1267 lines
54 KiB
HTML
1267 lines
54 KiB
HTML
<h1 id="awesome-research-tools">Awesome Research Tools</h1>
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<p><a href="https://github.com/sindresorhus/awesome"><img
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src="https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg"
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alt="Awesome" /></a></p>
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<p>A list of tools for research. Also available on <a
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href="https://tools.kausalflow.com/tools/">https://tools.kausalflow.com/tools/</a>.</p>
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<h2 id="toc">TOC</h2>
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<ul>
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<li><a href="#be-organized">Be Organized</a>
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<ul>
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<li><a href="#version-control-system">Version Control System</a></li>
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<li><a href="#pomodoro">Pomodoro</a></li>
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<li><a href="#gtd-task-manager">GTD-Task Manager</a></li>
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</ul></li>
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<li><a href="#cloud-services">Cloud Services</a>
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<ul>
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<li><a href="#math-and-programming-online">Math and Programming</a></li>
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<li><a href="#plotting-and-charting-online">Plots</a></li>
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<li><a href="#datasets">Data</a></li>
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<li><a href="#colors">Colors</a></li>
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</ul></li>
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<li><a href="#publishing-and-sharing">Publishing and Sharing</a>
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<ul>
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<li><a href="#writing">Writing</a></li>
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<li><a href="#hosting">Hosting</a></li>
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<li><a href="#blog-and-cms">Blog and CMS</a></li>
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<li><a href="#static-site-generator">Static Site Generator</a></li>
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</ul></li>
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<li><a href="#note-taking">Note Taking</a>
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<ul>
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<li><a href="#editors">Editors</a></li>
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<li><a href="#markdown">Markdown</a></li>
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<li><a href="#latex">LaTeX</a></li>
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<li><a href="#ipython-notebook">iPython Notebook</a></li>
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<li><a href="#mindmap">Mindmap</a></li>
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<li><a href="#concept-map-and-diagrams">Concept Map and
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Diagrams</a></li>
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<li><a href="#keep-the-notes">Keep The Notes</a></li>
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</ul></li>
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<li><a href="#presentation-tools">Presentation Tools</a>
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<ul>
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<li><a href="#online-load-and-edit">Online Load and Edit</a></li>
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<li><a href="#use-the-source">Use The Source</a></li>
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<li><a href="#ipython-notebook">IPython Notebook</a></li>
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<li><a href="#latex-beamer">LaTeX Beamer</a></li>
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<li><a href="#mathematica">Mathematica</a></li>
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<li><a href="#the-power-of-svg">The Power of SVG</a></li>
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<li><a href="#sharing-slides">Sharing Slides</a></li>
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</ul></li>
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<li><a href="#programming">Programming</a>
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<ul>
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<li><a href="#softwares">Softwares</a></li>
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<li><a href="#code-editors">Code Editors</a></li>
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<li><a href="#scientific-computing">Scientific Computing</a></li>
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<li><a href="#coding-is-fun">Coding is Fun</a></li>
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</ul></li>
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<li><a href="#academic">Academic</a>
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<ul>
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<li><a href="#self-plagiarism">Self-plagiarism</a></li>
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<li><a href="#investigate-papers">Investigate Papers</a></li>
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<li><a href="#get-yourself-a-citable-code-for-anything">Get Yourself A
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Citable Code for Anything</a></li>
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<li><a href="#open-science">Open Science</a></li>
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<li><a href="#tips-for-researchers">Tips for Researchers</a></li>
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</ul></li>
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<li><a href="#pacifier">Pacifier</a></li>
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<li><a href="#online-discussions">Online Discussions</a></li>
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<li><a href="#open-source">Open Source</a>
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<ul>
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<li><a href="#open-licenses">Open Licenses</a></li>
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<li><a href="#use-licenses">Use Licenses</a></li>
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<li><a href="#bibliography">Bibliography</a></li>
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</ul></li>
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<li><a href="#data-visualization-and-graph-making">Data Visualization
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and Graph Making</a>
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<ul>
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<li><a href="#data-visualization">Data Visualization</a></li>
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<li><a href="#graph-making">Graph Making</a></li>
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</ul></li>
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<li><a href="#latex-1">LaTeX</a>
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<ul>
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<li><a href="#tips">Tips</a></li>
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<li><a href="#symbols">Symbols</a></li>
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<li><a href="#graphing">Graphing</a></li>
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<li><a href="#fonts">Fonts</a></li>
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<li><a href="#templates">Templates</a></li>
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<li><a href="#references">References</a></li>
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</ul></li>
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<li><a href="#misc">MISC</a>
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<ul>
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<li><a href="#terminal">Terminal</a></li>
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<li><a href="#free-multimedia">Free Multimedia</a></li>
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<li><a href="#interesting-journals">Interesting Journals</a></li>
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<li><a href="#more">More</a></li>
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</ul></li>
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</ul>
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<h2 id="be-organized">Be-Organized</h2>
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<h3 id="version-control-system">Version Control System</h3>
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<blockquote>
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<p>First things first, everyone should know version control system, aka
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VCS. VCS helps us track changes in our documents as well as
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collaborations on the documents. Needless to say, version control is one
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of the most useful tools for scientists.</p>
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</blockquote>
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<ul>
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<li><strong>git</strong></li>
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<li>svn</li>
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<li>mercurial</li>
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</ul>
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<h4 id="online-git-service">Online Git Service</h4>
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<ul>
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<li><a href="https://github.com/">GitHub</a>: the most popular platform
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for git with social and collaborations built-in.
