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<h1 id="awesome-research-tools">Awesome Research Tools</h1>
<p><a href="https://github.com/sindresorhus/awesome"><img
src="https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg"
alt="Awesome" /></a></p>
<p>A list of tools for research. Also available on <a
href="https://tools.kausalflow.com/tools/">https://tools.kausalflow.com/tools/</a>.</p>
<h2 id="toc">TOC</h2>
<ul>
<li><a href="#be-organized">Be Organized</a>
<ul>
<li><a href="#version-control-system">Version Control System</a></li>
<li><a href="#pomodoro">Pomodoro</a></li>
<li><a href="#gtd-task-manager">GTD-Task Manager</a></li>
</ul></li>
<li><a href="#cloud-services">Cloud Services</a>
<ul>
<li><a href="#math-and-programming-online">Math and Programming</a></li>
<li><a href="#plotting-and-charting-online">Plots</a></li>
<li><a href="#datasets">Data</a></li>
<li><a href="#colors">Colors</a></li>
</ul></li>
<li><a href="#publishing-and-sharing">Publishing and Sharing</a>
<ul>
<li><a href="#writing">Writing</a></li>
<li><a href="#hosting">Hosting</a></li>
<li><a href="#blog-and-cms">Blog and CMS</a></li>
<li><a href="#static-site-generator">Static Site Generator</a></li>
</ul></li>
<li><a href="#note-taking">Note Taking</a>
<ul>
<li><a href="#editors">Editors</a></li>
<li><a href="#markdown">Markdown</a></li>
<li><a href="#latex">LaTeX</a></li>
<li><a href="#ipython-notebook">iPython Notebook</a></li>
<li><a href="#mindmap">Mindmap</a></li>
<li><a href="#concept-map-and-diagrams">Concept Map and
Diagrams</a></li>
<li><a href="#keep-the-notes">Keep The Notes</a></li>
</ul></li>
<li><a href="#presentation-tools">Presentation Tools</a>
<ul>
<li><a href="#online-load-and-edit">Online Load and Edit</a></li>
<li><a href="#use-the-source">Use The Source</a></li>
<li><a href="#ipython-notebook">IPython Notebook</a></li>
<li><a href="#latex-beamer">LaTeX Beamer</a></li>
<li><a href="#mathematica">Mathematica</a></li>
<li><a href="#the-power-of-svg">The Power of SVG</a></li>
<li><a href="#sharing-slides">Sharing Slides</a></li>
</ul></li>
<li><a href="#programming">Programming</a>
<ul>
<li><a href="#softwares">Softwares</a></li>
<li><a href="#code-editors">Code Editors</a></li>
<li><a href="#scientific-computing">Scientific Computing</a></li>
<li><a href="#coding-is-fun">Coding is Fun</a></li>
</ul></li>
<li><a href="#academic">Academic</a>
<ul>
<li><a href="#self-plagiarism">Self-plagiarism</a></li>
<li><a href="#investigate-papers">Investigate Papers</a></li>
<li><a href="#get-yourself-a-citable-code-for-anything">Get Yourself A
Citable Code for Anything</a></li>
<li><a href="#open-science">Open Science</a></li>
<li><a href="#tips-for-researchers">Tips for Researchers</a></li>
</ul></li>
<li><a href="#pacifier">Pacifier</a></li>
<li><a href="#online-discussions">Online Discussions</a></li>
<li><a href="#open-source">Open Source</a>
<ul>
<li><a href="#open-licenses">Open Licenses</a></li>
<li><a href="#use-licenses">Use Licenses</a></li>
<li><a href="#bibliography">Bibliography</a></li>
</ul></li>
<li><a href="#data-visualization-and-graph-making">Data Visualization
and Graph Making</a>
<ul>
<li><a href="#data-visualization">Data Visualization</a></li>
<li><a href="#graph-making">Graph Making</a></li>
</ul></li>
<li><a href="#latex-1">LaTeX</a>
<ul>
<li><a href="#tips">Tips</a></li>
<li><a href="#symbols">Symbols</a></li>
<li><a href="#graphing">Graphing</a></li>
<li><a href="#fonts">Fonts</a></li>
<li><a href="#templates">Templates</a></li>
<li><a href="#references">References</a></li>
</ul></li>
<li><a href="#misc">MISC</a>
<ul>
<li><a href="#terminal">Terminal</a></li>
<li><a href="#free-multimedia">Free Multimedia</a></li>
<li><a href="#interesting-journals">Interesting Journals</a></li>
<li><a href="#more">More</a></li>
</ul></li>
</ul>
<h2 id="be-organized">Be-Organized</h2>
<h3 id="version-control-system">Version Control System</h3>
<blockquote>
<p>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.</p>
</blockquote>
<ul>
<li><strong>git</strong></li>
<li>svn</li>
<li>mercurial</li>
</ul>
<h4 id="online-git-service">Online Git Service</h4>
<ul>
<li><a href="https://github.com/">GitHub</a>: the most popular platform
for git with social and collaborations built-in.
<ul>
<li>GitHub also provides GitHub Actions. With Actions one could automate
processes.</li>
<li>GitHub provides GitHub Pages. With GitHub Pages, on could host
static files as well as <a href="https://jekyllrb.com">Jekyll</a> built
websites.</li>
</ul></li>
<li><a href="https://about.gitlab.com/">GitLab</a>: similar to GitHub,
GitLab provides git hosting, collaborations, social, automations, and
more. GitLab can be both cloud-based and self-hosted using its
open-source code.
<ul>
<li>GitLab includes unlimited free private repositories.</li>
<li>GitLab comes with a continuous integration tool that is more
powerful than GitHub Actions.</li>
</ul></li>
<li><a href="https://bitbucket.org">BitBucket</a>: Alternative to GitHub
and GitLab with free private repositories.</li>
</ul>
<h4 id="self-hosted-git-server">Self-hosted Git Server</h4>
<ul>
<li><a href="http://gitlab.org/">GitLab</a>: See above at <a
href="#online-git-service">Online Git Service</a>.</li>
<li><a href="https://gitea.io/en-us/">Gitea</a>: Painless self-hosted
Git service written in Go.</li>
<li><a href="https://gogs.io/">Gogs</a>: A painless self-hosted Git
service.</li>
</ul>
<h4 id="enterprise-git-service">Enterprise Git Service</h4>
<ul>
<li><a href="https://rhodecode.com/">RhodeCode</a>: Centralized control
for distributed repositories. Mercurial, Git, and Subversion under a
single roof.</li>
</ul>
<h3 id="pomodoro">Pomodoro</h3>
<blockquote>
<p><a href="https://en.wikipedia.org/wiki/Pomodoro_Technique">Pomodoro
Technique</a> can be used to boost your productivity and probably
improve your health. There are almost infinite choices for the
tools.</p>
</blockquote>
<ul>
<li><a href="https://pomotodo.com/">Pomotodo</a>
(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>,<code>Chrome</code>):
A mix of todo list and pomodoro timer, with sync across devices and
weekly report [Free].</li>
<li><a href="https://tadamapp.com/">Tadam</a> (<code>Mac</code>): Simple
and elegant pomodoro timer [USD$ 4.99].</li>
<li><a
href="https://play.google.com/store/apps/details?id=com.wlxd.pomochallenge&amp;hl=en">Productivity
Challenge Timer</a> (<code>Android</code>): Pomodoro timer with great
gamification features [Free].</li>
</ul>
<h3 id="gtd-task-manager">GTD-Task Manager</h3>
<blockquote>
<p>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 (<a
href="https://en.wikipedia.org/wiki/Getting_Things_Done">Wikipedia</a>).
Tasks can be classified in contexts (<span class="citation"
data-cites="home">@home</span>, <span class="citation"
data-cites="computer">@computer</span>, <span class="citation"
data-cites="office">@office</span>, etc), time of action (now, next
actions, scheduled or someday) and projects. <a
href="https://hamberg.no/gtd/">Here</a> we have a good pragmatic guide
to GTD and <a
href="https://gettingthingsdone.com/pdfs/tt_workflow_chart.pdf">here</a>
is a flowchart.</p>
</blockquote>
<ul>
<li><a href="https://todo.microsoft.com/tasks">Microsoft To Do</a>
(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>,<code>Win Store</code>,<code>Chrome OS</code>):
Almost perfect todo lists with cooperation and sharing.</li>
<li><a href="https://keep.google.com/">Google
Keep</a>(<code>Cloud</code>,<code>Android</code>,<code>iOS</code>,<code>Chrome OS</code>)</li>
<li><a href="https://evernote.com/">Evernote</a>
(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>,<code>Win Store</code>):
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.</li>
<li><a href="https://www.any.do/">Anydo</a>
(<code>Cloud</code>,<code>Mac</code>,<code>Android</code>,<code>iOS</code>):
Good because it has a very good daily review which can help users
remember what to do.</li>
<li><a href="https://todoist.com/">Todoist</a>
(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>):
Todoist invented the karma system which keeps track of the tasks
done.</li>
<li><a href="https://taskade.com/">Taskade</a>
(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Chrome OS</code>,<code>Firefox</code>,<code>Android</code>,<code>iOS</code>):
Taskade is a collaborative task list and outliner for team
projects.</li>
<li><a href="https://agenda.com/">Agenda</a>(<code>Mac</code>):
Date-focused note taking.</li>
</ul>
<h2 id="cloud-services">Cloud Services</h2>
<p><em>For self-hosted services, check out <a
href="https://github.com/Kickball/awesome-selfhosted">awesome-selfhosted</a>
on GitHub.</em></p>
<h3 id="math-and-programming-online">Math and Programming Online</h3>
<blockquote>
<p>There are many tools that allows use of code, perform numerical
calculations or analytical derivation online.</p>
</blockquote>
<ul>
<li><a href="https://colab.research.google.com/">Google Colab</a>: free
jupyter notebook online. Google Colab also comes with free GPU hours.
<ul>
<li>Free and powerful.</li>
<li>Share and collaborate on the same notebook.</li>
<li>Can be saved in GitHub or Google Drive.</li>
</ul></li>
<li><a href="https://nextjournal.com/">NextJournal</a>: the notebook for
reproducible research.
<ul>
<li>Basically, NextJournal runs almost anything.</li>
<li>Focusing on reproducibility.</li>
</ul></li>
<li><a href="https://www.kaggle.com/">Kaggle</a>: kaggle has built-in
free jupyter notebook.
<ul>
<li>One can also connect to Google BigQuery to access big data.</li>
</ul></li>
<li><a href="https://notebooks.azure.com/">Azure Notebooks</a>: online
jupyter notebooks.</li>
<li><a href="https://datalore.io/">Datalore</a>: online jupyter notebook
by JetBrains.</li>
<li><a href="https://cocalc.com/">CoCalc (SageMathCloud)</a>: LaTeX, R,
iPython Notebook, etc.</li>
<li><a href="https://aws.amazon.com/sagemaker/">SageMaker</a>: AWS
service with a lot of tools integrated. Sagemaker comes with the
Sagemake Studio which provides jupyter notebook for programmer and other
charting and data management tools.</li>
<li><a href="https://www.wolframalpha.com/">WolframAlpha</a>: Excellent
engine to do mathematical derivation online and search.</li>
<li><a href="https://www.wolfram.com/mathematica/online/">Mathematica
Online</a>: Bring Mathematica to life in the cloud.</li>
</ul>
<h3 id="plotting-and-charting-online">Plotting and Charting Online</h3>
<blockquote>
<p>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.</p>
</blockquote>
<ul>
<li><a href="https://plot.ly/">plot.ly</a>: Online plotting with many
cloud services integrated.</li>
<li><a href="https://www.desmos.com/calculator">Desmos</a>: Graphs for
functions.</li>
<li><a href="https://www.geogebra.org">GeoGebra</a>: very old but still
very good. GeoGebra can be used for precise charting as well as
calculations.</li>
<li><a href="http://graph.tk/">graph.tk</a>: Online plotting with rich
features.</li>
<li><a href="http://www.wolframalpha.com/">Wolfram Alpha</a>: Make
graphs for functions, from your data and even more.</li>
</ul>
<h3 id="datasets">Datasets</h3>
<blockquote>
<p>Nature hosts a list of recommended data repositories <a
href="https://www.nature.com/sdata/policies/repositories">here</a>.</p>
</blockquote>
<h4 id="general-and-interdisciplinary">General and
Interdisciplinary</h4>
<ul>
<li><a href="http://datadryad.org/">DRYAD</a> (<code>Storage</code>,
<code>Lookup</code>): The Dryad Digital Repository stores curated
data.</li>
<li><a href="https://figshare.com/">Figshare</a> (<code>Storage</code>,
<code>Lookup</code>): Data sharing and storage</li>
<li><a href="https://data.gov">Data.gov</a> (<code>Lookup</code>): Data
by US Federal Government</li>
</ul>
<h4 id="life-science">Life Science</h4>
<ul>
<li><a href="https://www.ncbi.nlm.nih.gov/genbank/">GenBank</a>
(<code>Lookup</code>): Genetic sequence database</li>
<li><a href="https://www.ncei.noaa.gov/">National Centers for
Environmental Information</a> (<code>Lookup</code>): Weather, climate,
coasts, oceans, and geophysics etc</li>
<li><a href="http://www.geoportal.org">GEOSS Portal</a>
(<code>Lookup</code>): Earth science data</li>
</ul>
<h4 id="physical-sciences">Physical Sciences</h4>
<ul>
<li><a href="http://www.usvao.org/">US Virtual Astronomical
Observatory</a> (<code>Lookup</code>)</li>
<li><a
href="https://mast.stsci.edu/portal/Mashup/Clients/Mast/portal.html">MAST:
Barbara A. Mikulski Archive for Space Telescopes</a>
(<code>Lookup</code>)</li>
<li><a href="http://archive.stsci.edu/">Mikulski Archive for Space
Telescopes</a> (<code>Lookup</code>)</li>
</ul>
<h4 id="arts-and-humanities">Arts and Humanities</h4>
<ul>
<li><a href="http://archaeologydataservice.ac.uk/">Archaeology Data
Service</a> (<code>Lookup</code>): Certified repository</li>
</ul>
<h4 id="engineering">Engineering</h4>
<ul>
<li><a href="http://en.openei.org/wiki/Main_Page">Open Energy
Information (OpenEI)</a> (<code>Lookup</code>): Wiki of collections of
energy information</li>
</ul>
<h4 id="social-sciences">Social Sciences</h4>
<ul>
<li><a href="https://www.icpsr.umich.edu/web/pages/">Inter-university
Consortium for Political and Social Research (ICPSR)</a>
(<code>Lookup</code>)</li>
<li><a href="http://library.harvard.edu/gdc">Institute for Quantitative
Social Science (IQSS)</a> (<code>Lookup</code>)</li>
</ul>
<h3 id="colors">Colors</h3>
<blockquote>
<p>Pick a pleasing color for your presentations and notes. Refer to <a
href="#data-visualization-and-graph-making">Data Visualization and Graph
Making</a></p>
</blockquote>
<ul>
<li><a href="http://colorbrewer2.org">ColorBrewer</a></li>
<li><a href="http://paletton.com">Paletton</a></li>
<li><a href="https://www.sessions.edu/color-calculator/">Color
Calculator</a></li>
</ul>
<h2 id="publishing-and-sharing">Publishing and Sharing</h2>
<blockquote>
<p>Make use of <a href="http://github.com">GitHub</a> to cooperate with
others. <a href="https://pages.github.com/">GitHub pages</a> is also
good for hosting static contents. GitHub provides Education perks so
students could get free pro version which comes with private repos.</p>
</blockquote>
<h3 id="writing">Writing</h3>
<p><strong>Markdown is one of the best languages for writing.</strong>
Check out these editor in <a href="#markdown">Markdown section</a>.</p>
<p><strong>Make use of these programs for publishing:</strong></p>
<ul>
<li><a href="http://sphinx-doc.org">Sphinx</a>: RestructuredText as
source files, powerful, flexible and modularized.</li>
<li><a href="https://www.gitbook.com/">Gitbook</a>: 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.</li>
<li><a href="https://github.com/schacon/git-scribe">Git-scribe</a>: Good
for writing ebooks.</li>
<li><a href="#static-site-generator">Static Site Generator</a>: For more
please refer to <a href="#static-site-generator">Static Site
Generator</a>.</li>
</ul>
<p><strong>Sphinx Themes and configurations</strong></p>
<ul>
<li><a href="https://github.com/snide/sphinx_rtd_theme">rtd theme</a>:
Developed by ReadtheDocs.org</li>
<li><a href="https://github.com/bitprophet/alabaster">Alabaster</a>:
Clean and simple</li>
<li><a
href="https://ryan-roemer.github.io/sphinx-bootstrap-theme/">Bootstrap
theme</a></li>
</ul>
<p><strong>Science Books Using Sphinx</strong></p>
<blockquote>
<p>Here are some examples of how sphinx can be used for research.</p>
</blockquote>
<ul>
<li><a href="https://github.com/certik/theoretical-physics">Theoretical
Physics</a></li>
<li><a
href="https://github.com/emptymalei/statisticalphysics">Statistical
Physics</a></li>
<li><a href="https://github.com/NeuPhysics/neutrino">Neutrino
Physics</a></li>
</ul>
<p><strong>Writing Tools</strong></p>
<blockquote>
<p>Just use <a href="https://code.visualstudio.com/">Visual Studio
Code</a>.</p>
</blockquote>
<ul>
<li><a href="https://hemingwayapp.com/">Hemingway App</a>: Highlights
complex sentences, point out passive voice, and suggests alternative
words.</li>
<li><a href="https://github.com/amperser/proselint">proselint</a>: A
linter for English prose using advice from <em>Garner’s Modern American
Usage</em> and more.</li>
<li><a href="https://github.com/btford/write-good">write good</a>: Naive
JavaScript linter for English prose.</li>
<li><a
href="https://github.com/sachac/artbollocks-mode">artbollocks-mode</a>:
Emacs minor mode for avoiding cliches and bad grammar when writing about
art (or other topics).</li>
<li><a
href="https://jugad2.blogspot.com/2015/07/cut-crap-absolutely-essential-tool-for.html"><code>cut_the_crap.py</code></a>:
Simple Python script to flag redundant words and gives alternative
suggestions.</li>
<li><a href="https://github.com/GitbookIO/rousseau">Rousseau</a>:
Lightweight proofreader written in JavaScript.</li>
<li><a
href="https://github.com/azu/textlint-rule-rousseau">textlint-rule-rousseau</a>:
A textlint rule to check English sentences using Rousseau.</li>
<li><a href="http://scienceandpublic.com/">De-Jargonizer</a>: Paste your
article or upload file to analyze the amount of jargon in your
writing.</li>
</ul>
<h3 id="hosting">Hosting</h3>
<blockquote>
<p>Host your articles, notes and more. Research is also about
communications.</p>
</blockquote>
<ul>
<li><a href="http://readthedocs.org/">ReadtheDocs</a>: Turn your
reStructuredText source to HTML, PDF, and epub, all done online.</li>
<li><a href="https://pages.github.com/">GitHub pages</a>: Integrated
with Jekyll and turns markdown posts automatically. Jekyll is a tool for
blogging.</li>
<li><a href="http://github.com">GitHub</a>: Just put markdown,
reStructuredText, PDF or IPython/Jupyter notebook files on GitHub. All
these formats can be previewed online. <strong>The thing to mention is
that the math in IPython notebook can be rendered on
GitHub.</strong></li>
<li><a href="https://surge.sh/">Surge</a>: One command upload your
static website to make it live. Surge also integrates GitHub hooks.</li>
<li><a href="https://www.heroku.com/">Heroku</a>: The one that needs no
explanation.</li>
<li><a href="https://aws.amazon.com/">AWS</a>: Amazon AWS provide
student perks.</li>
</ul>
<blockquote>
<p>Other services such as <a
href="https://www.digitalocean.com/">Digital Ocean</a> are also useful
when it comes to dynamic websites and cloud computing.</p>
</blockquote>
<h3 id="blog-and-cms">Blog and CMS</h3>
<blockquote>
<p>Before doing the investigation on platforms, just remind
yourself:</p>
<p><strong>I want to write, not to run blogging software.</strong></p>
</blockquote>
<p><strong>Blog/CMS Software</strong></p>
<blockquote>
<p>These programs are running on the server and can be <a
href="#hosting">hosted using these services</a>.</p>
</blockquote>
<ul>
<li><a href="https://www.gitbook.com/">GitBook</a> (<code>Cloud</code>):
write in Markdown and collaborate with the team. GitBook integrates with
GitHub so no content will be lost.</li>
<li><a href="https://github.com/tryghost/Ghost">Ghost</a>
(<code>Node.js</code>): Open, Simple, non-profit; write with markdown
and live preview.</li>
<li><a href="https://github.com/picocms/Pico">Pico</a>
(<code>PHP</code>): Lightweight cms, open source, no database.</li>
<li><a href="https://github.com/circa75/dropplets">Dropplets</a>
(<code>PHP</code>): Open source, simple, and elegant blog system; write
in Markdown.</li>
<li><a href="https://wordpress.org/">Wordpress</a> (<code>PHP</code>):
Very popular but requires a lot of maintenance.</li>
</ul>
<p><strong>These Blog/CMS software can be hosted on <a
href="https://www.digitalocean.com/">Digital Ocean</a>.</strong></p>
<h3 id="static-site-generator">Static Site Generator</h3>
<blockquote>
<p><a href="https://staticsitegenerators.net/">Here is a nice
website</a> that tells you all the static site generators. Nonetheless
here is a list of the most popular ones.</p>
</blockquote>
<ul>
<li><a href="http://jekyllrb.com/">Jekyll</a> (Written in
<code>Ruby</code>)(<code>Markdown</code>): 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.</li>
<li><a href="http://octopress.org/">Octopress</a> (Written in
<code>Ruby</code>)(<code>Markdown</code>): Octopress is easier to use
compared with Jekyll while being somewhat compatible with Jekyll.</li>
<li><a href="https://hexo.io/">Hexo</a> (Written in
<code>Node.js</code>)(<code>Markdown</code>): “A fast, simple &amp;
powerful blog framework” as they say on their website. It supports
GFM.</li>
<li><a href="http://getpelican.com">Pelican</a> (Written in
<code>Python</code>)(<code>reStructuredText</code>,<code>Markdown</code>,<code>AsciiDoc</code>):
Pelican is a modularized framework and is perfect for blogging.
<ul>
<li><a href="https://github.com/wting/pelican-svbtle">Pelican Svbtle
Theme</a></li>
</ul></li>
<li><a href="https://getnikola.com/">Nikola</a> (Written in
<code>Python</code>)(<code>reStructuredText</code>,<code>Markdown</code>,<code>IPython Notebook/Jupyter</code>,<code>PHP</code>,
etc): It takes in multiple input formats including reStructuredText and
many others.</li>
<li><a href="http://gohugo.io/">Hugo</a>(Written in
<code>Go</code>)(<code>Markdown</code>): Easy to use and really fast. It
also supports more input formats through plugins.</li>
<li><a href="https://hyperdraft.rosano.ca">Hyperdraft</a>(Written in
<code>JavaScript</code>)(<code>Markdown</code>): Automatically generate
a website as you type plaintext or Markdown.</li>
</ul>
<blockquote>
<p>The site generated by these programs can be hosted on <a
href="https://pages.github.com/">GitHub Pages</a>.</p>
</blockquote>
<h2 id="note-taking">Note Taking</h2>
<h3 id="notebooks-for-researchers">Notebooks for Researchers</h3>
<ul>
<li><a href="https://findingsapp.com">Findings</a>: Your research
assistant &amp; lab notebook, all in one app.</li>
</ul>
<h3 id="editors">Editors</h3>
<blockquote>
<p>Markdown, LaTeX, and reStructuredText are the three useful languages.
<strong>In most cases, a tweakable text editor such as <a
href="https://code.visualstudio.com">Visual Studio Code, aka vscode</a>
is good enough.</strong> In fact vscode comes with a enormous amount of
extensions which can be used to build your own IDE.</p>
</blockquote>
<h4 id="markdown">Markdown</h4>
<ul>
<li><a href="https://hackmd.io">Hackmd.io</a> (<code>Cloud</code>):
Basically ships with everything you expect from the most complete online
markdown editor.</li>
<li><a href="https://stackedit.io/">StackEdit</a>(<code>Cloud</code>):
StackEdit is a Markdown editor with many integrated services such as
math (MathJax), Google Drive, Dropbox, and GitHub.</li>
<li><a href="https://www.zybuluo.com/mdeditor">CMD
markdown</a>(<code>Cloud</code>): CMD is a Markdown editor with math
(MathJax) support. What is special is that it keeps edit history.
(Chinese UI.)</li>
<li><a href="https://www.penflip.com/">Penflip</a>(<code>Cloud</code>):
Penflip is designed to be a GitHub for writers. It is Markdown-based and
git like without math support.</li>
<li><a
href="https://www.authorea.com/">Authorea</a>(<code>Cloud</code>): A
much more powerful Markdown and LaTeX online editor that can be used to
produce nice academic papers.</li>
<li><a href="http://dillinger.io/">Dillinger</a>(<code>Cloud</code>):
Markdown editor but no math mode.</li>
<li><a href="http://pandoc.herokuapp.com/">Pandoc
Markdown</a>(<code>Cloud</code>): Just another Markdown editor with math
(MathJax) support.</li>
<li><a
href="http://marxi.co/">Marxico</a>(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Chrome</code>):
Markdown editor that integrates with Evernote, generates pdf and works
offline. <a
href="https://maxiang.io/">马克飞象</a>(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Chrome</code>)
is the Chinese version。</li>
<li><a
href="https://www.madoko.net/">Madoko</a>(<code>Cloud</code>,<code>Chrome</code>):
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.</li>
<li><a href="http://markx.herokuapp.com/">Markx</a>(<code>Cloud</code>):
Markdown editor for scientific writing. Batteries included.</li>
<li><a
href="https://www.typora.io/">typora</a>(<code>Mac</code>,<code>Win</code>):
Beautiful UI and in-situ live preview.</li>
<li><a
href="http://pad.haroopress.com/">Haroopad</a>(<code>Mac</code>,<code>Win</code>,<code>Linux</code>):
A powerful github flavored markdown editor with useful extensions. Math
(mathjax) is supported.</li>
<li><a
href="http://jbt.github.io/markdown-editor/">jbt/markdown-editor</a>(<code>Cloud</code>):
Just another online Markdown editor without math support.</li>
<li><a href="http://markdownpad.com/">MarkdownPad</a>
(<code>Win</code>): If you have no bad feelings about .NET, this is
pretty good.</li>
<li><a href="https://github.com/retext-project/retext">ReText</a>
(<code>Mac</code>,<code>Win</code>,<code>Linux</code>): ReText one of
the best, even on Linux. It also supports reStructuredText input.</li>
<li><a href="https://www.madoko.net/">Madoko</a> (<code>Cloud</code>):
<strong>LaTeX</strong> × Markdown ²</li>
<li><a href="https://github.com/egoist/eme">eme</a>
(<code>Win</code>,<code>Mac</code>,<code>Linux</code>): Math
support.</li>
<li><a href="https://moeditor.org/">Moeditor</a>
(<code>Win</code>,<code>Mac</code>,<code>Linux</code>): All purpose
markdown editor.</li>
</ul>
<p>Notebook softwares that you can write in Markdown:</p>
<ul>
<li><a href="https://boostnote.io/">boostnote</a>
(<code>Win</code>,<code>Mac</code>,<code>Linux</code>): Math + Markdown,
with snippet note support.</li>
<li><a href="http://happenapps.com/">Quiver</a>
(<code>Mac</code>,<code>iOS</code>): Programmer’s notebook, math +
Markdown, code snippet.</li>
<li><a href="http://findingsapp.com/">Findings</a> (<code>Mac</code>):
Notebook for experimentalists, organized research materials and
notes.</li>
<li><a href="https://www.notion.so/">Notion</a>
(<code>Win</code>,<code>Mac</code>,<code>iOS</code>,<code>Android</code>):
Notetaking with kanban, math, calendar, table, etc.</li>
<li><a href="https://agenda.com/">Agenda</a>
(<code>Mac</code>,<code>iOS</code>): Notes and GTD.</li>
</ul>
<h4 id="latex">LaTeX</h4>
<ul>
<li><a
href="https://www.overleaf.com/">Overleaf</a>(<code>Cloud</code>): Built
in version control, Dropbox and GitHub integration, preview,
cooperation, simple UI. It also provides a lot of templates.</li>
<li><a
href="https://www.authorea.com/">Authorea</a>(<code>Cloud</code>): Easy
to use UI. Supports both Markdown and LaTeX.</li>
<li><a href="https://www.papeeria.com">Papeeria</a>(<code>Cloud</code>):
Just another online LaTeX and Markdown with plot compiler and
collaborations.</li>
<li><a href="http://jaxedit.com/">JaxEdit</a>(<code>Cloud</code>):
JaxEdit doesn’t provide full LaTeX support but is good enough for simple
LaTeX documents and slides.</li>
</ul>
<p><strong>You can also host one using your own machine.</strong></p>
<ul>
<li><a href="https://github.com/overleaf/overleaf">Overleaf Source
Code</a>: Overleaf open sourced their codes. This is a great move I
would say.</li>
<li><a href="http://www.texstudio.org">TeXStudio</a> - Cross-platform
LaTeX editor that stems from TeXMaker.</li>
<li><a href="http://www.winedt.com">WinEdt</a> - The LaTeX editor many
people swear by.</li>
<li><a href="http://www.texniccenter.org">TeXnicCenter</a> - A quite old
but free and decent editor for LaTeX.</li>
<li><a href="https://www.lyx.org">LyX</a> - Cross-platform WYSIWYM
editor that uses LaTeX behind the scenes to render documents.</li>
<li><a href="http://pages.uoregon.edu/koch/texshop/">TeXshop</a> -
No-nonsense editor for LaTeX documents which is included in MacTeX.</li>
<li><a href="https://www.tug.org/texworks/">TeXWorks</a> - No-nonsense
editor for LaTeX code, modeled after TeXShop, but this one is
cross-platform.</li>
</ul>
<p><strong>You can also add notes directly to academic
papers</strong></p>
<ul>
<li><a href="https://synthical.com">Synthical</a> - aggregates all
papers from arXiv, medRxiv, bioRxiv, and chemRxiv with ability to
highlight and leave notes.</li>
</ul>
<h3 id="ipython-notebook">IPython Notebook</h3>
<p>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.</p>
