awesome-research

Research tools catalog

A curated list of tools to help researchers manage their work and stay organized.

seedling a curated list of tools to help you with your research/life; I built a front end around this repo, please use the link below [This repo is deprecated. Instead, I maintain all the contents using the following website]

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Awesome Research Tools / Be-Organized / Version Control System

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

Awesome Research Tools / Be-Organized / Version Control System / GitHub

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

Awesome Research Tools / Be-Organized / Version Control System

GitLab : 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
BitBucket : Alternative to GitHub and GitLab with free private repositories
GitLab : See above at
Gitea : Painless self-hosted Git service written in Go
Gogs : A painless self-hosted Git service
RhodeCode : Centralized control for distributed repositories. Mercurial, Git, and Subversion under a single roof

Awesome Research Tools / Be-Organized / Pomodoro

Pomotodo ( , , , , , ): A mix of todo list and pomodoro timer, with sync across devices and weekly report [Free]
Tadam ( ): Simple and elegant pomodoro timer [USD$ 4.99]
Productivity Challenge Timer ( ): Pomodoro timer with great gamification features [Free]

Awesome Research Tools / Be-Organized / GTD-Task Manager

Microsoft To Do ( , , , , , , ): Almost perfect todo lists with cooperation and sharing
Google Keep ( , , , )
Evernote ( , , , , , ): 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 ( , , , ): Good because it has a very good daily review which can help users remember what to do
Todoist ( , , , , ): Todoist invented the karma system which keeps track of the tasks done
Taskade ( , , , , , , ): Taskade is a collaborative task list and outliner for team projects
Agenda ( ): Date-focused note taking

Awesome Research Tools / Cloud Services / Math and Programming Online

Google Colab : free jupyter notebook online. Google Colab also comes with free GPU hours
NextJournal : the notebook for reproducible research
Kaggle : kaggle has built-in free jupyter notebook
Azure Notebooks : online jupyter notebooks
Datalore : online jupyter notebook by JetBrains
CoCalc (SageMathCloud) : LaTeX, R, iPython Notebook, etc
SageMaker : 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
WolframAlpha : Excellent engine to do mathematical derivation online and search
Mathematica Online : Bring Mathematica to life in the cloud

Awesome Research Tools / Cloud Services / Plotting and Charting Online

plot.ly : Online plotting with many cloud services integrated
Desmos : Graphs for functions
GeoGebra : very old but still very good. GeoGebra can be used for precise charting as well as calculations
graph.tk : Online plotting with rich features
Wolfram Alpha : Make graphs for functions, from your data and even more

Awesome Research Tools / Cloud Services / Datasets

DRYAD ( , ): The Dryad Digital Repository stores curated data
Figshare ( , ): Data sharing and storage
Data.gov ( ): Data by US Federal Government
GenBank ( ): Genetic sequence database
National Centers for Environmental Information ( ): Weather, climate, coasts, oceans, and geophysics etc
GEOSS Portal ( ): Earth science data
US Virtual Astronomical Observatory ( )
MAST: Barbara A. Mikulski Archive for Space Telescopes ( )
Mikulski Archive for Space Telescopes ( )
Archaeology Data Service ( ): Certified repository
Open Energy Information (OpenEI) ( ): Wiki of collections of energy information
Inter-university Consortium for Political and Social Research (ICPSR) ( )
Institute for Quantitative Social Science (IQSS) ( )

Awesome Research Tools / Cloud Services / Colors

ColorBrewer
Paletton
Color Calculator

Awesome Research Tools / Publishing and Sharing / Writing

Sphinx : RestructuredText as source files, powerful, flexible and modularized
Gitbook : 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 1,353 about 1 year ago : Good for writing ebooks
rtd theme 4,800 8 days ago : Developed by ReadtheDocs.org
Alabaster 735 4 months ago : Clean and simple
Bootstrap theme
Theoretical Physics 223 3 months ago
Statistical Physics 44 10 months ago
Neutrino Physics 8 over 2 years ago
Hemingway App : Highlights complex sentences, point out passive voice, and suggests alternative words
proselint 4,360 4 months ago : A linter for English prose using advice from and more
write good 4,955 over 2 years ago : Naive JavaScript linter for English prose
artbollocks-mode 74 over 6 years ago : Emacs minor mode for avoiding cliches and bad grammar when writing about art (or other topics)
cut_the_crap.py : Simple Python script to flag redundant words and gives alternative suggestions
Rousseau 180 over 2 years ago : Lightweight proofreader written in JavaScript
textlint-rule-rousseau 7 5 months ago : A textlint rule to check English sentences using Rousseau
De-Jargonizer : Paste your article or upload file to analyze the amount of jargon in your writing

Awesome Research Tools / Publishing and Sharing / Hosting

ReadtheDocs : Turn your reStructuredText source to HTML, PDF, and epub, all done online
GitHub pages : Integrated with Jekyll and turns markdown posts automatically. Jekyll is a tool for blogging
GitHub : Just put markdown, reStructuredText, PDF or IPython/Jupyter notebook files on GitHub. All these formats can be previewed online
Surge : One command upload your static website to make it live. Surge also integrates GitHub hooks
Heroku : The one that needs no explanation
AWS : Amazon AWS provide student perks

Awesome Research Tools / Publishing and Sharing / Blog and CMS

GitBook ( ): write in Markdown and collaborate with the team. GitBook integrates with GitHub so no content will be lost
Ghost 47,509 6 days ago ( ): Open, Simple, non-profit; write with markdown and live preview
Pico 3,851 11 months ago ( ): Lightweight cms, open source, no database
Dropplets 1,627 almost 2 years ago ( ): Open source, simple, and elegant blog system; write in Markdown
Wordpress ( ): Very popular but requires a lot of maintenance

Awesome Research Tools / Publishing and Sharing / Static Site Generator

Jekyll (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
Octopress (Written in )( ): Octopress is easier to use compared with Jekyll while being somewhat compatible with Jekyll
Hexo (Written in )( ): "A fast, simple & powerful blog framework" as they say on their website. It supports GFM
Pelican (Written in )( , , ): Pelican is a modularized framework and is perfect for blogging

Awesome Research Tools / Publishing and Sharing / Static Site Generator / Pelican

Pelican Svbtle Theme 152 over 8 years ago

Awesome Research Tools / Publishing and Sharing / Static Site Generator

Nikola (Written in )( , , , , etc): It takes in multiple input formats including reStructuredText and many others
Hugo (Written in )( ): Easy to use and really fast. It also supports more input formats through plugins
Hyperdraft (Written in )( ): Automatically generate a website as you type plaintext or Markdown

Awesome Research Tools / Note Taking / Notebooks for Researchers

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

Awesome Research Tools / Note Taking / Editors

Hackmd.io ( ): Basically ships with everything you expect from the most complete online markdown editor
StackEdit ( ): StackEdit is a Markdown editor with many integrated services such as math (MathJax), Google Drive, Dropbox, and GitHub
CMD markdown ( ): CMD is a Markdown editor with math (MathJax) support. What is special is that it keeps edit history. (Chinese UI.)
Penflip ( ): Penflip is designed to be a GitHub for writers. It is Markdown-based and git like without math support
Authorea ( ): A much more powerful Markdown and LaTeX online editor that can be used to produce nice academic papers
Dillinger ( ): Markdown editor but no math mode
Pandoc Markdown ( ): Just another Markdown editor with math (MathJax) support
Marxico ( , , , ): Markdown editor that integrates with Evernote, generates pdf and works offline. ( , , , ) is the Chinese version。
Madoko ( , ): 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
Markx ( ): Markdown editor for scientific writing. Batteries included
typora ( , ): Beautiful UI and in-situ live preview
Haroopad ( , , ): A powerful github flavored markdown editor with useful extensions. Math (mathjax) is supported
jbt/markdown-editor ( ): Just another online Markdown editor without math support
MarkdownPad ( ): If you have no bad feelings about .NET, this is pretty good
ReText 1,882 about 2 months ago ( , , ): ReText one of the best, even on Linux. It also supports reStructuredText input
Madoko ( ): × Markdown ²
eme 2,048 almost 2 years ago ( , , ): Math support
Moeditor ( , , ): All purpose markdown editor
boostnote ( , , ): Math + Markdown, with snippet note support
Quiver ( , ): Programmer's notebook, math + Markdown, code snippet
Findings ( ): Notebook for experimentalists, organized research materials and notes
Notion ( , , , ): Notetaking with kanban, math, calendar, table, etc
Agenda ( , ): Notes and GTD
Overleaf ( ): Built in version control, Dropbox and GitHub integration, preview, cooperation, simple UI. It also provides a lot of templates
Authorea ( ): Easy to use UI. Supports both Markdown and LaTeX
Papeeria ( ): Just another online LaTeX and Markdown with plot compiler and collaborations
JaxEdit ( ): JaxEdit doesn't provide full LaTeX support but is good enough for simple LaTeX documents and slides
Overleaf Source Code 14,127 6 days ago : Overleaf open sourced their codes. This is a great move I would say
TeXStudio Cross-platform LaTeX editor that stems from TeXMaker
WinEdt The LaTeX editor many people swear by
TeXnicCenter A quite old but free and decent editor for LaTeX
LyX Cross-platform WYSIWYM editor that uses LaTeX behind the scenes to render documents
TeXshop No-nonsense editor for LaTeX documents which is included in MacTeX
TeXWorks No-nonsense editor for LaTeX code, modeled after TeXShop, but this one is cross-platform
Synthical aggregates all papers from arXiv, medRxiv, bioRxiv, and chemRxiv with ability to highlight and leave notes

Awesome Research Tools / Note Taking / IPython Notebook

Scientific Python Lectures 3,503 about 1 year ago
Reproduced Papers
More 16,311 6 days ago : For more IPython notebook on GitHub please read this enormous list

Awesome Research Tools / Note Taking / Mindmap

KityMinder By Baidu 4,434 over 5 years ago : Chinese Interface
my-mind : repo
beautiful Mind : repo
Mindmup : repo
mindmaps : repo
gojs
jsmind 3,473 about 1 month ago
jsmind
mindmaps 2,780 almost 2 years ago

Awesome Research Tools / Note Taking / Concept Map and Diagrams

Gliffy : all kinds of diagrams
ProcessOn : all kinds of diagrams
Draw.io : all kinds of diagrams

Awesome Research Tools / Note Taking / Keep The Notes

Raneto : Raneto is an open source Knowledgebase platform that uses static Markdown files to power your Knowledgebase. This one has a nice looking
Realms : Git based wiki written in Python Inspired by Gollum, Ghost, and Dillinger. Basic authentication and registration included
Tiddlywiki : A unique non-linear notebook for capturing, organizing and sharing complex information

Awesome Research Tools / Presentation Tools / Keep You Computer Awake

Caffeine ( ): As simple as a single click
Amphetamine ( ): More configurations involved and more intelligent

Awesome Research Tools / Presentation Tools / Online Load and Edit

Prezi if you can
slides.com : Easy to use with remote controlled page presentation
Slideas : the easiest way to create a beautiful Markdown Presentation, with all the features you need
Google Drive : no introduction needed
Sway : Microsoft
Strut 1,821 11 months ago
Impressionist 693 over 11 years ago
hovercraft 1,491 over 2 years ago

Awesome Research Tools / Presentation Tools / Use The Source

Impress.js : more about it
Jimpress : A jQuery version of impress.js
Reveal.js 67,906 10 days ago
Beckpoke.js 4,688 about 4 years ago
CSSS 1,733 about 1 month ago
Scrolldeck 671 about 3 years ago
Deck.js 5,423 almost 6 years ago
Shower 4,800 28 days ago
Flowtime.js 1,341 5 months ago
Slides 496 over 1 year ago
remark

Awesome Research Tools / Presentation Tools / LaTeX Beamer

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

Awesome Research Tools / Presentation Tools / Mathematica

Mathematica slides can be made interactive

Awesome Research Tools / Presentation Tools / The Power of SVG

ext-sozi 28 over 11 years ago
Inkscape ( , , )
GIMP ( , , )