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<ul>
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<li>GitHub also provides GitHub Actions. With Actions one could automate
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processes.</li>
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<li>GitHub provides GitHub Pages. With GitHub Pages, on could host
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static files as well as <a href="https://jekyllrb.com">Jekyll</a> built
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websites.</li>
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</ul></li>
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<li><a href="https://about.gitlab.com/">GitLab</a>: similar to GitHub,
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GitLab provides git hosting, collaborations, social, automations, and
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more. GitLab can be both cloud-based and self-hosted using its
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open-source code.
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<ul>
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<li>GitLab includes unlimited free private repositories.</li>
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<li>GitLab comes with a continuous integration tool that is more
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powerful than GitHub Actions.</li>
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</ul></li>
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<li><a href="https://bitbucket.org">BitBucket</a>: Alternative to GitHub
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and GitLab with free private repositories.</li>
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</ul>
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<h4 id="self-hosted-git-server">Self-hosted Git Server</h4>
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<ul>
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<li><a href="http://gitlab.org/">GitLab</a>: See above at <a
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href="#online-git-service">Online Git Service</a>.</li>
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<li><a href="https://gitea.io/en-us/">Gitea</a>: Painless self-hosted
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Git service written in Go.</li>
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<li><a href="https://gogs.io/">Gogs</a>: A painless self-hosted Git
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service.</li>
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</ul>
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<h4 id="enterprise-git-service">Enterprise Git Service</h4>
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<ul>
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<li><a href="https://rhodecode.com/">RhodeCode</a>: Centralized control
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for distributed repositories. Mercurial, Git, and Subversion under a
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single roof.</li>
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</ul>
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<h3 id="pomodoro">Pomodoro</h3>
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<blockquote>
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<p><a href="https://en.wikipedia.org/wiki/Pomodoro_Technique">Pomodoro
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Technique</a> can be used to boost your productivity and probably
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improve your health. There are almost infinite choices for the
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tools.</p>
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</blockquote>
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<ul>
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<li><a href="https://pomotodo.com/">Pomotodo</a>
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(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>,<code>Chrome</code>):
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A mix of todo list and pomodoro timer, with sync across devices and
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weekly report [Free].</li>
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<li><a href="https://tadamapp.com/">Tadam</a> (<code>Mac</code>): Simple
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and elegant pomodoro timer [USD$ 4.99].</li>
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<li><a
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href="https://play.google.com/store/apps/details?id=com.wlxd.pomochallenge&hl=en">Productivity
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Challenge Timer</a> (<code>Android</code>): Pomodoro timer with great
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gamification features [Free].</li>
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</ul>
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<h3 id="gtd-task-manager">GTD-Task Manager</h3>
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<blockquote>
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<p>The GTD (Getting Things Done) method unloads the todo lists off the
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mind by recording them using external tools. It allows one to focus on
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one active task instead of on all of them (<a
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href="https://en.wikipedia.org/wiki/Getting_Things_Done">Wikipedia</a>).
