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Awesome Research Tools

a curated list of tools to help you with your research/life; I built a front end around this repo, please use the link

Here you can see meta information about this topic like the time we last updated this page, the original creator of the awesome list and a link to the original GitHub repository.

Last Update: Dec. 1, 2020, 9:03 a.m.

Thank you emptymalei & contributors
View Topic on GitHub:
emptymalei/awesome-research

Search for resources by name or description.
Simply type in what you are looking for and the results will be filtered on the fly.

Further filter the resources on this page by type (repository/other resource), number of stars on GitHub and time of last commit in months.

Online Git Service

Transform your plain text into static websites and blogs.

Plant your code in the cloud. Watch it grow.

Self-hosted Git Server

Self Hosted Git repository management, code reviews, issue tracking, activity feeds and wikis. (Demo, Source Code) MIT Ruby

Painless self-hosted Git service written in Go.

A Self Hosted Git Service in the Go Programming Language.

Enterprise Git Service

enterprise source code management platform. It applies unified user control, permissions, code reviews, and tool integration across Mercurial, Git, and Subversion repositories. Large and growing software teams all over the world use RhodeCode to collaborate in a secure, behind-the-firewall environment.

Pomodoro

Cloud,Mac,Win,Android,iOS,Chrome`): A mix of todo list and pomodoro timer, with sync across devices and weekly report [Free].

Mac`): Simple and elegant pomodoro timer [USD$ 4.99].

Android`): Pomodoro timer with great gamification features [Free].

GTD-Task Manager

Cloud,Mac,Win,Android,iOS,Win Store,Chrome OS`): Almost perfect todo lists with cooperation and sharing.

Cloud,Android,iOS,Chrome OS`)

Infamous note-taking app, available on many platforms. ![Freeware][Freeware Icon]

Cloud,Mac,Android,iOS`): Good because it has a very good daily review which can help users remember what to do.

Powerful and cross-platform productivity tool.

Smart task lists with real-time cross-platform syncing and team collaboration. ![Freeware][freeware icon]

Date-focused note taking app for both planning and documenting your projects. ![App Store][app-store Icon]

Cloud Services

A list of Free Software network services and web applications which can be hosted locally. Selfhosting is the process of hosting and managing applications instead of renting from Software-as-a-Service providers

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Math and Programming Online

free jupyter notebook online. Google Colab also comes with free GPU hours.

the notebook for reproducible research.

online jupyter notebooks.

online jupyter notebook by JetBrains.

formerly SageMathCloud at cloud.sagemath.com) — Collaborative calculation in the cloud. Browser access to full Ubuntu with built-in collaboration and lots of free software for mathematics, science, data science, preinstalled: Python, LaTeX, Jupyter Notebooks, SageMath, scikitlearn, etc.

AWS service with a lot of tools integrated. Sagemaker comes with the Sagemake Studio which provides jupyter notebook for programmer and other charting and data management tools.

Excellent engine to do mathematical derivation online and search.

Bring Mathematica to life in the cloud.

Plotting and Charting Online

very old but still very good. GeoGebra can be used for precise charting as well as calculations.

Online plotting with rich features.

General and Interdisciplinary

Storage,Lookup`): The Dryad Digital Repository stores curated data.

Lookup`): Data by US Federal Government

Life Science

Lookup`): Genetic sequence database

Lookup`): Weather, climate, coasts, oceans, and geophysics etc

Lookup`): Earth science data

Physical Sciences

Arts and Humanities

Engineering

Lookup`): Wiki of collections of energy information

Social Sciences

Colors

Writing

basically the best way to write an ebook

1.35K
125
6y 11m
MIT

Sphinx theme for readthedocs.org

3.54K
1.45K
1d
n/a

Lightweight, configurable Sphinx theme. Now the Sphinx default!

580
156
10m
n/a

Source code of the Theoretical Physics Reference online book

156
35
2y 104d
MIT

notes on statistical physics

19
5
63d
MIT

Neutrino research

5
4
11m
n/a

A linter for prose.

3.59K
164
2y 96d
BSD-3-Clause

Naive linter for English prose

4.17K
194
60d
MIT

Emacs mode for highlighting weasel words

62
9
2y 9m
AGPL-3.0

Lightweight proofreader in JS

153
15
4y 5m
Apache-2.0

textlint rule check english sentence using rousseau

7
0
1y 4m
MIT

RestructuredText as source files, powerful, flexible and modularized.

A modern publishing toolchain. Simply taking you from ideas to finished, polished books.

Highlights complex sentences, point out passive voice, and suggests alternative words.

Simple Python script to flag redundant words and gives alternative suggestions.

Paste your article or upload file to analyze the amount of jargon in your writing.

Hosting

Turn your reStructuredText source to HTML, PDF, and epub, all done online.