Awesome Research Tools / Presentation Tools / Sharing Slides

GitHub pages : For Html based slides
Speaker Deck by GitHub: PDF slides. Can be displayed online or embeded

Awesome Research Tools / Programming / Code Editors

Visual Studio Code, aka VS Code ( , , ): same technology as atom but faster than atom, and Microsoft made
Atom ( , , ): electron based editor with numerous plugins and easy modifications. Cross-platform with settings and plugins synchronized through the plugin
Sublime Text ( , , ): cross-platform, fast, and with plugins. Not free but can be freely used forever
JetBrains ( , , ): beautiful IDE's with many debugging and editing modes integrated
vim 36,652 6 days ago ( , , ): no words can describe the almighty vim

Awesome Research Tools / Programming / Code Editors / vim

Vundle 23,934 4 months ago : the vim plugin manager
vimrc from amix 30,752 about 2 months ago : "The ultimate Vim configuration: vimrc"

Awesome Research Tools / Programming / Softwares

Synthical : AI-powered collaborative research environment
Mathematica : One Software to Rule Them All
iPython Notebook ( ): a useful tool for inline calculation, making graphs and writing notes

Awesome Research Tools / Programming / Softwares / iPython Notebook

wakari.io is a comercial one mostly aimed for data analysis
jiffylab 188 over 3 years ago is an open source one but not that well done
supervised-ipython-nbserver 6 about 11 years ago is a multiuser version of notebook using Django/Pinax

Awesome Research Tools / Programming / Softwares

Matlab
Maple
RStudio ( )

Awesome Research Tools / Programming / Scientific Computing

Python

Awesome Research Tools / Programming / Scientific Computing / Python

scipy : scientific computing made easy
SnakeViz : A nice tool for python debugging and performance improvement

Awesome Research Tools / Programming / Scientific Computing

Julia
R
Rust

Awesome Research Tools / Programming / Coding is Fun

Code Fights

Awesome Research Tools / Academic / Self-plagiarism

wikipedia:Plagiarism#Self-plagiarism

Awesome Research Tools / Academic / Investigate Papers

Synthical : 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
Paperscape : Finding interesting papers
Peerus : Monitor specific topics or journal for new and relevant papers
SciRate : An front-end for arXiv with rates from readers
ArXiv Sanity Preserver : Accelerate research through arXiv specific for many things machine learning by Andrej Karpathy
Iris.ai : Explore scientific papers and how they connect to a paper of your choice
Publish or Perish : Retrieves and analyzes academic citations designed to empower individual academics to present their case for research impact to its best advantage
PubChase : Life sciences and medical literature recommendation engine
Connected Papers : 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

Awesome Research Tools / Academic / Get Yourself A Citable Code for Anything

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

Awesome Research Tools / Academic / Get Yourself A Unique and Persistent Digital Identifier

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

Awesome Research Tools / Academic / Add Citations to Your Code

duecredit 238 4 months ago : Allows you to add decorators to Python functions that encode bibliographic details

Awesome Research Tools / Academic / Open Science

Open Science Framework : A open science tool with a lot of integrations

Awesome Research Tools / Academic / Bibliography

ReadCube/Papers : A all platform app for reference mamagement, note-taking, and more. The former Papers has been rebanded as ReadCube Papers
Mendeley : A bibliography reference manager with cloud storage and BibTeX support
Zotero : An open source bibliography reference manager with syncing and BibTeX support
Zotero Style Repository : Find any style you need
JabRef : An open source bibliography reference manager for the BibTeX format
doi2bib : Retrieves a BibTeX entry from a DOI
crossref : Makes research outputs easy to find, cite, link, and assess
org-ref 1,367 about 2 months ago : Citations, cross-references, indexes, glossaries, and bibtex utitlies for org-mode in Emacs

Awesome Research Tools / Academic / Tips for Researchers

Ten Simple Rules by PLoS One : 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 19,077 11 days ago Check the of the for search engines to search for papers

