Suggest edit — research-tools

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# Research Tools

**repo:** [emptymalei/awesome-research](https://github.com/emptymalei/awesome-research)  
**category:** [[miscellaneous|Miscellaneous]]

---

# Awesome Research Tools

[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome)

A list of tools for research. Also available on [https://tools.kausalflow.com/tools/](https://tools.kausalflow.com/tools/).

## TOC

* [Be Organized](#be-organized)
  * [Version Control System](#version-control-system)
  * [Pomodoro](#pomodoro)
  * [GTD-Task Manager](#gtd-task-manager)
* [Cloud Services](#cloud-services)
  * [Math and Programming](#[math](/@harrisonqian/awesome/wiki/theory/math)-and-programming-online)
  * [Plots](#plotting-and-[charting](/@harrisonqian/awesome/wiki/front-end-development/charting)-online)
  * [Data](#datasets)
  * [Colors](#colors)
* [Publishing and Sharing](#publishing-and-sharing)
  * [Writing](#writing)
  * [Hosting](#hosting)
  * [Blog and CMS](#blog-and-cms)
  * [Static Site Generator](#static-site-generator)
* [Note Taking](#note-taking)
  * [Editors](#editors)
  * [Markdown](#markdown)
  * [LaTeX](#latex)
  * [iPython Notebook](#ipython-notebook)
  * [Mindmap](#mindmap)
  * [Concept Map and Diagrams](#concept-map-and-diagrams)
  * [Keep The Notes](#keep-the-notes)
* [Presentation Tools](#presentation-tools)
  * [Online Load and Edit](#online-load-and-edit)
  * [Use The Source](#use-the-source)
  * [IPython Notebook](#ipython-notebook)
  * [LaTeX Beamer](#[latex](/@harrisonqian/awesome/wiki/miscellaneous/latex)-beamer)
  * [Mathematica](#mathematica)
  * [The Power of SVG](#the-power-of-svg)
  * [Sharing Slides](#sharing-slides)
* [Programming](#programming)
  * [Softwares](#softwares)
  * [Code Editors](#code-editors)
  * [Scientific Computing](#scientific-computing)
  * [Coding is Fun](#coding-is-fun)
* [Academic](#academic)
  * [Self-plagiarism](#self-plagiarism)
  * [Investigate Papers](#investigate-papers)
  * [Get Yourself A Citable Code for Anything](#get-yourself-a-citable-code-for-anything)
  * [Open Science](#open-science)
  * [Tips for Researchers](#[tips](/@harrisonqian/awesome/wiki/programming-languages/tips)-for-researchers)
* [Pacifier](#pacifier)
* [Online Discussions](#online-discussions)
* [Open Source](#open-source)
  * [Open Licenses](#open-licenses)
  * [Use Licenses](#use-licenses)
  * [Bibliography](#bibliography)
* [Data Visualization and Graph Making](#data-visualization-and-graph-making)
  * [Data Visualization](#data-visualization)
  * [Graph Making](#graph-making)
* [LaTeX](#[latex](/@harrisonqian/awesome/wiki/miscellaneous/latex)-1)
  * [Tips](#tips)
  * [Symbols](#symbols)
  * [Graphing](#graphing)
  * [Fonts](#fonts)
  * [Templates](#templates)
  * [References](#references)
* [MISC](#misc)
  * [Terminal](#terminal)
  * [Free Multimedia](#free-multimedia)
  * [Interesting Journals](#interesting-journals)
  * [More](#more)

## Be-Organized

### Version Control System

> 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.

* **git**
* svn
* mercurial

#### Online Git Service

* [GitHub](https://github.com/): the most popular platform for git with social and collaborations built-in.
  * [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) also provides [GitHub Actions](/@harrisonqian/awesome/wiki/development-environment/github-actions). With Actions one could automate processes.
  * [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) provides [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) Pages. With GitHub Pages, on could host static files as well as [Jekyll](https://jekyllrb.com) built websites.
* [GitLab](https://about.gitlab.com/): similar to [GitHub](/@harrisonqian/awesome/wiki/development-environment/github), GitLab provides git hosting, collaborations, social, automations, and more. GitLab can be both cloud-based and self-hosted using its open-source code.
  * GitLab includes unlimited free private repositories.
  * GitLab comes with a continuous [integration](/@harrisonqian/awesome/wiki/platforms/integration) tool that is more powerful than [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) Actions.
* [BitBucket](https://bitbucket.org): Alternative to [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) and GitLab with free private repositories.