Websites for you and your projects.

Just put markdown, reStructuredText, PDF or IPython/Jupyter notebook files on GitHub. All these formats can be previewed online. The thing to mention is that the math in IPython notebook can be rendered on GitHub.

A powerful alternative to GitHub Pages.

Platform where to host an exported game as a static website - Free/Paid.

Documentation](https://devcenter.heroku.com/articles/getting-started-with-laravel))

Rent cloud servers for more timeconsuming calculations (r4.xlarge server is a good place to start).

Blog and CMS

👻 The #1 headless Node.js CMS for professional publishing

35.59K
7.77K
1d
MIT

Pico is a stupidly simple, blazing fast, flat file CMS.

3.34K
579
20d
MIT

Welcome to an easier way to blog. - A minimalist markdown blogging platform.

1.62K
234
4m
GPL-3.0

A modern publishing toolchain. Simply taking you from ideas to finished, polished books.

A blogging platform and CMS.

A cheap and quality VPS hosting company.

Static Site Generator

A clean room copy of Svbtle.com's design for use with Pelican.

151
38
4y 9m
MIT

Written in Ruby)(Markdown): Jekyll is the most widely used one. The best part about Jekyll is that one just deploy to GitHub Pages by pushing the source to GitHub.

Written in Ruby)(Markdown): Octopress is easier to use compared with Jekyll while being somewhat compatible with Jekyll.

Fast, simple and powerful blog framework, powered by Node.js. (Source Code) MIT Nodejs

Written in Python)(reStructuredText,Markdown,AsciiDoc): Pelican is a modularized framework and is perfect for blogging.

Written in Python)(reStructuredText,Markdown,IPython Notebook/Jupyter,PHP, etc): It takes in multiple input formats including reStructuredText and many others.

Fast and Modern Static Website Engine.

Notebooks for Researchers

Your research assistant & lab notebook, all in one app.

Markdown

ReText: Simple but powerful editor for Markdown and reStructuredText

1.34K
169
23d
GPL-3.0

Elegant Markdown Editor.

1.94K
166
50d
MIT

A collaborative, powerful, real-time online markdown editor with preview.

Cloud`): StackEdit is a Markdown editor with many integrated services such as math (MathJax), Google Drive, Dropbox, and GitHub.

Cloud`): CMD is a Markdown editor with math (MathJax) support. What is special is that it keeps edit history. (Chinese UI.)

Collaborative writing and version control, powered by GitLab (similar to GitHub).

Cloud`): A much more powerful Markdown and LaTeX online editor that can be used to produce nice academic papers.

The last Markdown editor, ever. (Source Code) MIT Nodejs

Cloud`): Just another Markdown editor without math support.

Cloud`): Just another Markdown editor with math (MathJax) support.

Cloud,Mac,Win,Chrome): Markdown editor that integrates with Evernote, generates pdf and works offline. [马克飞象](https://maxiang.io/)(Cloud,Mac,Win,Chrome`) is the Chinese version。

Cloud,Chrome`): A Markdown editor with math support, where images are inserted easily with one click, while your files are saved on Dropbox, GitHub, OneDrive or local disk. It generates pdf and HTML page and works offline using browser's local storage. One can even import LaTeX files.

Cloud`): Markdown editor for scientific writing. Batteries included.

Mac,Win`): Beautiful UI and in-situ live preview.

Markdown editor with live preview.

Cloud`): Just another online Markdown editor without math support.

Mou

Mac`): Mou used to be the best Markdown editor on Mac. It is not bad but DO NOT preorder Mou 1.0. This project is dead, unofficially. 了解为什么死掉,请阅读此文。

Win`): If you have no bad feelings about .NET, this is pretty good.

Win,Mac,Linux`): All purpose markdown editor.

Note-taking app made for programmers. ![Open-Source Software][OSS Icon]

Mac,iOS`): Programmer's notebook, math + Markdown, code snippet.

Mac`): Notebook for experimentalists, organized research materials and notes.

Notion is the all-in-one workspace. From notes, tasks, wikis, to database, Notion is all you need. Works great for teams and individuals.

Date-focused note taking app for both planning and documenting your projects. ![App Store][app-store Icon]

LaTeX

FlyLatex: A Realtime Collaborative Environment (with a concurrent editor) in node-js.

770
89
4y 8m
n/a

A web-based collaborative LaTeX editor

7.61K
848
12d
AGPL-3.0

Cloud`): Dropbox and GitHub integration, preview, cooperation, simple UI. It also provides a lot of templates.

Web-based collaborative LaTeX editor. (Source Code) AGPL-3.0 Ruby

Cloud`): A much more powerful Markdown and LaTeX online editor that can be used to produce nice academic papers.

Cloud`): Just another online LaTeX and Markdown with plot compiler and collaborations.

