awesome-research

: the most popular platform for git with social and collaborations built-in

GitHub provides GitHub Pages. With GitHub Pages, on could host static files as well as built websites

: similar to GitHub, GitLab provides git hosting, collaborations, social, automations, and more. GitLab can be both cloud-based and self-hosted using its open-source code

: Alternative to GitHub and GitLab with free private repositories

: See above at

: Painless self-hosted Git service written in Go

: A painless self-hosted Git service

: Centralized control for distributed repositories. Mercurial, Git, and Subversion under a single roof

( , , , , , ): A mix of todo list and pomodoro timer, with sync across devices and weekly report [Free]

( ): Simple and elegant pomodoro timer [USD$ 4.99]

( ): Pomodoro timer with great gamification features [Free]

( , , , , , , ): Almost perfect todo lists with cooperation and sharing

( , , , )

( , , , , , ): 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

( , , , ): Good because it has a very good daily review which can help users remember what to do

( , , , , ): Todoist invented the karma system which keeps track of the tasks done

( , , , , , , ): Taskade is a collaborative task list and outliner for team projects

( ): Date-focused note taking

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

: the notebook for reproducible research

: kaggle has built-in free jupyter notebook

: online jupyter notebooks

: online jupyter notebook by JetBrains

: LaTeX, R, iPython Notebook, 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

: Online plotting with many cloud services integrated

: Graphs for functions

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

: Online plotting with rich features

: Make graphs for functions, from your data and even more

( , ): The Dryad Digital Repository stores curated data

( , ): Data sharing and storage

( ): Data by US Federal Government

( ): Genetic sequence database

( ): Weather, climate, coasts, oceans, and geophysics etc

( ): Earth science data

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( ): Certified repository

( ): Wiki of collections of energy information

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: RestructuredText as source files, powerful, flexible and modularized

: A new but promising tool for HTML, pdf, and epub with both online editors and local editors. Plugins like quizzes and math can be helpful to writing science

Git-scribe

: Good for writing ebooks

rtd theme

: Developed by ReadtheDocs.org

Alabaster

: Clean and simple

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

proselint

: A linter for English prose using advice from and more

write good

: Naive JavaScript linter for English prose

artbollocks-mode

: Emacs minor mode for avoiding cliches and bad grammar when writing about art (or other topics)

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

Rousseau

: Lightweight proofreader written in JavaScript

textlint-rule-rousseau

: A textlint rule to check English sentences using Rousseau

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

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

: Integrated with Jekyll and turns markdown posts automatically. Jekyll is a tool for blogging

: Just put markdown, reStructuredText, PDF or IPython/Jupyter notebook files on GitHub. All these formats can be previewed online

: One command upload your static website to make it live. Surge also integrates GitHub hooks

: The one that needs no explanation

: Amazon AWS provide student perks

( ): write in Markdown and collaborate with the team. GitBook integrates with GitHub so no content will be lost

Ghost

( ): Open, Simple, non-profit; write with markdown and live preview

Pico

( ): Lightweight cms, open source, no database

Dropplets

( ): Open source, simple, and elegant blog system; write in Markdown

( ): Very popular but requires a lot of maintenance

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

(Written in )( ): "A fast, simple & powerful blog framework" as they say on their website. It supports GFM

(Written in )( , , ): Pelican is a modularized framework and is perfect for blogging

(Written in )( , , , , etc): It takes in multiple input formats including reStructuredText and many others

(Written in )( ): Easy to use and really fast. It also supports more input formats through plugins

(Written in )( ): Automatically generate a website as you type plaintext or Markdown

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

( ): Basically ships with everything you expect from the most complete online markdown editor

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

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

( ): Penflip is designed to be a GitHub for writers. It is Markdown-based and git like without math support

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

( ): Markdown editor but no math mode

( ): Just another Markdown editor with math (MathJax) support

( , , , ): Markdown editor that integrates with Evernote, generates pdf and works offline. ( , , , ) is the Chinese version。

( , ): 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

( ): Markdown editor for scientific writing. Batteries included

( , ): Beautiful UI and in-situ live preview

( , , ): A powerful github flavored markdown editor with useful extensions. Math (mathjax) is supported

( ): Just another online Markdown editor without math support

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

ReText

( , , ): ReText one of the best, even on Linux. It also supports reStructuredText input

( ): × Markdown ²

eme

( , , ): Math support

( , , ): All purpose markdown editor

( , , ): Math + Markdown, with snippet note support

( , ): Programmer's notebook, math + Markdown, code snippet

( ): Notebook for experimentalists, organized research materials and notes

( , , , ): Notetaking with kanban, math, calendar, table, etc

( , ): Notes and GTD

( ): Built in version control, Dropbox and GitHub integration, preview, cooperation, simple UI. It also provides a lot of templates