#### Self-hosted Git Server

* [GitLab](http://gitlab.org/): See above at [Online Git Service](#online-git-service).
* [Gitea](https://gitea.io/en-us/): Painless self-hosted Git service written in Go.
* [Gogs](https://gogs.io/): A painless self-hosted Git service.

#### Enterprise Git Service

* [RhodeCode](https://rhodecode.com/): Centralized control for distributed repositories. Mercurial, Git, and Subversion under a single roof.

### Pomodoro

> [Pomodoro Technique](https://en.wikipedia.org/wiki/Pomodoro_Technique) can be used to boost your productivity and probably improve your health. There are almost infinite choices for the tools.

* [Pomotodo](https://pomotodo.com/) (`Cloud`,`Mac`,`Win`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`,`Chrome`): A mix of todo list and pomodoro timer, with sync across devices and weekly report [Free].
* [Tadam](https://tadamapp.com/) (`Mac`): Simple and elegant pomodoro timer [USD$ 4.99].
* [Productivity Challenge Timer](https://play.google.com/store/apps/details?id=com.wlxd.pomochallenge&hl=en) (`[Android](/@harrisonqian/awesome/wiki/platforms/android)`): Pomodoro timer with great gamification features [Free].

### GTD-Task Manager

> The GTD (Getting Things Done) method unloads the todo lists off the mind by recording them using external tools. It allows one to focus on one active task instead of on all of them ([Wikipedia](https://en.wikipedia.org/wiki/Getting_Things_Done)).
> Tasks can be classified in contexts (@home, @computer, @office, etc), time of action (now, next actions, scheduled or someday) and projects. [Here](https://hamberg.no/gtd/) we have a good pragmatic guide to GTD and [here](https://gettingthingsdone.com/pdfs/tt_workflow_chart.pdf) is a flowchart.

* [Microsoft To Do](https://todo.microsoft.com/tasks) (`Cloud`,`Mac`,`Win`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`,`Win Store`,`Chrome OS`): Almost perfect todo lists with cooperation and sharing.
* [Google Keep](https://keep.google.com/)(`Cloud`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`,`Chrome OS`)
* [Evernote](https://evernote.com/) (`Cloud`,`Mac`,`Win`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`,`Win Store`): Not so lightweight but still very good for managing life especially since it has got a lot of integrations from a lot of other services.
* [Anydo](https://www.any.do/) (`Cloud`,`Mac`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`): Good because it has a very good daily review which can help users remember what to do.
* [Todoist](https://todoist.com/) (`Cloud`,`Mac`,`Win`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`): Todoist invented the karma system which keeps track of the tasks done.
* [Taskade](https://taskade.com/) (`Cloud`,`Mac`,`Win`,`Chrome OS`,`Firefox`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`,`iOS`): Taskade is a collaborative task list and outliner for team projects.
* [Agenda](https://agenda.com/)(`Mac`): Date-focused note taking.

## Cloud Services

*For self-hosted services, check out [awesome-selfhosted](https://github.com/Kickball/awesome-selfhosted) on GitHub.*

### Math and Programming Online

> There are many tools that allows use of code, perform numerical calculations or analytical derivation online.

* [Google Colab](https://colab.research.google.com/): free [jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebook online. Google Colab also comes with free GPU hours.
  * Free and powerful.
  * Share and collaborate on the same notebook.
  * Can be saved in [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) or Google Drive.
* [NextJournal](https://nextjournal.com/): the notebook for reproducible research.
  * Basically, NextJournal runs almost anything.
  * Focusing on reproducibility.
* [Kaggle](https://www.kaggle.com/): kaggle has built-in free [jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebook.
  * One can also connect to Google BigQuery to access [big data](/@harrisonqian/awesome/wiki/big-data/big-data).
* [Azure Notebooks](https://notebooks.azure.com/): online [jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebooks.
* [Datalore](https://datalore.io/): online [jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebook by JetBrains.
* [CoCalc (SageMathCloud)](https://cocalc.com/): [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex), R, iPython Notebook, etc.
* [SageMaker](https://aws.amazon.com/sagemaker/): AWS service with a lot of tools integrated. Sagemaker comes with the Sagemake Studio which provides [jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebook for programmer and other [charting](/@harrisonqian/awesome/wiki/front-end-development/charting) and data management tools.
* [WolframAlpha](https://www.wolframalpha.com/): Excellent engine to do mathematical derivation online and search.
* [Mathematica Online](https://www.wolfram.com/mathematica/online/): Bring Mathematica to life in the cloud.

### Plotting and Charting Online

> While one could use these online jupyter notebooks mentioned above to make plots, there are many easy to use too that could be used for simple plotting.

* [plot.ly](https://plot.ly/): Online plotting with many cloud services integrated.
* [Desmos](https://www.desmos.com/calculator): Graphs for functions.
* [GeoGebra](https://www.geogebra.org): very old but still very good. GeoGebra can be used for precise [charting](/@harrisonqian/awesome/wiki/front-end-development/charting) as well as calculations.
* [graph.tk](http://graph.tk/): Online plotting with rich features.
* [Wolfram Alpha](http://www.wolframalpha.com/): Make graphs for functions, from your data and even more.
* [SankeyDiagram.net](https://sankeydiagram.net/): Web-based tool for creating & sharing Sankey Diagrams from data (open-source)

### Datasets

> Nature hosts a list of recommended data repositories [here](https://www.nature.com/sdata/policies/repositories).

#### General and Interdisciplinary

* [DRYAD](http://datadryad.org/) (`Storage`, `Lookup`): The Dryad Digital Repository stores curated data.
* [Figshare](https://figshare.com/) (`Storage`, `Lookup`): Data sharing and storage
* [Data.gov](https://data.gov) (`Lookup`): Data by US Federal Government

#### Life Science

* [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) (`Lookup`): Genetic sequence [database](/@harrisonqian/awesome/wiki/databases/database)
* [National Centers for Environmental Information](https://www.ncei.noaa.gov/) (`Lookup`): Weather, climate, coasts, oceans, and geophysics etc
* [GEOSS Portal](http://www.geoportal.org) (`Lookup`): [Earth](/@harrisonqian/awesome/wiki/miscellaneous/earth) science data

#### Physical Sciences

* [US Virtual Astronomical Observatory](http://www.usvao.org/) (`Lookup`)
* [MAST: Barbara A. Mikulski Archive for Space Telescopes](https://mast.stsci.edu/portal/Mashup/Clients/Mast/portal.html) (`Lookup`)
* [Mikulski Archive for Space Telescopes](http://archive.stsci.edu/) (`Lookup`)

#### Arts and Humanities

* [Archaeology Data Service](http://archaeologydataservice.ac.uk/) (`Lookup`): Certified repository

#### Engineering

* [Open Energy Information (OpenEI)](http://en.openei.org/wiki/Main_Page) (`Lookup`): Wiki of collections of energy information

#### Social Sciences

* [Inter-university Consortium for Political and Social Research (ICPSR)](https://www.icpsr.umich.edu/web/pages/) (`Lookup`)
* [Institute for Quantitative Social Science (IQSS)](http://library.harvard.edu/gdc) (`Lookup`)

### Colors

> Pick a pleasing color for your presentations and notes.
> Refer to [Data Visualization and Graph Making](#data-visualization-and-graph-making)

* [ColorBrewer](http://colorbrewer2.org)
* [Paletton](http://paletton.com)
* [Color Calculator](https://www.sessions.edu/color-calculator/)

## Publishing and Sharing

> Make use of [GitHub](http://github.com) to cooperate with others. [GitHub pages](https://pages.github.com/) is also good for hosting static contents.
> GitHub provides Education perks so students could get free pro version which comes with private repos.

### Writing

**Markdown is one of the best languages for writing.** Check out these editor in [Markdown section](#markdown).

**Make use of these programs for publishing:**

* [Sphinx](http://sphinx-doc.org): RestructuredText as source files, powerful, flexible and modularized.
* [Gitbook](https://www.gitbook.com/): A new but promising tool for HTML, pdf, and epub with both online editors and local editors. Plugins like quizzes and [math](/@harrisonqian/awesome/wiki/theory/math) can be helpful to writing science.
* [Git-scribe](https://github.com/schacon/git-scribe): Good for writing ebooks.
* [Static Site Generator](#static-site-generator): For more please refer to [Static Site Generator](#static-site-generator).