Awesome Research Tools / Pacifier

Rainy Mood ( , , ): rainy day rainy mood, simple but with excellent white noise; a new beautiful soundtrack each day
Coffitivity ( , , , ): a rather simple but useful coffee shop noise library; premium has more three more soundtracks; elegant UI; scientific research powered
Brain.fm ( ): Improve Focus, Relaxation & Sleep with audio brainwave training. Not free but worth every penny
Noizio ( , ): a handy white noise tool that stays in your Mac status bar
Noisli ( , , , ): 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
Soundrown ( ): free mixing of multiple tracks
Muji Sleep ( , )
A Soft Murmur ( ): free mixing of multiple tracks; simple UI; Timer provided; Meander available
mynoise ( , ): a noise generator; a lot of choices (too many actually); detailed equalizer
Rainy Cafe ( ): not much to say just a combination of rainy mood and coffitivity
Sleep Pillow ( , ): click and play style preloaded scenes; easy to use; beautiful design
A youtube audio track of coffee shop (really long)
A youtube audio track of 10 hours rain fall
TaoMix ( ): sound mixings to concentrate
Calm ( , , ): to help you calming down
Raining ( , , ): raining and thunder
focus@will ( , , ): music to boost your brain; paid services now
iSerenity : multiple choices but not that good (just my feeling)
Rany by simply noise : just rain
Natural Sound player : many natural sounds, cool
NatureSoundsFor.Me : make your own track, so many kinds of sounds
White.Noise : several different tracks
ambient mixer : make ambient sound easily
white noise mp3s : listen and download

Awesome Research Tools / Online Discussions / Forums and Q&A's

Physics.StackExchange
Biostars : StackOverflow style Q&A site for bioinformatics
NeuroStars : StackOverflow style Q&A site for neuroinformatics
SEQanswers : Forum for next generation sequencing community

Awesome Research Tools / Open Source / Open Licenses

Open Definition : Read the license and pick the one you like

Awesome Research Tools / Open Source / Use Licenses

Choose a License which helps you decide which license to use through several steps
Guokr Badge 23 over 10 years ago : Green CC License badges. ( )

Awesome Research Tools / Data Visualization and Graph Making / Data Visualization

D3 js ( )
Highcharts ( ): Line charts, area charts, column and bar charts, pie charts, scatter and bubble charts and more
Flot ( )
Raphaël ( )
JavaScript InfoVis Toolkit ( )
Paper.js ( )

Awesome Research Tools / Data Visualization and Graph Making / Graph Making

GeoGebra ( , , , , , , ): Geogebra is a very cool tool to make math graphs both 2D and 3D
LaTeXDraw 430 almost 4 years ago ( ): "A vector drawing editor for LaTeX."
TikZ ( )
BoxPlotR ( ): A web-tool for generation of box plots
Graphviz ( ): Open source graph visualization software
colorcet 689 2 months ago can be used to investigate colormaps

Awesome Research Tools / LaTeX / Tips

wikibooks - LaTeX : A good manual

Awesome Research Tools / LaTeX / Symbols

Detexify : find out what the symbol is by drawing online

Awesome Research Tools / LaTeX / Graphing

TeX Example (Tikz/PGF)

Awesome Research Tools / LaTeX / Fonts

Font Catalogue

Awesome Research Tools / LaTeX / Templates

LaTeX Templates

Awesome Research Tools / LaTeX / References

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

Awesome Research Tools / MISC / Terminal

plot in terminal 1,867 5 months ago
asciinema : Command line recording
bashplot 1,867 5 months ago : plot in terminal
fuck 385 about 4 years ago : correct the command by typing in fuck

Awesome Research Tools / MISC / Free Multimedia

CC Search : Search engine for images under CC License
Unsplash : Free high resolution images
Academicons
Phylopic

Awesome Research Tools / MISC / More

QR Code Generator : Adding a QR code to your poster can help you get more audience
SHIELDS.io : Make a beautiful badge by yourself
TitleCap : Not sure which word to capitalize in the title? is right for you
On Being a Scientist : A guide to responsible conduct in research
DiRT Directory : Registry of digital research tools for scholarly use
Online Whiteboard : A simple online whiteboard that users can collaborate; Good for online meetings
MapInSeconds.com : Create maps with corresponding data quickly by copy-pasting from a spreadsheet
Unpay Wall : legally download research papers for free

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