests.