Daniel Himmelstein (@dhimmel)
Biomedical Graduate Studies Orientation
University of Pennsylvania
BRB Auditorium
August 22, 2019 at 2:00 PM
slides.com/dhimmel/bgs
slides released under CC BY 4.0
http://www.greenelab.com/
Outline:
files (especially text files) and directories
computational notebooks (e.g. Jupyter or R Markdown)
version control
code review on gitlab / github
open source
manubot
2019-08-22
2019-08-22_bgs-presentation.pdf
2019-08-23_all-of-my-secrets.txt
01.download-data.ipynb 02.process-data.ipynb 03.visualize-data.ipynb
git log \ --pretty=short \ --abbrev-commit
Control packages
Control OS + packages
convert rms-fsf-slide-propreitary.png -channel RGB -negate -transparent black rms-fsf-slide-propreitary-negated.png
FreeSoftware TEDx slides. (2014) Reused under CC BY 3.0
FreeSoftware TEDx slides. (2014) Reused under CC BY 3.0
convert rms-fsf-slide.png -channel RGB -negate -transparent black rms-fsf-slide-negated.png
Recommendations:
Beyond the PDF First Day Notes
By De Jongens van de Tekeningen
Licensed under CC BY 3.0
Modified to invert colors
This is a sentence with 5 citations [ @doi:10.1038/nbt.3780; @pmid:29424689; @pmcid:PMC5938574; @arxiv:1407.3561; @url:https://greenelab.github.io/meta-review/ ].
This is a sentence with 5 citations [1,2,3,4,5].
https://manubot.org/catalog/
@dhimmel
0000-0002-3012-7446
Slides
https://slides.com/dhimmel/bgs