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Tasks can be classified in contexts (<span class="citation"
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data-cites="home">@home</span>, <span class="citation"
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data-cites="computer">@computer</span>, <span class="citation"
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data-cites="office">@office</span>, etc), time of action (now, next
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actions, scheduled or someday) and projects. <a
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href="https://hamberg.no/gtd/">Here</a> we have a good pragmatic guide
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to GTD and <a
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href="https://gettingthingsdone.com/pdfs/tt_workflow_chart.pdf">here</a>
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is a flowchart.</p>
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</blockquote>
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<ul>
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<li><a href="https://todo.microsoft.com/tasks">Microsoft To Do</a>
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(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>,<code>Win Store</code>,<code>Chrome OS</code>):
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Almost perfect todo lists with cooperation and sharing.</li>
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<li><a href="https://keep.google.com/">Google
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Keep</a>(<code>Cloud</code>,<code>Android</code>,<code>iOS</code>,<code>Chrome OS</code>)</li>
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<li><a href="https://evernote.com/">Evernote</a>
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(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>,<code>Win Store</code>):
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Not so lightweight but still very good for managing life especially
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since it has got a lot of integrations from a lot of other
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services.</li>
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<li><a href="https://www.any.do/">Anydo</a>
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(<code>Cloud</code>,<code>Mac</code>,<code>Android</code>,<code>iOS</code>):
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Good because it has a very good daily review which can help users
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remember what to do.</li>
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<li><a href="https://todoist.com/">Todoist</a>
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(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Android</code>,<code>iOS</code>):
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Todoist invented the karma system which keeps track of the tasks
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done.</li>
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<li><a href="https://taskade.com/">Taskade</a>
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(<code>Cloud</code>,<code>Mac</code>,<code>Win</code>,<code>Chrome OS</code>,<code>Firefox</code>,<code>Android</code>,<code>iOS</code>):
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Taskade is a collaborative task list and outliner for team
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projects.</li>
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<li><a href="https://agenda.com/">Agenda</a>(<code>Mac</code>):
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Date-focused note taking.</li>
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</ul>
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<h2 id="cloud-services">Cloud Services</h2>
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<p><em>For self-hosted services, check out <a
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href="https://github.com/Kickball/awesome-selfhosted">awesome-selfhosted</a>
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on GitHub.</em></p>
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<h3 id="math-and-programming-online">Math and Programming Online</h3>
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<blockquote>
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<p>There are many tools that allows use of code, perform numerical
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calculations or analytical derivation online.</p>
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</blockquote>
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<ul>
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<li><a href="https://colab.research.google.com/">Google Colab</a>: free
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jupyter notebook online. Google Colab also comes with free GPU hours.
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<ul>
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<li>Free and powerful.</li>
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<li>Share and collaborate on the same notebook.</li>
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<li>Can be saved in GitHub or Google Drive.</li>
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</ul></li>
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<li><a href="https://nextjournal.com/">NextJournal</a>: the notebook for
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reproducible research.
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<ul>
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<li>Basically, NextJournal runs almost anything.</li>
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<li>Focusing on reproducibility.</li>
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</ul></li>
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<li><a href="https://www.kaggle.com/">Kaggle</a>: kaggle has built-in
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free jupyter notebook.
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<ul>
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<li>One can also connect to Google BigQuery to access big data.</li>
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</ul></li>
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<li><a href="https://notebooks.azure.com/">Azure Notebooks</a>: online
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jupyter notebooks.</li>
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<li><a href="https://datalore.io/">Datalore</a>: online jupyter notebook
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by JetBrains.</li>
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<li><a href="https://cocalc.com/">CoCalc (SageMathCloud)</a>: LaTeX, R,
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iPython Notebook, etc.</li>
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<li><a href="https://aws.amazon.com/sagemaker/">SageMaker</a>: AWS
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service with a lot of tools integrated. Sagemaker comes with the
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Sagemake Studio which provides jupyter notebook for programmer and other
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charting and data management tools.</li>
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<li><a href="https://www.wolframalpha.com/">WolframAlpha</a>: Excellent
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engine to do mathematical derivation online and search.</li>
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<li><a href="https://www.wolfram.com/mathematica/online/">Mathematica
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Online</a>: Bring Mathematica to life in the cloud.</li>
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</ul>
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<h3 id="plotting-and-charting-online">Plotting and Charting Online</h3>
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<blockquote>
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<p>While one could use these online jupyter notebooks mentioned above to
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make plots, there are many easy to use too that could be used for simple
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plotting.</p>
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</blockquote>
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<ul>
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<li><a href="https://plot.ly/">plot.ly</a>: Online plotting with many
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cloud services integrated.</li>
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<li><a href="https://www.desmos.com/calculator">Desmos</a>: Graphs for
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functions.</li>
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<li><a href="https://www.geogebra.org">GeoGebra</a>: very old but still
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very good. GeoGebra can be used for precise charting as well as
