Keeping your scientific data and analysis scripts in order is not only good style but a prerequisite to enable reproducible and accessible scientific evidence. Beyond that, keeping your manuscripts and literature in order is a simple matter of efficiency in your daily routine.
How do you organize your data, scripts, manuscripts and literature? What folder structure or database do you use? What software do you use? What is your personal piece of advise for keeping your scientific data safe, accessible and properly documented?
check out scrivener. i partially used it for a while.
it is good way to organise your publishing. designer types like it
brad
For me the version control software Git has proven to be the best solution for organizing code as well as manuscripts. An introduction to Git can be found here http://git-scm.com/book/en/v2/Getting-Started-Git-Basics
Hi Andreas,
I suggest you to read the article:
"The R software environment in reproducible geoscientific research".
DOI: 10.1029/2012EO160003
As mentioned by the authors, "A typical workflow may consist of: (1) reading data, (2) manipulating data, (3) analysing data, computing statistics, generating figures, maps and/or graphs , and (4) exporting all results to a manuscript."
I my case, I use:
1) R (http://www.r-project.org/) for reading and manipulating data (http://www.statmethods.net/input/importingdata.html), computing statistics and producing maps (http://cran.r-project.org/web/views/Spatial.html) and figures (http://www.statmethods.net/graphs/).
2) LaTex (http://www.andy-roberts.net/writing/latex/) for generating pure text-and-figures manuscripts. You can combine LaTex with GitHub (https://github.com/) for having version control of your documents. In particular, ShareLaTex (https://www.sharelatex.com/project) is very good for writing collaborative documents in LaTex.
3) LaTex + Sweave (https://www.stat.uni-muenchen.de/~leisch/Sweave/) or LaTex + Knitr (http://kbroman.org/knitr_knutshell/pages/latex.html) for producing manuscripts with text and calls to pieces of R code, which will produce on-the-fly analysis/figures to be put in the text.
4) Beamer (http://en.wikibooks.org/wiki/LaTeX/Presentations) for presentations.
5) Referencer (https://apps.ubuntu.com/cat/applications/precise/referencer/) or JabRef (http://jabref.sourceforge.net/) as citation mananager.
You can find additional info on:
*) http://cran.r-project.org/web/views/ReproducibleResearch.html
*) https://www.coursera.org/course/repdata
IHTH,
I'd like to suggest Zotero for organizing literature, sources of data, etc. It even allows one to export references as a bib file, very useful when using LaTeX.
In my workflow, i often use Dropbox synchronized with several computers. git is on the way (and github is excellent).
As for scripting/coding: my codes contain more comments than code...so my suggestion is always "comment, comment, comment".
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