Software for scientists: community-edited list of general-purpose software for scientists.

Software for scientists

Some things takes much less time and stress once you know the right tool. Below, there is a community edited list of software for scientists.

Text editors

in General purpose text/code editors. It may be better to have a good editor for everything, than different ones for different languages, scripts, notes.

Sublime Text 2
- License: paid, unlimited trial
- Powerful but easy to start
- Good environment of plugins, including ones for science, e.g.:
  - LaTeXTools
  - Using Sublime Text 2 for R
Notepad++
- Open source, for Windows
- Quite powerful, simple (no steep learning curve), and very stable
- Useful block-select functions
Vim
- Open source
- Powerful, but steep learning curve
- Type vimtutor in terminal to learn basics (or if you want to have some fun vim-adventures)
- TODO: some materials for science (e.g. complete setup to use it with LaTeX)
Emacs
- More of a powerful programmagle text environment, than an editor
- Includes mutt (first mail client that supported threading), IRC client, many programming modes, Tramp (SSH), terminal emulator (great for Windows users!)
- Includes a powerful note-taking and Organization tool: Org mode
- LaTex mode with realtime preview of output PDF is awesome
Gedit
- open source

Note-taking

As we all take a lot of notes. Some links from this: http://academia.stackexchange.com/questions/8002/how-to-manage-theorists-labbook.

TiddlyWiki
- Interactive personal wiki in one file. A lot of plugins.
- See http://boolesrings.org/krautzberger/2010/11/10/tiddlywiki-or-the-end-of-my-latex-notes/
Evernote
- Synchronization with computer, web and devices. No tree structure or LaTeX support.
Gitit
- Personal wiki with Git, notes in separate files.
Rednotebook
- A journal/diary in one file. It allows to export the journal to PDF, HTML, Latex or plain text
DebateGraph
- Organize a graph of notes
- Include structured conversations around each node
- Each node has its own rich text editor (no LaTeX)
- Known issue: no way to export

As a general thing, Markdown format may be convenient. It can be read on any system, and it is easy to cenvert it to HTML, PDF of DOC using Pandoc.

Collaborative writing

Some discusion here: http://academia.stackexchange.com/questions/1261/simplest-way-to-jointly-write-a-manuscript

(see also: Sharing code and Version control)

Non-LaTeX

GoogleDrive
- Usually much nicer than sending back and forth docs
- Also nice for brainstorming (use your own colour)
Hackpad
- Content-oriented (same font), simple but productive features
- Great for brainstorming (names are visible, e-mail notifications)
- Examples: https://hackpad.com/New-scientific-markup-language-utAjFcYuvvB
Etherpad (software)
- e.g. at Titanpad

LaTeX

ShareLaTeX
- Open source
- Git and Dropbox support in paid version
- Basic features are free
WriteLatex
- Perhaps the best way to introduce people to LaTeX (no installation required, starts with a full working example)
Authorea
- nice interface designed for writing full, scientific papers
- also can use Markdown
- underlying git repo, so good history management
- public articles + one private free
StackEdit
- Web editor with Markdown and LaTeX, synchronizes with GoogleDocs and GitHub
- Maybe good to introduce people to Markdown
http://mathb.in/
- Short math notes

Collaborative reading

PeerLibrary
- Collaborative reading of academic publications
- Sharing, highlighting, annotations, discussions
- Displays PDFs in the browser
- Still in development, open source
SciRate
- tracking of new papers from arXiv
- you can recommend and comment preprints

Version control

Crucial for code. Often helps a lot with writing LaTeX documents (see some discussion here: http://academia.stackexchange.com/questions/5277/why-use-version-control-systems-for-writing-a-paper). Much more pleasant than e-mailing back and forth changes!