Cloud`): JaxEdit doesn't provide full LaTeX support but is good enough for simple LaTeX documents and slides.

Cross-platform LaTeX editor that stems from TeXMaker.

The LaTeX editor many people swear by.

A quite old but free and decent editor for LaTeX.

LyX

Cross-platform WYSIWYM editor that uses LaTeX behind the scenes to render documents.

No-nonsense editor for LaTeX documents which is included in MacTeX.

No-nonsense editor for LaTeX code, modeled after TeXShop, but this one is cross-platform.

IPython Notebook

Lectures on scientific computing with python, as IPython notebooks.

2.95K
1.66K
3y 1d
n/a

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

14.36K
4.03K
94d
n/a

Mindmap

百度脑图

3.75K
1.57K
5y 113d
BSD-3-Clause

Javascript version of mind mapping

1.87K
575
4d
n/a

An open source, offline capable, mind mapping application leveraging HTML5 technologies

2.08K
498
2y 5m
AGPL-3.0

Unlimited mind maps for free, and store them in the cloud. Your mind maps are available everywhere, instantly, from any device.

Concept Map and Diagrams

Online diagrams: flowchart, UML, wireframe,... Also plugins for Jira and Confluence. 5 diagrams and 2 MB free

Keep The Notes

Raneto is an open source Knowledgebase platform that uses static Markdown files to power your Knowledgebase. MIT Nodejs

Git based wiki written in Python Inspired by Gollum, Ghost, and Dillinger. Basic authentication and registration included.

Reusable non-linear personal web notebook. (Source Code) BSD-3-Clause Nodejs

Keep You Computer Awake

Mac`): As simple as a single click.

Mac`): More configurations involved and more intelligent.

Online Load and Edit

Strut - An Impress.js and Bespoke.js Presentation Editor

1.58K
496
10m
n/a

Visual tool to create impress.js presentations

592
134
7y 5m
n/a

Make dynamic impressive presentations from text files!

1.31K
209
41d
MIT

Online presentations with really transitions that can zoom and rotate.

A place for creating, presenting and sharing slide decks.

the easiest way to create a beautiful Markdown Presentation, with all the features you need.

no introduction needed

HTML+CSS+JS

The HTML Presentation Framework

54.37K
15.19K
50d
MIT

DIY Presentation Micro-Framework

4.57K
461
84d
MIT

Lean, hackable, extensible slide deck framework. Previously known as CSSS.

1.59K
256
1d
MIT

jQuery plugin for making scrolling presentation decks

685
142
4y 11m
n/a

Modern HTML Presentations

5.41K
664
4y 7m
MIT

Shower HTML presentation engine

4.54K
861
4m
n/a

Flowtime.js HTML5/CSS3/JS Websites and Presentation Framework

1.3K
239
62d
MIT

A slide presentation framework in HTML, JS, and OOCSS

484
140
4y 4m
n/a

A jQuery version of impress.js

LaTeX Beamer

Shipped with standard LaTeX installations. A lot of themes has been invented. Start editing with one click on

Web-based collaborative LaTeX editor. (Source Code) AGPL-3.0 Ruby

Mathematica

The Power of SVG

Sozi extension for SVG-Edit -- Discontinued until I have time to update for latest Sozi & SVG-Edit

29
9
8y 8m
MIT

Popular cross-platform open source vector graphics editor.

Mac,Win,Linux`)

Sharing Slides

Websites for you and your projects.

Upload your slides as a PDF, and get an online, shareable presentation.

Code Editors

The official Vim repository

22.04K
3.22K
1d
n/a

Vundle, the plug-in manager for Vim

21.88K
2.46K
1y 107d
MIT

The ultimate Vim configuration (vimrc)

23.23K
6.25K
4m
MIT

Microsoft's free & open-source editor, TypeScript friendly, VSCode Plugins. ![Open-Source Software][OSS Icon] ![Freeware][Freeware Icon] ![Awesome List][awesome-list Icon]

A hackable text editor for the 21st Century. ![Open-Source Software][oss icon] ![Freeware][freeware icon]

Free for Students,Cross-platform,Plugins`): beautiful IDE's with many debugging and editing modes integrated.

Softwares

zero configuration Python/Unix web based teaching env

187
24
6y 8m
n/a

Mass management of IPython notebook servers with Supervisord and a Django/Pinax front-end

7
1
7y 26d
MIT

One Software to Rule Them All

Python`): a useful tool for inline calculation, making graphs and writing notes.

is a comercial one mostly aimed for data analysis.

Scientific Computing

Python 3 is the best option.

A Python-based ecosystem of open-source software for mathematics, science, and engineering.

A nice tool for python debugging and performance improvement.

The R Project for Statistical Computing.

