A list of tools for research. Also available on http://tools.kausalflow.com/tools/.
First things first, everyone should know version control system, aka VCS. VCS helps us track changes in our documents as well as collaborations on the documents. Needless to say, version control is one of the most useful tools for scientists.
Pomodoro Technique can be used to boost your productivity and probably improve your health. There are almost infinite choices for the tools.
Cloud,Mac,Win,Android,iOS,Chrome):
A mix of todo list and pomodoro timer, with sync across devices and
weekly report [Free].
Mac): Simple and
elegant pomodoro timer [USD$ 4.99].
Android): Pomodoro timer with great gamification features
[Free].
The GTD (Getting Things Done) method unloads the todo lists off the mind by recording them using external tools. It allows one to focus on one active task instead of on all of them (Wikipedia). Tasks can be classified in contexts (@home, @computer, @office, etc), time of action (now, next actions, scheduled or someday) and projects. Here we have a good pragmatic guide to GTD and here is a flowchart.
Cloud,Mac,Win,Android,iOS,Win Store,Chrome OS): Almost perfect todo lists with cooperation
and sharing.
Cloud,Android,iOS,Chrome OS)
Cloud,Mac,Win,Android,iOS,Win Store): Not so lightweight but still very good for managing life especially
since it has got a lot of integrations from a lot of other services.
Cloud,Mac,Android,iOS):
Good because it has a very good daily review which can help users
remember what to do.
Cloud,Mac,Win,Android,iOS):
Todoist invented the karma system which keeps track of the tasks done.
Cloud,Mac,Win,Chrome OS,Firefox,Android,iOS): Taskade
is a collaborative task list and outliner for team projects.
Mac): Date-focused
note taking.
For self-hosted services, check out awesome-selfhosted on GitHub.
There are many tools that allows use of code, perform numerical calculations or analytical derivation online.
While one could use these online jupyter notebooks mentioned above to make plots, there are many easy to use too that could be used for simple plotting.
Nature hosts a list of recommended data repositories here.
Storage,
Lookup): The Dryad Digital Repository stores curated data.
Storage,
Lookup): Data sharing and storage
Lookup): Data by
US Federal Government
Lookup): Genetic sequence database
Lookup): Weather, climate, coasts, oceans, and geophysics
etc
Lookup): Earth science data
Lookup)
Lookup)
Lookup)
Lookup): Certified repository
Lookup): Wiki of collections of energy information
Lookup)
Lookup)
Pick a pleasing color for your presentations and notes. Refer to Data Visualization and Graph Making
Make use of GitHub to cooperate with others. GitHub pages is also good for hosting static contents. GitHub provides Education perks so students could get free pro version which comes with private repos.
Markdown is one of the best languages for writing. Check out these editor in Markdown section.
Make use of these programs for publishing:
Sphinx Themes and configurations
Science Books Using Sphinx
Here are some examples of how sphinx can be used for research.
Writing Tools
Just use Visual Studio Code.
cut_the_crap.py: Simple Python script to flag redundant words and gives alternative
suggestions.
Host your articles, notes and more. Research is also about communications.
Other services such as Digital Ocean are also useful when it comes to dynamic websites and cloud computing.
Before doing the investigation on platforms, just remind yourself:
I want to write, not to run blogging software.
Blog/CMS Software
These programs are running on the server and can be hosted using these services.
Cloud):
write in Markdown and collaborate with the team. GitBook integrates with
GitHub so no content will be lost.
Node.js): Open, Simple, non-profit; write with markdown
and live preview.
PHP):
Lightweight cms, open source, no database.
PHP): Open source, simple, and elegant blog system; write
in Markdown.
PHP): Very
popular but requires a lot of maintenance.
These Blog/CMS software can be hosted on Digital Ocean.
Here is a nice website that tells you all the static site generators. Nonetheless here is a list of the most popular ones.
Ruby)(Markdown): Jekyll is the most widely
used one. The best part about Jekyll is that one just deploy to GitHub
Pages by pushing the source to GitHub.
Ruby)(Markdown): Octopress is easier to use
compared with Jekyll while being somewhat compatible with Jekyll.
Node.js)(Markdown): “A fast, simple &
powerful blog framework” as they say on their website. It supports GFM.
Python)(reStructuredText,Markdown,AsciiDoc):
Pelican is a modularized framework and is perfect for blogging.
Python)(reStructuredText,Markdown,IPython Notebook/Jupyter,PHP, etc): It takes in multiple input formats including
reStructuredText and many others.
Go)(Markdown): Easy to use and really fast. It
also supports more input formats through plugins.
The site generated by these programs can be hosted on GitHub Pages.
Markdown, LaTeX, and reStructuredText are the three useful languages. In most cases, a tweakable text editor such as Visual Studio Code, aka vscode is good enough. In fact vscode comes with a enormous amount of extensions which can be used to build your own IDE.
Cloud):
Basically ships with everything you expect from the most complete online
markdown editor.
Cloud):
StackEdit is a Markdown editor with many integrated services such as
math (MathJax), Google Drive, Dropbox, and GitHub.
Cloud): CMD is a Markdown editor with math (MathJax)
support. What is special is that it keeps edit history. (Chinese UI.)
Cloud):
Penflip is designed to be a GitHub for writers. It is Markdown-based and
git like without math support.
Cloud): A
much more powerful Markdown and LaTeX online editor that can be used to
produce nice academic papers.
Cloud):
Markdown editor but no math mode.
Cloud): Just another Markdown editor without math
support.
Cloud): Just another Markdown editor with math (MathJax)
support.
Cloud,Mac,Win,Chrome):
Markdown editor that integrates with Evernote, generates pdf and works
offline.