<ul>
<li><a
href="https://github.com/jrjohansson/scientific-python-lectures">Scientific
Python Lectures</a></li>
<li><a href="http://reproduced-papers.github.io/">Reproduced
Papers</a></li>
<li><a
href="https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks">More</a>:
For more IPython notebook on GitHub please read this enormous list.</li>
</ul>
<h3 id="mindmap">Mindmap</h3>
<p><strong>Standalone</strong></p>
<ul>
<li>Mind Manager</li>
<li>XMind</li>
<li>Docear</li>
</ul>
<p><strong>Online</strong></p>
<ul>
<li><a href="https://github.com/fex-team/kityminder">KityMinder By
Baidu</a> : Chinese Interface</li>
<li><a href="http://my-mind.github.io/">my-mind</a>: repo <a
href="https://github.com/ondras/my-mind">here</a>.</li>
<li><a href="http://beautifulmind.io/">beautiful Mind</a>: repo <a
href="https://github.com/ierror/BeautifulMind.io">here</a></li>
<li><a href="https://www.mindmup.com/">Mindmup</a>: repo <a
href="https://github.com/mindmup">here</a></li>
<li><a href="http://drichard.org/mindmaps/">mindmaps</a>: repo <a
href="https://github.com/drichard/mindmaps">here</a></li>
</ul>
<p><strong>MINDMAP HTML</strong></p>
<ul>
<li><a href="http://gojs.net/latest/samples/mindMap.html">gojs</a></li>
<li><a href="https://github.com/hizzgdev/jsmind">jsmind</a></li>
<li><a href="http://sourceforge.net/projects/jsmind/">jsmind</a></li>
<li><a href="https://github.com/drichard/mindmaps">mindmaps</a></li>
</ul>
<h3 id="concept-map-and-diagrams">Concept Map and Diagrams</h3>
<ol type="1">
<li><a href="https://www.gliffy.com/">Gliffy</a>: all kinds of
diagrams</li>
<li><a href="http://www.processon.com/">ProcessOn</a>: all kinds of
diagrams</li>
<li><a href="http://www.draw.io/">Draw.io</a>: all kinds of
diagrams</li>
</ol>
<h3 id="keep-the-notes">Keep The Notes</h3>
<blockquote>
<p>It’s alway better to keep track the changes of your notes and
<strong>git</strong> is a nice choice. Therefore, <a
href="http://github.com">GitHub</a> is the almost perfect place.</p>
<p>As for LaTeX, <a
href="http://www.ctan.org/tex-archive/support/latexdiff/">latexdiff</a>
is a tool for checking the diff.</p>
</blockquote>
<blockquote>
<p><strong>Some programs allows you to keep the markdown notes on a
server.</strong></p>
</blockquote>
<ul>
<li><a href="http://raneto.com/">Raneto</a>: Raneto is an open source
Knowledgebase platform that uses static Markdown files to power your
Knowledgebase. This one has a nice looking.</li>
<li><a href="http://realms.io/">Realms</a>: Git based wiki written in
Python Inspired by Gollum, Ghost, and Dillinger. Basic authentication
and registration included.</li>
<li><a href="http://tiddlywiki.com/">Tiddlywiki</a>: A unique non-linear
notebook for capturing, organizing and sharing complex information.</li>
<li>Some other <a href="#static-generator">static site
generators</a>.</li>
</ul>
<p>For experimental research, eLabFTW made a online labnote system: <a
href="https://www.elabftw.net/">eLabFTW</a>.</p>
<h2 id="presentation-tools">Presentation Tools</h2>
<h3 id="keep-you-computer-awake">Keep You Computer Awake</h3>
<blockquote>
<p>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.</p>
</blockquote>
<ul>
<li><a
href="https://itunes.apple.com/us/app/caffeine/id411246225">Caffeine</a>
(<code>Mac</code>): As simple as a single click.</li>
<li><a
href="https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12">Amphetamine</a>
(<code>Mac</code>): More configurations involved and more
intelligent.</li>
</ul>
<h3 id="online-load-and-edit">Online Load and Edit</h3>
<ul>
<li><a href="https://prezi.com/">Prezi</a> if you can.</li>
<li><a href="http://slides.com/">slides.com</a>: Easy to use with remote
controlled page presentation.</li>
<li><a href="https://www.slideas.app/">Slideas</a>: the easiest way to
create a beautiful Markdown Presentation, with all the features you
need.</li>
<li><a href="https://drive.google.com/">Google Drive</a>: no
introduction needed</li>
<li><a href="https://sway.com/">Sway</a>: Microsoft</li>
<li><a href="https://github.com/tantaman/Strut">Strut</a></li>
<li><a
href="https://github.com/harish-io/Impressionist">Impressionist</a></li>
<li><a href="https://github.com/regebro/hovercraft">hovercraft</a></li>
</ul>
<h3 id="use-the-source">Use The Source</h3>
<blockquote>
<p>Requires a few front-end techniques.</p>
</blockquote>
<h4 id="htmlcssjs">HTML+CSS+JS</h4>
<blockquote>
<p>Use <a href="https://github.com/mrmrs/colors">colors</a> to make your
HTML feels better.</p>
</blockquote>
<ul>
<li><a href="http://impress.github.io/impress.js/">Impress.js</a>: more
about it <a href="https://github.com/impress/impress.js/wiki">impress
wiki page</a>.</li>
<li><a href="http://jmpressjs.github.io/jmpress.js/">Jimpress</a>: A
jQuery version of impress.js</li>
<li><a href="https://github.com/hakimel/reveal.js">Reveal.js</a></li>
<li><a href="https://github.com/bespokejs/bespoke">Beckpoke.js</a></li>
<li><a href="https://github.com/LeaVerou/CSSS">CSSS</a></li>
<li><a
href="https://github.com/johnpolacek/scrolldeck.js">Scrolldeck</a></li>
<li><a href="https://github.com/imakewebthings/deck.js">Deck.js</a></li>
<li><a href="https://github.com/shower/shower">Shower</a></li>
<li><a
href="https://github.com/marcolago/flowtime.js">Flowtime.js</a></li>
<li><a href="https://github.com/briancavalier/slides">Slides</a></li>
<li><a href="https://remarkjs.com">remark</a></li>
</ul>
<h3 id="ipythonjupyter-notebook">IPython/Jupyter Notebook</h3>
<blockquote>
<p>Python, Julia, R, Scala and more languages are supported in <a
href="https://jupyter.org/">IPython/Jupyter Notebook</a> which can also
be used to give presentations.</p>
<p>Refer to <a href="#math-and-programming-online">math and programming
online</a> for cloud-based Jupyter Notebooks.</p>
</blockquote>
<h3 id="latex-beamer">LaTeX Beamer</h3>
<ul>
<li><a href="https://bitbucket.org/rivanvx/beamer/wiki/Home">Beamer</a>:
Shipped with standard LaTeX installations. A lot of themes has been
invented. Start editing with one click on <a
href="https://www.overleaf.com/">Overleaf</a></li>
</ul>
<h3 id="mathematica">Mathematica</h3>
<ul>
<li><a
href="http://reference.wolfram.com/language/howto/CreateASlideShow.html">Mathematica
slides</a> can be made interactive.</li>
</ul>
<h3 id="the-power-of-svg">The Power of SVG</h3>
<p><strong>Online SVG editors:</strong></p>
<ul>
<li><a href="https://github.com/asyazwan/ext-sozi">ext-sozi</a></li>
</ul>
<p><strong>Local SVG editors:</strong></p>
<ul>
<li><a
href="https://inkscape.org">Inkscape</a>(<code>Mac</code>,<code>Win</code>,<code>Linux</code>)</li>
<li><a
href="https://www.gimp.org">GIMP</a>(<code>Mac</code>,<code>Win</code>,<code>Linux</code>)</li>
</ul>
<h3 id="sharing-slides">Sharing Slides</h3>
<ul>
<li><a href="https://pages.github.com/">GitHub pages</a>: For Html based
slides.</li>
<li><a href="https://speakerdeck.com/">Speaker Deck</a> by GitHub: PDF
slides. Can be displayed online or embeded.</li>
</ul>
<h2 id="programming">Programming</h2>
<h3 id="code-editors">Code Editors</h3>
<ul>
<li><a href="https://code.visualstudio.com/">Visual Studio Code, aka VS
Code</a>(<code>Free</code>,<code>Cross-platform</code>,<code>Plugins</code>):
same technology as atom but faster than atom, and Microsoft made.</li>
<li><a
href="https://atom.io/">Atom</a>(<code>Free</code>,<code>Cross-platform</code>,<code>Plugins</code>):
electron based editor with numerous plugins and easy modifications.
