Doing science in the open, 2013 edition

2013/03/06      no responses

(For the 2011 edition, see Doing science in the open.)

Understanding open science

Open science is about sharing — papers, data, software, ideas… Sharing promotes replicability, transparency, knowledge accumulation, love…
But it is only meaningful when open standards are implemented. Examples:

General idea — Use tools that are as independent as possible:

Note: This is a general preference, not absolute. Your particular problem might have different requirements.


(dev indicates that I do not consider the tool to be mature yet. It may change (e.g., become paid or change its API), it may disappear, or better (more widely accepted) tools of the same sort may emerge soon.)

Open Science Framework

A project (dev) closely related to the Reproducibility Project (Brian Nosek and friends):

Licenses (my recommendations)

Google Scholar

Alternatives: ResearchGate (and here’ how my profile looks like),, Facebook Profile / Facebook Page, Mendeley (my profile)

Reading publications

Limitations of PDFs:

(You may want to try text reflow for converting a PDF into text on the fly as a possible solution but I’m not aware of an app that would do the job well.)
But even worse is reading papers online in the HTML format :

(For a magazine-like HTML experience, try PubMed’s PubReader on your browser.)
Best solution so far is epub (an experimental paper format from PubMed):

Since 2008, NIH-funded scientists are required to submit their manuscripts and they’re published on PubMed within 12 months of the initial journal publication. Thus, epubs are already available for recent publications and appear pretty fast but, unfortunately, not instantaneously for the new ones.

Experiments on tablets

Alternative: online experiments (like L-POST) which you can learn to create them at Udacity


For collaboration: Google Drive

Writing, formatting, commenting: LyX

IPython for papers

import pandas
%load_ext rmagic
data = pandas.read_csv("data.csv")
# -i sends the variable to R, the rest is R code
%R -i data print(summary(data))

Open Science Paper (dev):

PythonTeX (dev)

If you still prefer Word documents, at least stop sending multiple versions around. Dropbox is your true friend:


Traditional: Scribus

Alternative: Inkscape


Browser-based (usually HTML+JS)

(but you may share pdfs of your presentations on figshare or slideshare (see my own example))

figshare (dev)

Disclaimer: I am a figshare advisor
Alternative: Your own website with copyright information (use CC BY)

Keeping file history

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