( ): Easy to use UI. Supports both Markdown and LaTeX

( ): Just another online LaTeX and Markdown with plot compiler and collaborations

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

Overleaf Source Code

: Overleaf open sourced their codes. This is a great move I would say

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

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

aggregates all papers from arXiv, medRxiv, bioRxiv, and chemRxiv with ability to highlight and leave notes

More

: For more IPython notebook on GitHub please read this enormous list

KityMinder By Baidu

: Chinese Interface

: repo

: repo

: repo

: repo

: all kinds of diagrams

: all kinds of diagrams

: all kinds of diagrams

: Raneto is an open source Knowledgebase platform that uses static Markdown files to power your Knowledgebase. This one has a nice looking

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

: A unique non-linear notebook for capturing, organizing and sharing complex information

( ): As simple as a single click

( ): More configurations involved and more intelligent

if you can

: Easy to use with remote controlled page presentation

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

: no introduction needed

: Microsoft

: more about it

: A jQuery version of impress.js

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

can be made interactive

( , , )

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: For Html based slides

by GitHub: PDF slides. Can be displayed online or embeded

( , , ): same technology as atom but faster than atom, and Microsoft made

( , , ): electron based editor with numerous plugins and easy modifications. Cross-platform with settings and plugins synchronized through the plugin

( , , ): cross-platform, fast, and with plugins. Not free but can be freely used forever

( , , ): beautiful IDE's with many debugging and editing modes integrated

vim

( , , ): no words can describe the almighty vim

Vundle

: the vim plugin manager

vimrc from amix

: "The ultimate Vim configuration: vimrc"

: AI-powered collaborative research environment

: One Software to Rule Them All

( ): a useful tool for inline calculation, making graphs and writing notes

is a comercial one mostly aimed for data analysis

jiffylab

is an open source one but not that well done

supervised-ipython-nbserver

is a multiuser version of notebook using Django/Pinax

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: scientific computing made easy

: A nice tool for python debugging and performance improvement

: 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

: Finding interesting papers

: Monitor specific topics or journal for new and relevant papers

: An front-end for arXiv with rates from readers

: 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

: 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

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

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

duecredit

: Allows you to add decorators to Python functions that encode bibliographic details

: A open science tool with a lot of integrations

: 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

: An open source bibliography reference manager with syncing and BibTeX support

: Find any style you need

: An open source bibliography reference manager for the BibTeX format

: Retrieves a BibTeX entry from a DOI

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

org-ref

: Citations, cross-references, indexes, glossaries, and bibtex utitlies for org-mode in Emacs

: 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

Academic Resources and Grey Literature List

Check the of the for search engines to search for papers

( , , ): rainy day rainy mood, simple but with excellent white noise; a new beautiful soundtrack each day

( , , , ): a rather simple but useful coffee shop noise library; premium has more three more soundtracks; elegant UI; scientific research powered

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

( , ): a handy white noise tool that stays in your Mac status bar

( , , , ): 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

( ): free mixing of multiple tracks

( , )

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

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

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

( , ): click and play style preloaded scenes; easy to use; beautiful design

( ): sound mixings to concentrate

( , , ): to help you calming down

( , , ): raining and thunder

( , , ): music to boost your brain; paid services now

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

: just rain

: many natural sounds, cool

: make your own track, so many kinds of sounds

: several different tracks

: make ambient sound easily

: listen and download

: StackOverflow style Q&A site for bioinformatics

: StackOverflow style Q&A site for neuroinformatics

: Forum for next generation sequencing community

: Read the license and pick the one you like

which helps you decide which license to use through several steps

Guokr Badge

: Green CC License badges. ( )

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( ): Line charts, area charts, column and bar charts, pie charts, scatter and bubble charts and more

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( , , , , , , ): Geogebra is a very cool tool to make math graphs both 2D and 3D

LaTeXDraw

( ): "A vector drawing editor for LaTeX."

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( ): A web-tool for generation of box plots

( ): Open source graph visualization software

colorcet

can be used to investigate colormaps

: A good manual

: find out what the symbol is by drawing online

(Tikz/PGF)

: This is a great book for math related typography. This is copyright material. Please DO NOT redistribute

: Command line recording

bashplot

: plot in terminal

fuck

: correct the command by typing in fuck

: Search engine for images under CC License

: Free high resolution images

: 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? 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