Git
- steep learnign curve, especially on Windows
- Tutorials:
  - Interactive tutorial: http://try.github.io/
  - Relatively simple intro: http://www.ralfebert.de/tutorials/git/
  - Version Control with Git - Software Carpentry - especially for scientists
  - Git for Scientists: A Tutorial
  - How to contribute to GitHub projects
  - Adv. interactive tutorial for branching: http://pcottle.github.io/learnGitBranching/
- An easy to use interface for Win is TortoiseGit
Mercurial
- Pure Python, so it works nicely on Windows (Linux and Mac OS X as well)
- Similar to git but with less steep learning curve
- Hg Init: a Mercurial tutorial by Joel Spolsky

While for small-to-medium size both are equally powerful (so pick any and you will be happy!), an older version control system Subversion (SVN) is less powerful, but not necessarily simpler (so when starting a new repository, use Git or Mercurial). For older projects it is still fine (SVN version control is still much, much better than no version control!).

For both Git and Mercurial SourceTree is nice and free (though not open) graphical interface.

For hosting (for collaboration with others and backup), see Bitbucket and GitHub.

Website tools

For personal homepages, lab notebooks and conference websites.

WordPress - code and WordPress - hosting
- Examples:
Jekyll
- For writing blogs in Markdown and easily putting them on GitHub
- Tutorial for using LaTeX in it: http://cwoebker.com/posts/latex-math-magic
- Examples:
  - Open Lab Notebook in Jekyll
  - A homepage
Wikidot
- e.g http://offtopicarium.wikidot.com/
Wikispaces
- Simple wikis, very easy to create and manage
- Used as open science notebooks, for instance http://usefulchem.wikispaces.com/
Site44
- Showing small site by putting files into a Dropbox folder
GitHub Pages
- Static websites with Git
Instiki
- Wiki especially for mathematical collaboration (see features on Azimuth - how to blog - LaTeX, SVG, ...)
- Examples:
  - http://www.azimuthproject.org/
  - http://ncatlab.org/
WorkingWiki
- Wiki especially for mathematical collaboration
Sphinx
- Great for writing documentation
- Example (in Polish): http://django.carrots.pl/
Jekade
- Jekyll-like static pages with built-in LaTe support, in Node.JS

Survey tools

Google Forms of Google Drive
- easy, free, but for a limited number of responses
- easy way to set registration for a small event, or to get feedback
Survey Monkey

Reference managers

Mendeley
- With PDF, notes, arXiv field, BibTeX support, metadata extraction
- Free with large storage limit; owned by Elsevier
Zotero
- Strong browser integration - click a button in the URL bar to save a reference
- Syncs references between computers
- Open source
JabRef
- Cross-platform manager for BibTeX databases. Little integration with the web.
Bibdesk
- Mac OS X

Sharing and repositories

GitHub
- great for sharing code and not only; very open for collaboration
- examples:
  - a scientific open-source project QuTip: Quantum Toolbox in Python
  - the Linux itself
  - German Federal Law and Regulations (vide open data)
  - ...and even a book - "Two dozen mathematicians wrote a 600 page book in 6 months on GitHub" (http://homotopytypetheory.org/book/, see also a blog post on it)
- gist for posting short codes or notes on anything
BitBucket
- for Git, Mercurial and SVN
- less social/collaborative than GitHub
- unlimited number of private projects and collaborators with an academic e-mail http://atlassian.com/software/views/bitbucket-academic-license.jsp
Figshare
- For sharing negative data, plots, posters, etc; gives you a DOI.

Question and Answer sites

(list only related to academia or research-level)

Some Stack Exchange sites related to science, e.g.:
- MathOverflow
- Academia - StackExchange