**Sphinx Themes and configurations**

* [rtd theme](https://github.com/snide/sphinx_rtd_theme): Developed by ReadtheDocs.org
* [Alabaster](https://github.com/bitprophet/alabaster): Clean and simple
* [Bootstrap theme](https://ryan-roemer.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/sphinx-bootstrap-theme/)

**Science Books Using Sphinx**

> Here are some examples of how sphinx can be used for research.

* [Theoretical Physics](https://github.com/certik/theoretical-physics)
* [Statistical Physics](https://github.com/emptymalei/statisticalphysics)
* [Neutrino Physics](https://github.com/NeuPhysics/neutrino)

**Writing Tools**

> Just use [Visual Studio Code](https://code.visualstudio.com/).

* [Hemingway App](https://hemingwayapp.com/): Highlights complex sentences, point out passive voice, and suggests alternative words.
* [proselint](https://github.com/amperser/proselint): A linter for English prose using advice from *Garner's Modern American Usage* and more.
* [write good](https://github.com/btford/write-good): Naive [JavaScript](/@harrisonqian/awesome/wiki/programming-languages/javascript) linter for English prose.
* [artbollocks-mode](https://github.com/sachac/artbollocks-mode): [Emacs](/@harrisonqian/awesome/wiki/editors/emacs) minor mode for avoiding cliches and bad grammar when writing about art (or other topics).
* [`cut_the_crap.py`](https://jugad2.blogspot.com/2015/07/cut-crap-absolutely-essential-tool-for.html): Simple [Python](/@harrisonqian/awesome/wiki/programming-languages/python) script to flag redundant words and gives alternative suggestions.
* [Rousseau](https://github.com/GitbookIO/rousseau): Lightweight proofreader written in [JavaScript](/@harrisonqian/awesome/wiki/programming-languages/javascript).
* [textlint-rule-rousseau](https://github.com/azu/textlint-rule-rousseau): A textlint rule to check English sentences using Rousseau.
* [De-Jargonizer](http://scienceandpublic.com/): Paste your article or upload file to analyze the amount of jargon in your writing.

### Hosting

> Host your articles, notes and more. Research is also about communications.

* [ReadtheDocs](http://readthedocs.org/): Turn your reStructuredText source to HTML, PDF, and epub, all done online.
* [GitHub pages](https://pages.[github](/@harrisonqian/awesome/wiki/development-environment/github).com/): Integrated with Jekyll and turns [markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) posts automatically. Jekyll is a tool for blogging.
* [GitHub](http://github.com): Just put [markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown), reStructuredText, PDF or IPython/[Jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebook files on [GitHub](/@harrisonqian/awesome/wiki/development-environment/github). All these formats can be previewed online. **The thing to mention is that the [math](/@harrisonqian/awesome/wiki/theory/math) in IPython notebook can be rendered on GitHub.**
* [Surge](https://surge.sh/): One command upload your static website to make it live. Surge also integrates [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) hooks.
* [Heroku](https://www.[heroku](/@harrisonqian/awesome/wiki/platforms/heroku).com/): The one that needs no explanation.
* [AWS](https://aws.amazon.com/): Amazon AWS provide student perks.

> Other services such as [Digital Ocean](https://www.digitalocean.com/) are also useful when it comes to dynamic websites and cloud computing.

### Blog and CMS

> Before doing the investigation on platforms, just remind yourself:
>
> **I want to write, not to run blogging software.**

**Blog/CMS Software**

> These programs are running on the server and can be [hosted using these services](#hosting).

* [GitBook](https://www.gitbook.com/) (`Cloud`): write in [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) and collaborate with the team. GitBook integrates with [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) so no content will be lost.
* [Ghost](https://github.com/tryghost/Ghost) (`[Node.js](/@harrisonqian/awesome/wiki/platforms/node-js)`): Open, Simple, non-profit; write with [markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) and live preview.
* [Pico](https://github.com/picocms/Pico) (`PHP`): Lightweight cms, open source, no [database](/@harrisonqian/awesome/wiki/databases/database).
* [Dropplets](https://github.com/circa75/dropplets) (`PHP`): Open source, simple, and elegant blog system; write in [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown).
* [Wordpress](https://wordpress.org/) (`PHP`): Very popular but requires a lot of maintenance.

**These Blog/CMS software can be hosted on [Digital Ocean](https://www.digitalocean.com/).**

### Static Site Generator

> [Here is a nice website](https://staticsitegenerators.net/) that tells you all the static site generators. Nonetheless here is a list of the most popular ones.