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calculations.</li>
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<li><a href="http://graph.tk/">graph.tk</a>: Online plotting with rich
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features.</li>
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<li><a href="http://www.wolframalpha.com/">Wolfram Alpha</a>: Make
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graphs for functions, from your data and even more.</li>
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</ul>
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<h3 id="datasets">Datasets</h3>
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<blockquote>
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<p>Nature hosts a list of recommended data repositories <a
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href="https://www.nature.com/sdata/policies/repositories">here</a>.</p>
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</blockquote>
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<h4 id="general-and-interdisciplinary">General and
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Interdisciplinary</h4>
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<ul>
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<li><a href="http://datadryad.org/">DRYAD</a> (<code>Storage</code>,
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<code>Lookup</code>): The Dryad Digital Repository stores curated
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data.</li>
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<li><a href="https://figshare.com/">Figshare</a> (<code>Storage</code>,
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<code>Lookup</code>): Data sharing and storage</li>
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<li><a href="https://data.gov">Data.gov</a> (<code>Lookup</code>): Data
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by US Federal Government</li>
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</ul>
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<h4 id="life-science">Life Science</h4>
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<ul>
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<li><a href="https://www.ncbi.nlm.nih.gov/genbank/">GenBank</a>
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(<code>Lookup</code>): Genetic sequence database</li>
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<li><a href="https://www.ncei.noaa.gov/">National Centers for
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Environmental Information</a> (<code>Lookup</code>): Weather, climate,
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coasts, oceans, and geophysics etc</li>
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<li><a href="http://www.geoportal.org">GEOSS Portal</a>
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(<code>Lookup</code>): Earth science data</li>
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</ul>
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<h4 id="physical-sciences">Physical Sciences</h4>
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<ul>
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<li><a href="http://www.usvao.org/">US Virtual Astronomical
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Observatory</a> (<code>Lookup</code>)</li>
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<li><a
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href="https://mast.stsci.edu/portal/Mashup/Clients/Mast/portal.html">MAST:
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Barbara A. Mikulski Archive for Space Telescopes</a>
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(<code>Lookup</code>)</li>
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<li><a href="http://archive.stsci.edu/">Mikulski Archive for Space
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Telescopes</a> (<code>Lookup</code>)</li>
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</ul>
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<h4 id="arts-and-humanities">Arts and Humanities</h4>
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<ul>
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<li><a href="http://archaeologydataservice.ac.uk/">Archaeology Data
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Service</a> (<code>Lookup</code>): Certified repository</li>
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</ul>
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<h4 id="engineering">Engineering</h4>
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<ul>
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<li><a href="http://en.openei.org/wiki/Main_Page">Open Energy
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Information (OpenEI)</a> (<code>Lookup</code>): Wiki of collections of
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energy information</li>
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</ul>
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<h4 id="social-sciences">Social Sciences</h4>
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<ul>
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<li><a href="https://www.icpsr.umich.edu/web/pages/">Inter-university
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Consortium for Political and Social Research (ICPSR)</a>
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(<code>Lookup</code>)</li>
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<li><a href="http://library.harvard.edu/gdc">Institute for Quantitative
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Social Science (IQSS)</a> (<code>Lookup</code>)</li>
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</ul>
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<h3 id="colors">Colors</h3>
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<blockquote>
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<p>Pick a pleasing color for your presentations and notes. Refer to <a
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href="#data-visualization-and-graph-making">Data Visualization and Graph
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Making</a></p>
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</blockquote>
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<ul>
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<li><a href="http://colorbrewer2.org">ColorBrewer</a></li>
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<li><a href="http://paletton.com">Paletton</a></li>
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<li><a href="https://www.sessions.edu/color-calculator/">Color
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Calculator</a></li>
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</ul>
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<h2 id="publishing-and-sharing">Publishing and Sharing</h2>
|
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<blockquote>
|
||
<p>Make use of <a href="http://github.com">GitHub</a> to cooperate with
|
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others. <a href="https://pages.github.com/">GitHub pages</a> is also
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good for hosting static contents. GitHub provides Education perks so
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students could get free pro version which comes with private repos.</p>
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</blockquote>
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<h3 id="writing">Writing</h3>
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<p><strong>Markdown is one of the best languages for writing.</strong>
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Check out these editor in <a href="#markdown">Markdown section</a>.</p>
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<p><strong>Make use of these programs for publishing:</strong></p>
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<ul>
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<li><a href="http://sphinx-doc.org">Sphinx</a>: RestructuredText as
|
||
source files, powerful, flexible and modularized.</li>
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<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.
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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
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for writing ebooks.</li>
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<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>:
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||
Developed by ReadtheDocs.org</li>
|
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<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 &
|
||
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 & 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 & 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&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&A site for bioinformatics.</li>
|
||
<li><a href="https://neurostars.org/">NeuroStars</a>: StackOverflow
|
||
style Q&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>
|