General-purpose programming

Python
- Some great packages:
  - The SciPy ecosystem contains lots of useful libraries. A detailed course is online at http://scipy-lectures.github.io/
    - NumPy for numerics
    - Matplotlib for plots
    - Sympy for symbolic computations
  - IPython Notebook for interactive environment for exploration and presenting results $ ipython notebook --pylab inline
    - http://nbviewer.ipython.org/ for sharing notebooks
    - Introduction to IPython Notebook
  - http://pandas.pydata.org/ for data analysis (R-like)
  - Also: NLTK! http://nltk.org/
  - http://scikit-learn.org/stable/ for machine learning
- Python syntax intro: http://learnxinyminutes.com/docs/python/
- Intros to Python for scientists:
  - A Crash Course in Python for Scientists by Rick Mulle in IPython Notebook
  - Python for scientific computing: Where to start by Steve Byrnes
- More in depth science introductions:
  - Python Scientific Lecture Notes - great!
  - Materials by Nicolas P. Rougier
JavaScript
- For interactive applications and visualizations (works on any system, no installations required)
- Nice introduction: http://eloquentjavascript.net/

Plots and diagrams

Matplotlib for Python
- http://scipy-lectures.github.io/intro/matplotlib/matplotlib.html
- http://www.physics.ucdavis.edu/~dwittman/Matplotlib-examples/
gnuplot (free software)
R (for applied statistics, but also nice plots, free software)
- use together with RStudio http://www.rstudio.com/, powerfull IDE for R
- ggplot "a plotting system for R, based on the grammar of graphics", easier and nicer looking plotting, tutorial
D3.js - Data Driven Documents
- A JavaScript library any data visualizations (also interactive)
- Interactive intro
- Examples: http://biovisualize.github.io/d3visualization/
Gephi
- for graph anaysis and visualization
Origin
- Windows, commercial

Drawing diagrams

In LaTeX: TikZ library
- Examples: http://www.texample.net/tikz/examples/
- Introduction: Basic Drawing Using TikZ - ShareLaTeX blog, http://cremeronline.com/LaTeX/minimaltikz.pdf
- Manual: http://paws.wcu.edu/tsfoguel/tikzpgfmanual.pdf
Inkscape for *.svg (Scalable Vector Graphics)
- open source, GNU
The Ipe extensible drawing editor
- open source, GNU

Presentations

(except for the well-known office packages :), unless with some additional hints)

LaTeX/Beamer
- also: Beamer slides using Markdown: http://jeromyanglim.blogspot.com.es/2012/07/beamer-pandoc-markdown.html
Prezi
- zoomable prezentations
- for example: http://prezi.com/d3lswto1mebc/free-falling-through-prezi/
knitr combine R and markdown and export your report to pdf/doc/odt
Slidify
- combine R and Markdown and get beautiful HTML5 slides
- example
- easy share on GitHub or Github, Dropbox or Rpubs

Additional tools

Latexit for easily putting equations into Keynote/Powerpoint/Anything

Sharing slides

Sharing is bulit-in in Prezi and Slidify.

https://speakerdeck.com/
- people can view online and download pdfs (no registration or adverts, as of now)
- example

More generic: GitHub and Figshare

Posters

Inkscape for *.svg (Scalable Vector Graphics)
- GNU
LaTeX
- LaTeX Templates - Conference Posters

Math calculations

See also: General-purpose programming: Python. (And to reiterate: SciPy!)

Mathematica
- commercial
- for symbolic calculations
Wolfram Alpha
- for online simple plots, units changing, integrals etc. a "demo version" of Mathematica
MATLAB
- commercial
- for numerical calculations, supports scripting
Octave
- open source, GNU licence
- almost the same as MATLAB (sometimes incompatible), without graphical interface - only text
- may use Gnuplot for plots
Sage
- open source, licensed under the GPL
- mathematics software system (alternative to Magma, Maple, Mathematica and Matlab.) . It combines the power of many existing open-source packages into a common Python-based interface.
R
- for any kind of statistics

Productivity misc

Throw a pile of random programs (it is not a complete list)

Remember The Milk
- Todo list with easy synchronization
RescueTime
- to track how much time you spend on different activities on your computer (that is, how much you work, and how much you procrastinate)
Delicious and Pinboard
- bookmark managers
Dropbox
- backup, sharing and some crude collaboration and version control

Other similar listings

http://www.force11.org/tools

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