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

Outline

files & directories

ISO 8601

how to name files?

01.download-data.ipynb
02.process-data.ipynb
03.visualize-data.ipynb

notebooks

• restart & run all

• single script to run entire pipeline

caution

version control

code review

versioned environments

dhimmel/elevcan: repository for "Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen"

conquer your environment

open source

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

proprietary software:
the software controls the science

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

open source software:
the scientist controls the software

Recommendations:

1. release data under an open license
2. University researchers: commit to open in your resource sharing plan

manubot

Beyond the PDF First Day Notes

By De Jongens van de Tekeningen

Licensed under CC BY 3.0

Modified to invert colors

citation by persistent identifier

References

1. Reproducibility of computational workflows is automated using continuous analysis
   Brett K Beaulieu-Jones, Casey S Greene
   Nature Biotechnology (2017-03-13) https://doi.org/f9ttx6
   DOI: 10.1038/nbt.3780 · PMID: 28288103 · PMCID: PMC6103790
    
2. Sci-Hub provides access to nearly all scholarly literature.
   Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
   eLife (2018-03-01) https://www.ncbi.nlm.nih.gov/pubmed/29424689
   DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410
    
3. Opportunities and obstacles for deep learning in biology and medicine
   Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman, … Casey S. Greene
   Journal of the Royal Society Interface (2018-04) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574/
   DOI: 10.1098/rsif.2017.0387 · PMID: 29618526 · PMCID: PMC5938574
    
4. IPFS - Content Addressed, Versioned, P2P File System
   Juan Benet
   arXiv (2014-07-14) https://arxiv.org/abs/1407.3561v1
    
5. Open collaborative writing with Manubot
   Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
   (2018-08-03) https://greenelab.github.io/meta-review/

This is a sentence with 5 citations [1,2,3,4,5].

https://manubot.org/catalog/