马克飞象(Cloud,Mac,Win,Chrome)
is the Chinese version。
Cloud,Chrome): A Markdown editor with math
support, where images are inserted easily with one click, while your
files are saved on Dropbox, GitHub, OneDrive or local disk. It generates
pdf and HTML page and works offline using browser’s local storage. One
can even import LaTeX files.
Cloud):
Markdown editor for scientific writing. Batteries included.
Mac,Win): Beautiful UI and in-situ live
preview.
Mac,Win,Linux): A powerful
github flavored markdown editor with useful extensions. Math (mathjax)
is supported.
Cloud): Just another online Markdown editor without math
support.
Mac): Mou used to be
the best Markdown editor on Mac. It is not bad but DO NOT preorder Mou
1.0. This project is dead, unofficially.
了解为什么死掉，请阅读此文。
Win): If
you have no bad feelings about .NET, this is pretty good.
Mac,Win,Linux): ReText one of
the best, even on Linux. It also supports reStructuredText input.
Cloud):
LaTeX × Markdown ²
Win,Mac,Linux): Math support.
Win,Mac,Linux): All purpose
markdown editor.
Notebook softwares that you can write in Markdown:
Win,Mac,Linux): Math + Markdown,
with snippet note support.
Mac,iOS): Programmer’s notebook, math +
Markdown, code snippet.
Mac):
Notebook for experimentalists, organized research materials and notes.
Win,Mac,iOS,Android):
Notetaking with kanban, math, calendar, table, etc.
Mac,iOS): Notes and GTD.
Cloud): Dropbox and GitHub integration, preview,
cooperation, simple UI. It also provides a lot of templates.
Cloud):
Built in version control.
Cloud):
Easy to use UI. Supports both Markdown and LaTeX.
Cloud):
Just another online LaTeX and Markdown with plot compiler and
collaborations.
Cloud): JaxEdit
doesn’t provide full LaTeX support but is good enough for simple LaTeX
documents and slides.
You can also host one using your own machine.
Use IPython Notebook to help with your research. IPython Notebook can be previewed on GitHub directly. Here are some examples of how IPython notebook can be used.
Standalone
Online
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 a tool for checking the diff.
Some programs allows you to keep the markdown notes on a server.
For experimental research, eLabFTW made a online labnote system: eLabFTW.
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.
Mac): As simple as a single click.
Mac): More configurations involved and more intelligent.
Requires a few front-end techniques.
Use colors to make your HTML feels better.
Python, Julia, R, Scala and more languages are supported in IPython/Jupyter Notebook which can also be used to give presentations.
Refer to math and programming online for cloud-based Jupyter Notebooks.
Online SVG editors:
Local SVG editors:
Free,Cross-platform,Plugins):
same technology as atom but faster than atom, and Microsoft made.
Free,Cross-platform,Plugins):
electron based editor with numerous plugins and easy modifications.
Cross-platform with settings and plugins synchronized through the
sync-settings
plugin.
Free Evaluation,Cross-platform,Plugins): cross-platform,
fast, and with plugins. Not free but can be freely used forever.
Free for Students, Cross-platform,Plugins): beautiful IDE’s
with many debugging and editing modes integrated.
Free,Cross-platform,Plugins):
no words can describe the almighty vim.
Python): a useful tool for inline calculation, making
graphs and writing notes.
R)This might be not so straightforward but remember this. Reusing your own work doesn’t protect you from plagiarism! Read more on
Rainy Mood, Coffitivity and Noisli are the recommended ones.
iOS,
Android, Web): rainy day rainy mood, simple
but with excellent white noise; a new beautiful soundtrack each day
iOS,
Android, Web, Mac): a rather
simple but useful coffee shop noise library; premium has more three more
soundtracks; elegant UI; scientific research powered
Web): Improve
Focus, Relaxation & Sleep with audio brainwave training. Not free
but worth every penny.
iOS,
Mac): a handy white noise tool that stays in your Mac
status bar.
iOS,
Android, Web, Chrome): 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.
Web): free
mixing of multiple tracks
iOS,
Android)
Web):
free mixing of multiple tracks; simple UI; Timer provided; Meander
available
iOS, Web): a noise generator; a lot of
choices (too many actually); detailed equalizer
Web): not
much to say just a combination of rainy mood and coffitivity
iOS, Mac): click and play style preloaded
scenes; easy to use; beautiful design
Android): sound mixings to concentrate
iOS,
Android, Web): to help you calming down
iOS,
Android, Web): raining and thunder
iOS,
Android, Web): music to boost your brain; paid
services now
Some Other Related Stuff
StackExchange.com is a good place for professional discussions. Here is an example.
Open Source is great. Use git.
Generally, open licenses are part of
To choose a license, an easy way is to use
CC Licenses can be found at Creative Commons. For alternative badges or icons, check the following.
JS and jQuery
js)js): Line charts, area charts, column and bar charts, pie
charts, scatter and bubble charts and more.
jQuery)
js)js)
js)Python
bokeh: Internet required, interactive plotting.
itermplot: An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.
Professional graphs should be made using professional tools.
Cloud,Mac,Win,Linux,Android,iOS,Win Store): Geogebra is a very cool tool to make math graphs both 2D and 3D.
Linux): “A vector drawing editor for LaTeX.”
LaTeX)
Web): A web-tool for generation of box plots.
Linux,Win,Max,Solaris,FreeBSD): Open source graph
visualization software.
Choose percentually accurate colors for your research plots. Why? (1, 2)
Much much much better than Microsoft Word.
Math Typesetting
This is a CC BY-SA licensed project. Use the source! Keep the source open!