Coding is Fun

Practive programming and tackle out your next tech interview

Self-plagiarism

Investigate Papers

Finding interesting papers.

Monitor specific topics or journal for new and relevant papers.

Accelerate research through arXiv specific for many things machine learning by Andrej Karpathy.

Explore scientific papers and how they connect to a paper of your choice.

Retrieves and analyzes academic citations designed to empower individual academics to present their case for research impact to its best advantage.

Life sciences and medical literature recommendation engine.

Get Yourself A Citable Code for Anything

Make anything from GitHub citable by getting a DOI code here.

Get Yourself A Unique and Persistent Digital Identifier

Use your ORCID identifier in any research workflow to ensure you get credit for your work.

Add Citations to Your Code

Automated collection and reporting of citations for used software/methods/datasets

179
20
61d
n/a

Open Science

A open science tool with a lot of integrations.

Bibliography

org-mode modules for citations, cross-references, bibliographies in org-mode and useful bibtex tools to go with it.

881
187
5d
n/a

A all platform app for reference mamagement, note-taking, and more. The former Papers has been rebanded as ReadCube Papers.

A bibliography reference manager with cloud storage and BibTeX support.

Free, easy-to-use tool to help you collect, organize, cite, and share research.

Open source bibliography reference manager.

Retrieves a BibTeX entry from a DOI.

Makes research outputs easy to find, cite, link, and assess.

Tips for Researchers

A curated list of amazingly awesome OSINT

5.01K
1.16K
95d
n/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.

Pacifier

iOS,Android,Web`): rainy day rainy mood, simple but with excellent white noise; a new beautiful soundtrack each day

iOS,Android,Web,Mac`): a rather simple but useful coffee shop noise library; premium has more three more soundtracks; elegant UI; scientific research powered

Web`): Improve Focus, Relaxation & Sleep with audio brainwave training. Not free but worth every penny.

Ambient sound equalizer for relaxation or productivity.

iOS,Android,Web,Chrome`): free mixing of multiple tracks (which is similar to Soundrown but with much better UI). Users can save a customized setting for later use. I personally think this one has better fire sound tracks than soundrown.

Web`): free mixing of multiple tracks

Web`): free mixing of multiple tracks; simple UI; Timer provided; Meander available

iOS,Web`): a noise generator; a lot of choices (too many actually); detailed equalizer

Web`): not much to say just a combination of rainy mood and coffitivity

iOS,Mac`): click and play style preloaded scenes; easy to use; beautiful design

Android`): sound mixings to concentrate

iOS,Android,Web`): to help you calming down

iOS,Android,Web`): raining and thunder

iOS,Android,Web`): music to boost your brain; paid services now

multiple choices but not that good (just my feeling).

make your own track, so many kinds of sounds.

several different tracks

make ambient sound easily

Forums and Q&A's

StackOverflow style Q&A site for bioinformatics.

StackOverflow style Q&A site for neuroinformatics.

Forum for next generation sequencing community.

Open Licenses

Read the license here and pick the one you like.

Use Licenses

一些开放版权类 License 的 Badge,可以用于果壳的问答,日志,文章,小组等。当然也可以用于其他网站,如果颜色大小合适的话。「我们坚信分享改变世界」

22
4
6y 8m
n/a

which helps you decide which license to use through several steps.

Data Visualization

Handout for the tutorial "Creating publication-quality figures with matplotlib"

1.5K
239
2y 6d
n/a

An awesome iTerm2 backend for Matplotlib, so you can plot directly in your terminal.

1.24K
42
2y 5m
n/a

js`): Line charts, area charts, column and bar charts, pie charts, scatter and bubble charts and more.

A python visualization library based on matplotlib.

A Grammar of Graphics for Python

Internet required, interactive plotting.

Internet required, interactive plotting.

Graph Making

A vector drawing editor for LaTeX (JavaFX).

323
54
2d
GPL-3.0

A set of useful perceptually uniform colormaps for plotting scientific data

422
33
29d
n/a

Cloud,Mac,Win,Linux,Android,iOS,Win Store`): Geogebra is a very cool tool to make math graphs both 2D and 3D.

Web`): A web-tool for generation of box plots.

Tips

Symbols

find out what the symbol is by drawing online

Graphing

Fonts

Templates

Terminal

plotting in the terminal

1.48K
122
1y 6m
MIT

Fix command line spelling errors like it's 1999.

339
18
5y 4m
n/a

Free Multimedia

More

Adding a QR code to your poster can help you get more audience.

Make a beautiful badge by yourself.

Not sure which word to capitalize in the title? TitleCap is right for you.

A guide to responsible conduct in research.

Registry of digital research tools for scholarly use.

A simple online whiteboard that users can collaborate; Good for online meetings.

Create maps with corresponding data quickly by copy-pasting from a spreadsheet.

legally download research papers for free.