Cross-platform with settings and plugins synchronized through the <a
href="https://atom.io/packages/sync-settings">sync-settings</a>
plugin.</li>
<li><a href="https://www.sublimetext.com/">Sublime
Text</a>(<code>Free Evaluation</code>,<code>Cross-platform</code>,<code>Plugins</code>):
cross-platform, fast, and with plugins. Not free but can be freely used
forever.</li>
<li><a
href="https://www.jetbrains.com/">JetBrains</a>(<code>Free for Students</code>,
<code>Cross-platform</code>,<code>Plugins</code>): beautiful IDE’s with
many debugging and editing modes integrated.</li>
<li><a
href="https://github.com/vim/vim">vim</a>(<code>Free</code>,<code>Cross-platform</code>,<code>Plugins</code>):
no words can describe the almighty vim.
<ul>
<li><a href="https://github.com/VundleVim/Vundle.vim">Vundle</a>: the
vim plugin manager</li>
<li><a href="https://github.com/amix/vimrc">vimrc from amix</a>: “The
ultimate Vim configuration: vimrc”</li>
</ul></li>
</ul>
<h3 id="softwares">Softwares</h3>
<ul>
<li><a href="https://synthical.com">Synthical</a>: AI-powered
collaborative research environment</li>
<li><a href="http://www.wolfram.com/mathematica/">Mathematica</a>: One
Software to Rule Them All</li>
<li><a href="http://ipython.org/notebook.html">iPython Notebook</a>
(<code>Python</code>): a useful tool for inline calculation, making
graphs and writing notes.
<ul>
<li><a href="https://wakari.io/">wakari.io</a> is a comercial one mostly
aimed for data analysis.</li>
<li><a href="https://github.com/ptone/jiffylab">jiffylab</a> is an open
source one but not that well done.</li>
<li><a
href="https://github.com/writefaruq/supervised-ipython-nbserver">supervised-ipython-nbserver</a>
is a multiuser version of notebook using Django/Pinax.</li>
</ul></li>
<li><a href="http://www.mathworks.com/products/matlab/">Matlab</a></li>
<li><a href="https://www.maplesoft.com/index.aspx?L=E">Maple</a></li>
<li><a href="https://www.rstudio.com/">RStudio</a> (<code>R</code>)</li>
</ul>
<h3 id="scientific-computing">Scientific Computing</h3>
<ul>
<li><a href="https://www.python.org/">Python</a>
<ul>
<li><a href="https://www.scipy.org/">scipy</a>: scientific computing
made easy</li>
<li><a href="https://jiffyclub.github.io/snakeviz/">SnakeViz</a>: A nice
tool for python debugging and performance improvement.</li>
</ul></li>
<li><a href="http://julialang.org/">Julia</a></li>
<li><a href="http://www.r-project.org/">R</a></li>
<li><a href="https://www.rust-lang.org/en-US/">Rust</a></li>
</ul>
<h3 id="coding-is-fun">Coding is Fun</h3>
<ul>
<li><a href="https://codefights.com/">Code Fights</a></li>
</ul>
<h2 id="academic">Academic</h2>
<h3 id="self-plagiarism">Self-plagiarism</h3>
<blockquote>
<p>This might be not so straightforward but remember this. Reusing your
own work doesn’t protect you from plagiarism! Read more on</p>
</blockquote>
<ul>
<li><a
href="https://en.wikipedia.org/wiki/Plagiarism#Self-plagiarism">wikipedia:Plagiarism#Self-plagiarism</a>.</li>
</ul>
<h3 id="investigate-papers">Investigate Papers</h3>
<ul>
<li><a href="https://synthical.com">Synthical</a>: AI-powered
collaborative research environment. You can use it to get
recommendations of articles based on reading history, simplify papers,
find out what articles are trending, search articles by meaning (not
just keywords), create and share folders of articles, see lists of
articles from specific companies and universities, and add
highlights.</li>
<li><a href="http://paperscape.org/">Paperscape</a>: Finding interesting
papers.</li>
<li><a href="https://peer.us/">Peerus</a>: Monitor specific topics or
journal for new and relevant papers.</li>
<li><a href="https://scirate.com/">SciRate</a>: An front-end for arXiv
with rates from readers.</li>
<li><a href="http://arxiv-sanity.com/">ArXiv Sanity Preserver</a>:
Accelerate research through arXiv specific for many things machine
learning by Andrej Karpathy.</li>
<li><a href="https://the.iris.ai/">Iris.ai</a>: Explore scientific
papers and how they connect to a paper of your choice.</li>
<li><a href="https://harzing.com/resources/publish-or-perish">Publish or
Perish</a>: Retrieves and analyzes academic citations designed to
empower individual academics to present their case for research impact
to its best advantage.</li>
<li><a href="http://pubchase.com/">PubChase</a>: Life sciences and
medical literature recommendation engine.</li>
<li><a href="https://www.connectedpapers.com/">Connected Papers</a>:
Visualise connected papers with support for node colours, size and
distance from origin to distinguish whether a paper is useful and how
related it is.</li>
</ul>
<h3 id="get-yourself-a-citable-code-for-anything">Get Yourself A Citable
Code for Anything</h3>
<ul>
<li><a href="https://zenodo.org/">Zenodo</a>: Make anything from GitHub
citable by getting a DOI code here.</li>
</ul>
<h3 id="get-yourself-a-unique-and-persistent-digital-identifier">Get
Yourself A Unique and Persistent Digital Identifier</h3>
<ul>
<li><a href="http://orcid.org/">orcid</a>: Use your ORCID identifier in
any research workflow to ensure you get credit for your work.</li>
</ul>
<h3 id="add-citations-to-your-code">Add Citations to Your Code</h3>
<ul>
<li><a href="https://github.com/duecredit/duecredit">duecredit</a>:
Allows you to add decorators to Python functions that encode
bibliographic details.</li>
</ul>
<h3 id="open-science">Open Science</h3>
<ul>
<li><a href="https://osf.io/">Open Science Framework</a>: A open science
tool with a lot of integrations.</li>
</ul>
<h3 id="bibliography">Bibliography</h3>
<ul>
<li><a href="https://www.readcube.com/">ReadCube/Papers</a>: A all
platform app for reference mamagement, note-taking, and more. The former
Papers has been rebanded as ReadCube Papers.</li>
<li><a href="https://www.mendeley.com/">Mendeley</a>: A bibliography
reference manager with cloud storage and BibTeX support.</li>
<li><a href="https://www.zotero.org/">Zotero</a>: An open source
bibliography reference manager with syncing and BibTeX support.</li>
<li><a href="https://www.zotero.org/styles">Zotero Style Repository</a>:
Find any style you need.</li>
<li><a href="https://www.jabref.org/">JabRef</a>: An open source
bibliography reference manager for the BibTeX format.</li>
<li><a href="https://www.doi2bib.org/">doi2bib</a>: Retrieves a BibTeX