* [Jekyll](http://jekyllrb.com/) (Written in `[Ruby](/@harrisonqian/awesome/wiki/programming-languages/ruby)`)(`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`): Jekyll is the most widely used one. The best part about Jekyll is that one just deploy to [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) Pages by pushing the source to GitHub.
* [Octopress](http://octopress.org/) (Written in `[Ruby](/@harrisonqian/awesome/wiki/programming-languages/ruby)`)(`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`): Octopress is easier to use compared with Jekyll while being somewhat compatible with Jekyll.
* [Hexo](https://hexo.io/) (Written in `[Node.js](/@harrisonqian/awesome/wiki/platforms/node-js)`)(`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`): "A fast, simple & powerful blog framework" as they say on their website. It supports GFM.
* [Pelican](http://getpelican.com) (Written in `[Python](/@harrisonqian/awesome/wiki/programming-languages/python)`)(`reStructuredText`,`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`,`AsciiDoc`): Pelican is a modularized framework and is perfect for blogging.
  * [Pelican Svbtle Theme](https://github.com/wting/pelican-svbtle)
* [Nikola](https://getnikola.com/) (Written in `[Python](/@harrisonqian/awesome/wiki/programming-languages/python)`)(`reStructuredText`,`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`,`IPython Notebook/Jupyter`,`PHP`, etc): It takes in multiple input formats including reStructuredText and many others.
* [Hugo](http://gohugo.io/)(Written in `Go`)(`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`): Easy to use and really fast. It also supports more input formats through plugins.
* [Hyperdraft](https://hyperdraft.rosano.ca)(Written in `[JavaScript](/@harrisonqian/awesome/wiki/programming-languages/javascript)`)(`[Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)`): Automatically generate a website as you type plaintext or [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown).

> The site generated by these programs can be hosted on [GitHub Pages](https://pages.github.com/).

## Note Taking

### Notebooks for Researchers

* [Findings](https://findingsapp.com): Your research assistant & lab notebook, all in one app.
* [Learnly AI](https://learnlyai.co.uk/): AI-powered academic assistant for students, featuring smart note-taking from lectures, PDFs and videos, essay writing with literature review, and AI presentation generator.

### Editors

> Markdown, LaTeX, and reStructuredText are the three useful languages.
> **In most cases, a tweakable text editor such as [Visual Studio Code, aka vscode](https://code.visualstudio.com) is good enough.** In fact vscode comes with a enormous amount of extensions which can be used to build your own IDE.

#### Markdown

* [Hackmd.io](https://hackmd.io) (`Cloud`): Basically ships with everything you expect from the most complete online [markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor.
* [StackEdit](https://stackedit.io/)(`Cloud`): StackEdit is a [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor with many integrated services such as [math](/@harrisonqian/awesome/wiki/theory/math) (MathJax), Google Drive, Dropbox, and [GitHub](/@harrisonqian/awesome/wiki/development-environment/github).
* [CMD markdown](https://www.zybuluo.com/mdeditor)(`Cloud`): CMD is a [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor with [math](/@harrisonqian/awesome/wiki/theory/math) (MathJax) support. What is special is that it keeps edit history. (Chinese UI.)
* [Penflip](https://www.penflip.com/)(`Cloud`): Penflip is designed to be a [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) for writers. It is [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)-based and git like without [math](/@harrisonqian/awesome/wiki/theory/math) support.
* [Authorea](https://www.authorea.com/)(`Cloud`): A much more powerful [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) and [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) online editor that can be used to produce nice academic [papers](/@harrisonqian/awesome/wiki/computer-science/papers).
* [Dillinger](http://dillinger.io/)(`Cloud`): [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor but no [math](/@harrisonqian/awesome/wiki/theory/math) mode.
* [Pandoc Markdown](http://pandoc.herokuapp.com/)(`Cloud`): Just another [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor with [math](/@harrisonqian/awesome/wiki/theory/math) (MathJax) support.
* [Marxico](http://marxi.co/)(`Cloud`,`Mac`,`Win`,`Chrome`): [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor that integrates with Evernote, generates pdf and works offline. [马克飞象](https://maxiang.io/)(`Cloud`,`Mac`,`Win`,`Chrome`) is the Chinese version。
* [Madoko](https://www.madoko.net/)(`Cloud`,`Chrome`): A [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor with [math](/@harrisonqian/awesome/wiki/theory/math) support, where images are inserted easily with one click, while your files are saved on Dropbox, [GitHub](/@harrisonqian/awesome/wiki/development-environment/github), OneDrive or local disk. It generates pdf and HTML page and works offline using browser's local storage. One can even import [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) files.
* [Markx](http://markx.herokuapp.com/)(`Cloud`): [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor for [scientific writing](/@harrisonqian/awesome/wiki/miscellaneous/scientific-writing). Batteries included.
* [typora](https://www.typora.io/)(`Mac`,`Win`):  Beautiful UI and in-situ live preview.
* [Haroopad](http://pad.haroopress.com/)(`Mac`,`Win`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`): A powerful [github](/@harrisonqian/awesome/wiki/development-environment/github) flavored [markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor with useful extensions. [Math](/@harrisonqian/awesome/wiki/theory/math) (mathjax) is supported.
* [jbt/markdown-editor](http://jbt.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/markdown-editor/)(`Cloud`): Just another online [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor without [math](/@harrisonqian/awesome/wiki/theory/math) support.
* [MarkdownPad](http://markdownpad.com/) (`Win`): If you have no bad feelings about .NET, this is pretty good.
* [ReText](https://github.com/retext-project/retext) (`Mac`,`Win`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`): ReText one of the best, even on [Linux](/@harrisonqian/awesome/wiki/platforms/linux). It also supports reStructuredText input.
* [Madoko](https://www.madoko.net/) (`Cloud`): **[LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex)** &times; [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) &sup2;
* [eme](https://github.com/egoist/eme) (`Win`,`Mac`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`): [Math](/@harrisonqian/awesome/wiki/theory/math) support.
* [Moeditor](https://moeditor.org/) (`Win`,`Mac`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`): All purpose [markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) editor.

