The Data Biologist Cookbook

Daniel Himmelstein

September 17, 2015

visualization evolved using electric sheep

License: all original content CC0, reused content attributed via hyperlink

the allegory of academia

rising journal subscription costs in the UK

major variability
opaque market
access is not gauranteed
In 2012, UCSF paid $7,733 for 2 physical copies of Nature

Does copyright support continued availability and distribution?

From How Copyright Keeps Works Disappeared

Dissapearing decades: Amazon titles by decade

Works published prior to 1923 are public domain

open access citation advantage

SPARC identified 70 studies: 46 yes versus 17 no

code

data

articles

choosealicense.com

doaj.org

copyright — rights automatically granted creators of original work
copyright transfer — cornerstone of subscription publishing
no license — all rights reserved, copyright transfer

copyright and licensing

preprints

paper-now

PrePrints

Definition: a draft of an article that has not yet been peer reviewed for formal publication

Benefits:

establish precedence
citeable & versioned
receive feedback
compatible with most publishers
attention & openness

Stanford's Biomedical Computation Review mentions our research and preprint 6 months before publication

data repositories

Domain specific repositories: GEO, dbGaP

open scientists

Image: The National Gallery of Art, Washington D.C.

Incumbent view:

I deserve compensation for any profit derived from my work.

Revolutionary view:

I will judge the success of my work by

the benefit it creates for others
the effect it has on the future

Bee sting pain index by body location

Michael Smith

DOI: 10.7717/peerj.338

Alexandra Elbakyan

"the goal is to collect all research papers ever published, and make them free" [source]

Satoshi Nakamoto

computational tools

The less effort, the faster and more powerful you will be.

— Bruce Lee

Calligraphy: sho-shin beginner's mind by Hidy Ochiai

DOI: digital object identifier
Format: 10.registrant/identifier
Example: 10.7717/peerj.705
url: https://doi.org/10.7717/peerj.705
Issued by 9 agencies
crossref, datacite
metadata
citation

plain text editor

# markdown introduction

markdown was proposed by [John Gruber in 2004](http://daringfireball.net/projects/markdown/).
It is:

+ formatting language
+ no boilerplate
+ readable in plain text
+ supports *italics*, **bold**, and `code`
+ `.md` extension

Three websites that use markdown are:

1. GitHub
+ reddit
+ Trello

>>> import phd

general
powerful
elegant
3 > 2
conda + pip
testing (pytest)
practice zen

See Python for the modern biodata scientist for more

See R best practices for more

statistics
bioinformatics
hadleyverse
- dplyr, tidyr — data manipulation
- readr, readxl — io
- ggplot2 — plotting
- devtools, roxygen2 — development
you will pay in blood for using R
see dhimmel/snplentiful#3