/awesome-research

:seedling: a lot of tools to help you with the research/life

Awesome Research Tools

Awesome

A list of tools for research.

TOC

Be-Organized

Version Control System

First things first, everyone should know version control systems. Version control is one of the most useful tools for scientists.

  • git
  • svn
  • mercurial

Online Git Service

  • GitHub: No description needed.
  • BitBucket: Alternative to GitHub with free private repositories.
  • Taiga: Alternative to GitHub with some fun communication tools like drinking Iocaine.

Self-hosted Git Server

Enterprise Git Service

Pomodoro

Try Pomodoro Technique to gain efficiency and probably health.

GTD-Task Manager

  • Wunderlist (All platforms): almost perfect todo lists; cooperation
  • Evernote (All platforms): just perfect
  • Anydo (All platforms): good because it has a very good reminder system; cooperation
  • Todoist(All platforms)

Cloud Services

For self-hosted services, checkout awesome-selfhosted on GitHub.

Math and Programming

Coding/Numerical calculation/Analytical derivation online.

  • Sagemath: LaTeX, R, iPython Notebook, etc.
  • PiCloud: python, but it was aquired by Dropbox and has been shut down. The new site is Multyvac.
  • Multyvac: Kind of the sucessor of PiCloud but will be more powerful for sure.
  • WolframAlpha: Excellent engine to do mathematical derivation online and search.

Plots

  • plot.ly: Online plotting with many cloud services integrated.
  • Desmos: Graphs for functions.
  • graph.tk: Online plotting with rich features.
  • DataJoy: Developed by ShareLaTeX team; python & R at this moment.
  • Wolfram Alpha: Make graphs for functions, from your data and even more.

Data

Colors

Pick a pleasing color for your presentations and notes.

Publishing and Sharing

Make use of GitHub to cooperate with others. GitHub pages is also good for hosting static contents.

Writing

Markdown is one of the best languages for writing.

Make use of these softwares for publishing

  • Sphinx: RestructuredText as source files, powerful, flexible and modularized.
  • Gitbook: A new but promising tool for html, pdf and epub with both online editors and local editors. Plugins like quizzes and math can be helpful to writing science.
  • Git-scribe: Good for writing ebooks.
  • Wordsmith

Sphinx Themes and configurations

Science Books Using Sphinx

Hosting

Host your articles, notes and more.

  • ReadtheDocs: Turn your restructuredtext source to html, pdf and epub, all done online.
  • GitHub pages: Integrated with Jekyll and turns markdown posts automatically. Jekyll is a tool for blogging.
  • GitHub: Just put markdown, restructuredtext, pdf or ipython notebook files on GitHub. All these formats can be previewed online. The thing to mention is that the math in ipython notebook can rendered on GitHub.

Blog and CMS

Before doing the investigation on platforms, just remind yourself:

I want to write, not run blogging software.

Blog/CMS Softwares

These softwares are running on the server and can be

  • Wordpress (PHP): Very popular but requires a lot of maintenance.
  • Ghost (Node.js): Open, Simple, non-profit; write with markdown and live preview.
  • Pico (PHP): Lightweight cms, open source, no database.
  • Dropplets (PHP): Open source, simple, and elegant blog system; write in Markdown.

These Blog/CMS softwares can be hosted on Digital Ocean.

Static Generator

Here is a nice website that tells you all the static site generators.

  • Jekyll (Ruby): most widely used one I guess; easy to deply.
  • Octopress (Ruby): easier to use compared with jekyll; somewhat compatable with Jekyll.
  • Hexo (Node.js)
  • Peclican (Python)
  • Nikola (Python): multiple formats including restructuredtext; multiple purpose.
  • Tinkerer (Python)
  • Hugo(Go): easy to use and really fast.

The site generated by these softwares can be hosted on GitHub Pages.

Note Taking

Editors

Markdown, restructuredText and LaTeX are the three chosen languages.

Markdown

  • StackEdit(Cloud): Markdown and MathJax (LaTeX) support.
  • CMD markdown(Cloud): Markdown and MathJax (LaTeX) support. (Chinese UI.)
  • Penflip(Cloud): Markdown based and git like. No LaTeX support.
  • Authorea(Cloud): Markdown and LaTeX. A much more powerful markdown editor that can be used to produce nice academic papers.
  • Dillinger(Cloud): Markdown editor but no math mode.
  • Online Kramdown Editor(Cloud): No math support.
  • Pandoc Markdown(Cloud): Markdown and MathJax (LaTeX) support.
  • Marxico(Cloud,Mac,Windows,Chrome): Markdown that integrates with Evernote, generates pdf and works offline. 马克飞象(Cloud,Mac,Windows,Chrome) is the Chinese version。
  • Madoko(Cloud,Chrome): Markdown and Math support, images are inserted easily with one click, files saved on Dropbox, GitHub, OneDrive or local disk. It generates pdf and HTML page and works offline using browser's local storage, imports LaTeX files.
  • Markx(Cloud): Markdown editor for scientific writing. Batteries included.

LaTeX

  • ShareLaTeX(Cloud): Dropbox and GitHub integration, preview, cooperation, simple UI. It also provides a lot of templates.
  • Overleaf(Cloud): Built in version control.
  • Authorea(Cloud): Easy to use UI. Supports both Markdown and LaTeX.
  • JaxEdit(Cloud): JaxEdit doesn't provide full LaTeX support but is good enough for simple LaTeX.