Notebook softwares that you can write in Markdown:

* [boostnote](https://boostnote.io/) (`Win`,`Mac`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`): [Math](/@harrisonqian/awesome/wiki/theory/math) + [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown), with snippet note support.
* [Quiver](http://happenapps.com/) (`Mac`,`iOS`): Programmer's notebook, [math](/@harrisonqian/awesome/wiki/theory/math) + [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown), code snippet.
* [Findings](http://findingsapp.com/) (`Mac`): Notebook for experimentalists, organized research materials and notes.
* [Notion](https://www.notion.so/) (`Win`,`Mac`,`iOS`,`[Android](/@harrisonqian/awesome/wiki/platforms/android)`): Notetaking with kanban, [math](/@harrisonqian/awesome/wiki/theory/math), calendar, table, etc.
* [Agenda](https://agenda.com/) (`Mac`,`iOS`): Notes and GTD.

#### LaTeX

* [Overleaf](https://www.overleaf.com/)(`Cloud`): Built in version control, Dropbox and [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) [integration](/@harrisonqian/awesome/wiki/platforms/integration), preview, cooperation, simple UI. It also provides a lot of templates.
* [Authorea](https://www.authorea.com/)(`Cloud`): Easy to use UI. Supports both [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) and [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex).
* [Papeeria](https://www.papeeria.com)(`Cloud`): Just another online [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) and [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) with plot compiler and collaborations.
* [JaxEdit](http://jaxedit.com/)(`Cloud`): JaxEdit doesn't provide full [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) support but is good enough for simple [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) documents and slides.
* [SpicyChai LaTeX](https://latex.spicychai.com/)(`Cloud`): Online [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) editor with AI-powered template population, real-time PDF preview, and pre-built templates for resumes, [papers](/@harrisonqian/awesome/wiki/computer-science/papers), and more. Free anonymous renders without signup.

**You can also host one using your own machine.**

* [Overleaf Source Code](https://github.com/overleaf/overleaf): Overleaf open sourced their codes. This is a great [move](/@harrisonqian/awesome/wiki/programming-languages/move) I would say.
* [TeXStudio](http://www.texstudio.org) - [Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform) [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) editor that stems from TeXMaker.
* [WinEdt](http://www.winedt.com) - The [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) editor many people swear by.
* [TeXnicCenter](http://www.texniccenter.org) - A quite old but free and decent editor for [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex).
* [LyX](https://www.lyx.org) - [Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform) WYSIWYM editor that uses [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) behind the scenes to render documents.
* [TeXshop](http://pages.uoregon.edu/koch/texshop/) - No-nonsense editor for [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) documents which is included in MacTeX.
* [TeXWorks](https://www.tug.org/texworks/) - No-nonsense editor for [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) code, modeled after TeXShop, but this one is [cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform).