entry from a DOI.</li>
<li><a href="https://www.crossref.org/">crossref</a>: Makes research
outputs easy to find, cite, link, and assess.</li>
<li><a href="https://github.com/jkitchin/org-ref">org-ref</a>:
Citations, cross-references, indexes, glossaries, and bibtex utitlies
for org-mode in Emacs.</li>
</ul>
<h3 id="tips-for-researchers">Tips for Researchers</h3>
<ul>
<li><a href="http://collections.plos.org/ten-simple-rules">Ten Simple
Rules by PLoS One</a>: Series of quick “Ten Simple Rules” articles for
research scientists to manage challenges in their careers. Number of
articles are life-science specific, but rest the of articles are general
enough for any researcher.</li>
<li>Check the <a
href="https://github.com/jivoi/awesome-osint#-academic-resources-and-grey-literature">Academic
Resources and Grey Literature List</a> of the <a
href="https://github.com/jivoi/awesome-osint">Awesome Open-Source
Intelligence List</a> for search engines to search for papers.</li>
</ul>
<h2 id="pacifier">Pacifier</h2>
<blockquote>
<p><strong><a href="http://www.rainymood.com/">Rainy Mood</a>, <a
href="https://coffitivity.com/">Coffitivity</a> and <a
href="http://www.noisli.com/">Noisli</a> are the recommended
ones.</strong></p>
</blockquote>
<ul>
<li><a href="http://www.rainymood.com/">Rainy Mood</a>(<code>iOS</code>,
<code>Android</code>, <code>Web</code>): rainy day rainy mood, simple
but with excellent white noise; a new beautiful soundtrack each day</li>
<li><a href="http://coffitivity.com/">Coffitivity</a>(<code>iOS</code>,
<code>Android</code>, <code>Web</code>, <code>Mac</code>): a rather
simple but useful coffee shop noise library; premium has more three more
soundtracks; elegant UI; scientific research powered</li>
<li><a href="https://www.brain.fm/">Brain.fm</a>(<code>Web</code>):
Improve Focus, Relaxation &amp; Sleep with audio brainwave training. Not
free but worth every penny.</li>
<li><a href="http://noiz.io/">Noizio</a>(<code>iOS</code>,
<code>Mac</code>): a handy white noise tool that stays in your Mac
status bar.</li>
<li><a href="http://www.noisli.com/">Noisli</a> (<code>iOS</code>,
<code>Android</code>, <code>Web</code>, <code>Chrome</code>): 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.</li>
<li><a href="http://soundrown.com/">Soundrown</a>(<code>Web</code>):
free mixing of multiple tracks</li>
<li><a href="http://sleep.muji.net/">Muji Sleep</a>(<code>iOS</code>,
<code>Android</code>)</li>
<li><a href="http://asoftmurmur.com/">A Soft
Murmur</a>(<code>Web</code>): free mixing of multiple tracks; simple UI;
Timer provided; Meander available</li>
<li><a
href="https://mynoise.net/noiseMachines.php">mynoise</a>(<code>iOS</code>,
<code>Web</code>): a noise generator; a lot of choices (too many
actually); detailed equalizer</li>
<li><a href="http://rainycafe.com/">Rainy Cafe</a>(<code>Web</code>):
not much to say just a combination of rainy mood and coffitivity</li>
<li><a href="http://www.clearskyapps.com/portfolio/sleep">Sleep
Pillow</a>(<code>iOS</code>, <code>Mac</code>): click and play style
preloaded scenes; easy to use; beautiful design</li>
<li><a href="https://www.youtube.com/watch?v=KZV9FmHOsRg">A youtube
audio track of coffee shop (really long)</a></li>
<li><a href="https://www.youtube.com/watch?v=s_2FDRtFOAw">A youtube
audio track of 10 hours rain fall</a></li>
<li><a
href="https://play.google.com/store/apps/details?id=air.com.demute.TaoMix">TaoMix</a>
(<code>Android</code>): sound mixings to concentrate</li>
<li><a href="http://www.calm.com/">Calm</a>(<code>iOS</code>,
<code>Android</code>, <code>Web</code>): to help you calming down</li>
<li><a href="http://raining.fm">Raining</a>(<code>iOS</code>,
<code>Android</code>, <code>Web</code>): raining and thunder</li>
<li><a
href="https://www.focusatwill.com">focus@will</a>(<code>iOS</code>,
<code>Android</code>, <code>Web</code>): music to boost your brain; paid
services now</li>
</ul>
<p><strong>Some Other Related Stuff</strong></p>
<ul>
<li><a href="http://www.iserenity.com/">iSerenity</a>: multiple choices
but not that good (just my feeling).</li>
<li><a href="https://rain.simplynoise.com/">Rany by simply noise</a>:
just rain.</li>
<li><a href="http://www.naturesoundplayer.com/">Natural Sound
player</a>: many natural sounds, cool.</li>
<li><a href="http://naturesoundsfor.me/">NatureSoundsFor.Me</a>: make
your own track, so many kinds of sounds.</li>
<li><a href="http://whitenoise247.net/">White.Noise</a>: several
different tracks</li>
<li><a href="http://www.ambient-mixer.com/">ambient mixer</a>: make
ambient sound easily</li>
<li><a href="http://whitenoisemp3s.com/">white noise mp3s</a>: listen
and download</li>
</ul>
<h2 id="online-discussions">Online Discussions</h2>
<h3 id="forums-and-qas">Forums and Q&amp;A’s</h3>
<blockquote>
<p>StackExchange.com is a good place for professional discussions. Here
is an example.</p>
</blockquote>
<ul>
<li><a
href="http://physics.stackexchange.com/">Physics.StackExchange</a></li>
<li><a href="https://www.biostars.org/">Biostars</a>: StackOverflow
style Q&amp;A site for bioinformatics.</li>
<li><a href="https://neurostars.org/">NeuroStars</a>: StackOverflow
style Q&amp;A site for neuroinformatics.</li>
<li><a href="http://seqanswers.com/">SEQanswers</a>: Forum for next
generation sequencing community.</li>
</ul>
<h2 id="open-source">Open Source</h2>
<blockquote>
<p>Open Source is great. Use git.</p>
</blockquote>
<h3 id="open-licenses">Open Licenses</h3>
<blockquote>
<p>Generally, open licenses are part of</p>
</blockquote>
<ul>
<li><a href="http://opendefinition.org/">Open Definition</a>: Read the
license <a href="http://opendefinition.org/licenses/">here</a> and pick
the one you like.</li>
</ul>
<h3 id="use-licenses">Use Licenses</h3>
<blockquote>
<p>To choose a license, an easy way is to use</p>
</blockquote>
<ul>
<li><a href="http://choosealicense.com/">Choose a License</a> which
helps you decide which license to use through several steps.</li>
</ul>
<blockquote>
<p>CC Licenses can be found at <a
href="http://creativecommons.org/">Creative Commons</a>. For alternative
badges or icons, check the following.</p>
</blockquote>
<ul>
<li><a href="https://github.com/opentf/GuokrBadge">Guokr Badge</a>:
Green CC License badges. (<strong>Documentation is in