You can also host one using your own machine.

iPython Notebook

Use IPython Notebook to help with your research. IPython Notebook can be previewed on GitHub directly.

Mindmap

Standalone

  • Mind Manager
  • XMind
  • Docear

Online

MINDMAP HTML

Diagrams

  1. Gliffy: all kinds of diagrams
  2. ProcessOn: all kinds of diagrams
  3. Draw.io: all kinds of diagrams

Keep The Notes

It's alway better to keep track the changes of your notes and git is a nice choice. Therefore, GitHub is the almost perfect place.

As for LaTeX, latexdiff is the suitable tool for checking the diff.

Some softwares allows you to keep the markdown notes on a server.

  • Raneto: Raneto is an open source Knowledgebase platform that uses static Markdown files to power your Knowledgebase. This one has a nice looking.
  • Realms: Git based wiki written in Python Inspired by Gollum, Ghost, and Dillinger. Basic authentication and registration included.
  • Tiddlywiki: A unique non-linear notebook for capturing, organizing and sharing complex information.

Presentation Tools

Keep You Computer Awake

It is important to keep your computer awake during the presentation. Instead of changing the power options, the following tools can also do the job.

  • Caffeine (Mac): As simple as a single click.
  • Amphetamine (Mac): More configurations involved and more intelligent.

Online Load and Edit

Use The Source

Requires a few front-end techniques.

HTML+CSS+JS

Use colors to make your html feels better.

IPython Notebook

Julia or Python language, even R is supported in

LaTeX Beamer

  • Beamer: Shipped with standard LaTeX installations. A lot of themes has been invented. Start editing with one click on

Mathematica

Mathematica slides can be made interactive.

The Power of SVG

Online SVG Editor:

Sharing Slides

Programming

Softwares

Scientific Computing

Coding is Fun

Code Fights

Academic

Self-plagiarism

This might be not so straightforward but remember this. Reuse your own work doesn't protect you from plagiarism! Read it on

Investigate Papers

  • Paperscape: Finding interesting papers.
  • SciRate: An front-end for arXiv with rates from readers.

Get Yourself A Citable Code for Anything

  • Zenodo: Make anything from GitHub citable by getting a DOI code here.

Open Science

Pacifier

Rainy Mood, Coffitivity and Noisli are the recommended ones.

  • Rainy Mood(iOS, Android, Web): rainy day rainy mood, simple but with excellent white noise; a new beautiful soundtrack each day
  • Coffitivity(iOS, Android, Web, Mac): a rather simple but ellite cafe library; premium has more three more soundtracks; elegant UI; scientific research powered
  • Brain.fm(Web): Improve Focus, Relaxation & Sleep with audio brainwave training. Not free but worth every penny.
  • Noizio(iOS, Mac): a handy white noise tool that stays in your Mac status bar.
  • Noisli (Web): free mixing of multiple tracks (which is similar to Soundrown but with much better UI). Users can save a customized setting for later use. I personally think this one has better fire sound tracks than soundrown.
  • Soundrown(Web): free mixing of multiple tracks
  • Muji Sleep(iOS, Android)
  • A Soft Murmur(Web): free mixing of multiple tracks; simple UI; Timer provided; Meander available
  • mynoise(iOS, Web): a noise generator; a lot of choices (too many actually); detailed equalizer
  • Rainy Cafe(Web): not much to say just a combination of rainy mood and coffitivity
  • Sleep Pillow(iOS, Mac): click and play style preloaded scenes; easy to use; beautiful design
  • A youtube audio track of coffee shop (really long)
  • A youtube audio track of 10 hours rain fall
  • TaoMix (Android): sound mixings to concentrate
  • Calm(iOS, Android, Web): to help you calming down
  • Raining(iOS, Android, Web): raining and thunder
  • focus@will(iOS, Android, Web): music to boost your brain; payed services now

Some Other Related Stuff

Online Discussions

Forums and Q&A's

StackExchange.com is a good place for professional discussions. Here is an example.

Open Source

Open Source is great.

Open Licenses

Generally, open licenses are part of

Use Licenses

To choose a license, an easy way is to use

  • Choose a License which helps you decide which license to use through several steps.

CC Licenses can be found at Creative Commons. For alternative badges or icons, check the following.

  • Guokr Badge: Green CC License badges. (Documentation is in Chinese.)

Data Visualization

JS and jQuery

Python

Fun

Doing research is fun.

April Fools' Papers

Check arXiv.org today!

Physics

2014

2012

2010

2009

2008

2007

LaTeX

Tips

Symbols

  • Detexify: find out what the symbol is by drawing online

Graphing

Fonts

Templates

New Commands

New commands for Quantum Mechanics

\newcommand{\ud}[1]{{#1^{\dagger}}}
\newcommand{\bra}[1]{\left\langle #1\right|}
\newcommand{\ket}[1]{\left| #1\right\rangle}
\newcommand\Tr{\mathrm{Tr}}
\newcommand{\braket}[2]{\langle #1 \mid #2 \rangle}
\newcommand\d{\mathrm{d}}
\newcommand\I{\mathbb{I}}
\newcommand{\avg}[1]{\left< #1 \right>}

References

Math Typesetting

  • Math into Type: This is a great book for math related typography. This is copyright material. Please DO NOT redistribute.

MISC

Terminal

Free Multimedia

  • Unsplash: Free high resolution images.

Interesting Journals

More

This is a CC BY-SA licensed project. Use the source! Keep the source open!

CC BY-SA