**You can also add notes directly to academic papers**

* [Synthical](https://synthical.com) - aggregates all [papers](/@harrisonqian/awesome/wiki/computer-science/papers) from arXiv, medRxiv, bioRxiv, and chemRxiv with ability to highlight and leave notes.

### IPython Notebook

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.

* [Scientific [Python](/@harrisonqian/awesome/wiki/programming-languages/python) Lectures](https://github.com/jrjohansson/scientific-python-lectures)
* [Reproduced Papers](http://reproduced-[papers](/@harrisonqian/awesome/wiki/computer-science/papers).[github](/@harrisonqian/awesome/wiki/development-environment/github).io/)
* [More](https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks): For more IPython notebook on [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) please read this enormous list.

### Mindmap

**Standalone**

* Mind Manager
* XMind
* Docear

**Online**

* [KityMinder By Baidu](https://github.com/fex-team/kityminder) : Chinese Interface
* [my-mind](http://my-mind.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/): repo [here](https://github.com/ondras/my-mind).
* [beautiful Mind](http://beautifulmind.io/): repo [here](https://github.com/ierror/BeautifulMind.io)
* [Mindmup](https://www.mindmup.com/): repo [here](https://github.com/mindmup)
* [mindmaps](http://drichard.org/mindmaps/): repo [here](https://github.com/drichard/mindmaps)

**MINDMAP HTML**

* [gojs](http://gojs.net/latest/samples/mindMap.html)
* [jsmind](https://github.com/hizzgdev/jsmind)
* [jsmind](http://sourceforge.net/projects/jsmind/)
* [mindmaps](https://github.com/drichard/mindmaps)

### Concept Map and Diagrams

1. [Gliffy](https://www.gliffy.com/): all kinds of diagrams
2. [ProcessOn](http://www.processon.com/): all kinds of diagrams
3. [Draw.io](http://www.draw.io/): all kinds of diagrams

### Keep The Notes

> It's alway better to keep track the changes of your notes and **git** is a nice choice. Therefore, [GitHub](http://github.com) is the almost perfect place.
>
> As for LaTeX, [latexdiff](http://www.ctan.org/tex-archive/support/latexdiff/) is a tool for checking the diff.

> **Some programs allows you to keep the markdown notes on a server.**

* [Raneto](http://raneto.com/): Raneto is an open source Knowledgebase platform that uses static [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) files to power your Knowledgebase. This one has a nice looking.
* [Realms](http://realms.io/): Git based wiki written in [Python](/@harrisonqian/awesome/wiki/programming-languages/python) Inspired by Gollum, Ghost, and Dillinger. Basic authentication and registration included.
* [Tiddlywiki](http://tiddlywiki.com/): A unique non-linear notebook for capturing, organizing and sharing complex information.
* Some other [static site generators](#static-generator).

For experimental research, eLabFTW made a online labnote system: [eLabFTW](https://www.elabftw.net/).

## Presentation Tools

### Keep You Computer Awake

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

* [Caffeine](https://itunes.apple.com/us/app/caffeine/id411246225) (`Mac`): As simple as a single click.
* [Amphetamine](https://itunes.apple.com/us/app/amphetamine/id937984704?mt=12) (`Mac`): More configurations involved and more intelligent.

### Online Load and Edit

* [Prezi](https://prezi.com/) if you can.
* [slides.com](http://slides.com/): Easy to use with remote controlled page presentation.
* [Slideas](https://www.slideas.app/): the easiest way to create a beautiful [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) Presentation, with all the features you need.
* [Google Drive](https://drive.google.com/): no introduction needed
* [Sway](https://sway.com/): Microsoft
* [Strut](https://github.com/tantaman/Strut)
* [Impressionist](https://github.com/harish-io/Impressionist)
* [hovercraft](https://github.com/regebro/hovercraft)

### Use The Source

> Requires a few front-end techniques.

#### HTML+CSS+JS

> Use [colors](https://github.com/mrmrs/colors) to make your HTML feels better.

