A list of tools for research.
- Be Organized
- Cloud Services
- Publishing and Sharing
- Note Taking
- Presentation Tools
- Programming
- Academic
- Pacifier
- Online Discussions
- Open Source
- Data Visualization
- LaTeX
- MISC
First things first, everyone should know version control systems. Version control is one of the most useful tools for scientists.
- git
- svn
- mercurial
- GitHub: No description needed.
- BitBucket: Alternative to GitHub with free private repositories.
- Taiga: Alternative to GitHub with some fun communication tools like drinking Iocaine.
- GitLab: Similar to GitHub.
- Gitorious: Acquired by GitLab and discontinued, but the software can still be installed.
Try Pomodoro Technique to gain efficiency and probably health.
- 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)
For self-hosted services, checkout awesome-selfhosted on GitHub.
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.
- 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.
- Figshare: Data sharing and storage.
Pick a pleasing color for your presentations and notes.
Make use of GitHub to cooperate with others. GitHub pages is also good for hosting static contents.
Markdown is one of the best languages for writing.
- Cloud Based Markdown Editors
- Mou (
Mac) - MarkdownPad (
Win): if you have no bad feelings about .NET - ReText (
All platforms) - Madoko (
Cloud): LaTeX × Markdown ²
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
- Themes
- rtd theme: Developed by Readthedocs.org.
- some beautiful themes
- bootstrap theme: quite comfortable
Science Books Using Sphinx
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.
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.
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.
Markdown, restructuredText and LaTeX are the three chosen languages.
- 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.
- 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.
- FlyLaTeX: A free, open source version of sharelatex
- ShareLaTeX Source Code: ShareLaTeX open sourced their codes. This is a great move I would say.
Use IPython Notebook to help with your research. IPython Notebook can be previewed on GitHub directly.
Standalone
- Mind Manager
- XMind
- Docear
Online
- KityMinder By Baidu : Chinese Interface
- my-mind: repo here.
- beautiful Mind: repo here
- Mindmup: repo here
- mindmaps: repo here
MINDMAP HTML
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.
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.
- Prezi if you can.
- slides.com: Easy to use with remote controlled page presentation.
- Google Drive: no introduction needed
- Sway: Microsoft
- Strut
- Impressionist
- hovercraft
Requires a few front-end techniques.
Use colors to make your html feels better.
- Impress.js: more about it impress wiki page.
- Jimpress: A jQuery version of impress.js
- Reveal.js
- Beckpoke.js
- CSSS
- Scrolldeck
- Deck.js
- Shower
- HTML5 Rocks
- Flowtime.js
- Slides
Julia or Python language, even R is supported in
- Beamer: Shipped with standard LaTeX installations. A lot of themes has been invented. Start editing with one click on
Mathematica slides can be made interactive.
Online SVG Editor:
- GitHub pages: For Html based slides.
- Speaker Deck by GitHub: PDF slides. Can be displayed online or embeded.
- Mathematica: One Software to Rule Them All
- iPython Notebook (
Python): an useful tool for inline calculation, making graph and writing notes.- wakari.io is a comercial one mostly aimed for data analysis.
- jiffylab is an open source one but not that well done.
- supervised-ipython-nbserver is a multiuser version of notebook using Django/Pinax.
- Matlab
- RStudio (
R)
This might be not so straightforward but remember this. Reuse your own work doesn't protect you from plagiarism! Read it on
- Paperscape: Finding interesting papers.
- SciRate: An front-end for arXiv with rates from readers.
- Zenodo: Make anything from GitHub citable by getting a DOI code here.
- Open Science Framework: A open science tool with a lot of integrations.
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
- iSerenity: multiple choices but not that good (just my feeling).
- Rany by simply noise: just rain. simplynoise has other products.
- Natural Sound player: many natural sounds, cool.
- NatureSoundsFor.Me: make your own track, so many kinds of sounds.
- White.Noise: several different tracks
- ambient mixer: make ambient sound easily
- white noise mp3s: listen and download
StackExchange.com is a good place for professional discussions. Here is an example.
Open Source is great.
Generally, open licenses are part of
- Open Definition: Read the license here and pick the one you like.
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.)
JS and jQuery
- Highcharts (
js): Line charts, area charts, column and bar charts, pie charts, scatter and bubble charts and more. - Flot (
jQuery) - Raphaël (
js) - JavaScript InfoVis Toolkit (
js) - D3js (
js) - Paper.js (
js)
Python
- matplotlib
- ggplot for python
- statistical data vis
- plot.ly: Internet required, interactive plotting.
- bokeh: Internet required, interactive plotting.
- wikibooks - LaTeX: A good manual.
- Notetaking programs listed above
- Detexify: find out what the symbol is by drawing online
- TeX Example (Tikz/PGF)
Math Typesetting
- Math into Type: This is a great book for math related typography. This is copyright material. Please DO NOT redistribute.
- plot in terminal
- asciinema: Command line recording.
- bashplot: plot in terminal.
- fuck: correct the command by typing in fuck.
- Unsplash: Free high resolution images.
- QR Code Generator: Adding a QR code to your poster can help you get more audience.
- SHIELDS.io: Make a beautiful badge by yourself.
This is a CC BY-SA licensed project. Use the source! Keep the source open!