Chinese.</strong>)</li>
</ul>
<h2 id="data-visualization-and-graph-making">Data Visualization and
Graph Making</h2>
<h3 id="data-visualization">Data Visualization</h3>
<p><strong>JS and jQuery</strong></p>
<ul>
<li><a href="http://d3js.org/">D3 js</a> (<code>js</code>)</li>
<li><a href="http://www.highcharts.com/demo/bar-stacked">Highcharts</a>
(<code>js</code>): Line charts, area charts, column and bar charts, pie
charts, scatter and bubble charts and more.</li>
<li><a href="http://www.flotcharts.org/flot/examples/">Flot</a>
(<code>jQuery</code>)</li>
<li><a href="http://raphaeljs.com/">Raphaël</a> (<code>js</code>)</li>
<li><a href="http://philogb.github.io/jit/demos.html">JavaScript InfoVis
Toolkit</a> (<code>js</code>)</li>
<li><a href="http://paperjs.org/">Paper.js</a> (<code>js</code>)</li>
</ul>
<p><strong>Python</strong></p>
<ul>
<li><p><a
href="https://github.com/jbmouret/matplotlib_for_papers">matplotlib</a></p></li>
<li><p><a href="https://seaborn.pydata.org/">seaborn</a>: statistical
data visualization</p></li>
<li><p><a href="https://plotnine.readthedocs.io">Plotnine</a>: A Grammar
of Graphics for Python</p></li>
<li><p><a href="http://ggplot.yhathq.com/">ggplot for
python</a></p></li>
<li><p><a href="https://plot.ly/ipython-notebooks/">plot.ly</a>:
Internet required, interactive plotting.</p></li>
<li><p><a
href="http://bokeh.pydata.org/en/latest/docs/quickstart.html#quickstart">bokeh</a>:
Internet required, interactive plotting.</p></li>
<li><p><a href="https://github.com/daleroberts/itermplot">itermplot</a>:
An awesome iTerm2 backend for Matplotlib, so you can plot directly in
your terminal.</p></li>
</ul>
<h3 id="graph-making">Graph Making</h3>
<blockquote>
<p>Professional graphs should be made using professional tools.</p>
</blockquote>
<ul>
<li><a
href="http://www.geogebra.org/">GeoGebra</a>(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Linux</code>,<code>Android</code>,<code>iOS</code>,<code>Win Store</code>):
Geogebra is a very cool tool to make math graphs both 2D and 3D.</li>
<li><a
href="https://github.com/arnobl/latexdraw">LaTeXDraw</a>(<code>Linux</code>):
“A vector drawing editor for LaTeX.”</li>
<li><a
href="http://www.texample.net/tikz/">TikZ</a>(<code>LaTeX</code>)</li>
<li><a
href="http://shiny.chemgrid.org/boxplotr/">BoxPlotR</a>(<code>Web</code>):
A web-tool for generation of box plots.</li>
<li><a
href="https://www.graphviz.org/">Graphviz</a>(<code>Linux,Win,Max,Solaris,FreeBSD</code>):
Open source graph visualization software.</li>
</ul>
<blockquote>
<p>Choose percentually accurate colors for your research plots. Why? (<a
href="https://github.com/holoviz/colorcet/blob/master/examples/index.ipynb">1</a>,
<a href="https://bids.github.io/colormap/">2</a>)</p>
</blockquote>
<ul>
<li><a href="https://github.com/holoviz/colorcet">colorcet</a> can be
used to investigate colormaps.</li>
</ul>
<h2 id="latex-1">LaTeX</h2>
<blockquote>
<p>Much much much better than Microsoft Word.</p>
</blockquote>
<h3 id="tips">Tips</h3>
<ul>
<li><a href="https://en.wikibooks.org/wiki/LaTeX">wikibooks - LaTeX</a>:
A good manual.</li>
<li><a href="#latex">Notetaking programs listed above</a></li>
</ul>
<h3 id="symbols">Symbols</h3>
<ul>
<li><a href="http://detexify.kirelabs.org/classify.html">Detexify</a>:
find out what the symbol is by drawing online</li>
</ul>
<h3 id="graphing">Graphing</h3>
<ul>
<li><a href="http://www.texample.net/">TeX Example</a> (Tikz/PGF)</li>
</ul>
<h3 id="fonts">Fonts</h3>
<ul>
<li><a href="http://www.tug.dk/FontCatalogue/seriffonts.html">Font
Catalogue</a></li>
</ul>
<h3 id="templates">Templates</h3>
<ul>
<li><a href="http://www.latextemplates.com/">LaTeX Templates</a></li>
</ul>
<h3 id="references">References</h3>
<p><strong>Math Typesetting</strong></p>
<ul>
<li><a
href="ftp://ftp.ams.org/pub/author-info/documentation/howto/mit-2.pdf">Math
into Type</a>: This is a great book for math related typography. This is
copyright material. Please DO NOT redistribute.</li>
</ul>
<h2 id="misc">MISC</h2>
<h3 id="terminal">Terminal</h3>
<ul>
<li><a href="https://github.com/glamp/bashplotlib">plot in
terminal</a></li>
<li><a href="https://asciinema.org/">asciinema</a>: Command line
recording.</li>
<li><a href="https://github.com/glamp/bashplotlib">bashplot</a>: plot in
terminal.</li>
<li><a href="https://github.com/EricFreeman/fuck">fuck</a>: correct the
command by typing in fuck.</li>
</ul>
<h3 id="free-multimedia">Free Multimedia</h3>
<ul>
<li><a href="https://ccsearch.creativecommons.org/">CC Search</a>:
Search engine for images under CC License.</li>
<li><a href="https://unsplash.com/">Unsplash</a>: Free high resolution
images.</li>
<li><a
href="https://jpswalsh.github.io/academicons/">Academicons</a></li>
<li><a href="http://phylopic.org/">Phylopic</a></li>
</ul>
<h3 id="more">More</h3>
<ul>
<li><a href="https://www.unitag.io/qrcode">QR Code Generator</a>: Adding
a QR code to your poster can help you get more audience.</li>
<li><a href="http://shields.io/">SHIELDS.io</a>: Make a beautiful badge
by yourself.</li>
<li><a href="http://titlecapitalization.com/">TitleCap</a>: Not sure
which word to capitalize in the title? <a
href="http://titlecapitalization.com/">TitleCap</a> is right for
you.</li>
<li><a href="https://www.nap.edu/read/12192/">On Being a Scientist</a>:
A guide to responsible conduct in research.</li>
<li><a href="http://dirtdirectory.org/">DiRT Directory</a>: Registry of
digital research tools for scholarly use.</li>
<li><a href="https://awwapp.com">Online Whiteboard</a>: A simple online
whiteboard that users can collaborate; Good for online meetings.</li>
<li><a href="http://www.mapinseconds.com/">MapInSeconds.com</a>: Create
maps with corresponding data quickly by copy-pasting from a
spreadsheet.</li>
<li><a href="http://unpaywall.org/">Unpay Wall</a>: legally download
research papers for free.</li>
</ul>
<hr />
<p>This is a CC BY-SA licensed project. Use the source! Keep the source
open!</p>
<figure>
<img
src="https://raw.githubusercontent.com/emptymalei/awesome-research/master/assets/cc_bysa.flat.guokr.png"
alt="CC BY-SA" />
<figcaption aria-hidden="true">CC BY-SA</figcaption>
</figure>
<p><a href="https://github.com/emptymalei/awesome-research">research.md
Github</a></p>
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