* [Impress.js](http://impress.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/impress.js/): more about it [impress wiki page](https://github.com/impress/impress.js/wiki).
* [Jimpress](http://jmpressjs.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/jmpress.js/): A [jQuery](/@harrisonqian/awesome/wiki/front-end-development/jquery) version of impress.js
* [Reveal.js](https://github.com/hakimel/reveal.js)
* [Beckpoke.js](https://github.com/bespokejs/bespoke)
* [CSSS](https://github.com/LeaVerou/CSSS)
* [Scrolldeck](https://github.com/johnpolacek/scrolldeck.js)
* [Deck.js](https://github.com/imakewebthings/deck.js)
* [Shower](https://github.com/shower/shower)
* [Flowtime.js](https://github.com/marcolago/flowtime.js)
* [Slides](https://github.com/briancavalier/slides)
* [remark](https://remarkjs.com)

### IPython/Jupyter Notebook

> Python, Julia, R, Scala and more languages are supported in [IPython/Jupyter Notebook](https://jupyter.org/) which can also be used to give presentations.
>
> Refer to [math and programming online](#math-and-programming-online) for cloud-based Jupyter Notebooks.

### LaTeX Beamer

* [Beamer](https://bitbucket.org/rivanvx/beamer/wiki/Home): Shipped with standard [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) installations. A lot of themes has been invented. Start editing with one click on [Overleaf](https://www.overleaf.com/)

### Mathematica

* [Mathematica slides](http://reference.wolfram.com/language/howto/CreateASlideShow.html) can be made interactive.

### The Power of SVG

**Online SVG editors:**

* [ext-sozi](https://github.com/asyazwan/ext-sozi)

**Local SVG editors:**

* [Inkscape](https://inkscape.org)(`Mac`,`Win`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`)
* [GIMP](https://www.gimp.org)(`Mac`,`Win`,`[Linux](/@harrisonqian/awesome/wiki/platforms/linux)`)

### Sharing Slides

* [GitHub pages](https://pages.[github](/@harrisonqian/awesome/wiki/development-environment/github).com/): For Html based slides.
* [Speaker Deck](https://speakerdeck.com/) by [GitHub](/@harrisonqian/awesome/wiki/development-environment/github): PDF slides. Can be displayed online or embeded.

## Programming

### Code Editors

* [Visual Studio Code, aka VS Code](https://code.visualstudio.com/)(`Free`,`[Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform)`,`Plugins`): same technology as [atom](/@harrisonqian/awesome/wiki/editors/atom) but faster than atom, and Microsoft made.
* [Atom](https://atom.io/)(`Free`,`[Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform)`,`Plugins`): [electron](/@harrisonqian/awesome/wiki/platforms/electron) based editor with numerous plugins and easy modifications. [Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform) with settings and plugins synchronized through the [sync-settings](https://atom.io/packages/sync-settings) plugin.
* [Sublime Text](https://www.sublimetext.com/)(`Free Evaluation`,`[Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform)`,`Plugins`): cross-platform, fast, and with plugins. Not free but can be freely used forever.
* [JetBrains](https://www.jetbrains.com/)(`Free for Students`, `[Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform)`,`Plugins`): beautiful IDE's with many debugging and editing modes integrated.
* [vim](https://github.com/vim/vim)(`Free`,`[Cross-platform](/@harrisonqian/awesome/wiki/platforms/cross-platform)`,`Plugins`): no words can describe the almighty vim.
  * [Vundle](https://github.com/VundleVim/Vundle.vim): the vim plugin manager
  * [vimrc from amix](https://github.com/amix/vimrc): "The ultimate Vim configuration: vimrc"

### Softwares

* [Synthical](https://synthical.com): AI-powered collaborative research environment
* [Mathematica](http://www.wolfram.com/mathematica/): One Software to Rule Them All
* [iPython Notebook](http://ipython.org/notebook.html) (`[Python](/@harrisonqian/awesome/wiki/programming-languages/python)`): a useful tool for inline calculation, making graphs and writing notes.
  * [wakari.io](https://wakari.io/) is a comercial one mostly aimed for data analysis.
  * [jiffylab](https://github.com/ptone/jiffylab) is an open source one but not that well done.
  * [supervised-ipython-nbserver](https://github.com/writefaruq/supervised-ipython-nbserver) is a multiuser version of notebook using Django/Pinax.
* [Matlab](http://www.mathworks.com/products/matlab/)
* [Maple](https://www.maplesoft.com/index.aspx?L=E)
* [RStudio](https://www.rstudio.com/) (`R`)

### Scientific Computing

---
*truncated — [full list on GitHub](https://github.com/emptymalei/awesome-research)*