A list of tools for research. Also available on

GitHub

the most popular platform for git with social and collaborations built-in.; GitHub also provides GitHub Actions. With Actions one could automate processes.; GitHub provides GitHub Pages. With GitHub Pages, on could host static files as well as Jekyll built websites.

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.; GitLab includes unlimited free private repositories.; GitLab comes with a continuous integration tool that is more powerful…

BitBucket

Alternative to GitHub and GitLab with free private repositories.

GitLab

See above at Online Git Service.

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.

Pomodoro Technique

can be used to boost your productivity and probably improve your health. There are almost infinite choices for the tools.

Pomotodo

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

Tadam

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

Productivity Challenge Timer

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

Microsoft To Do

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

Google Keep

(Cloud,Android,iOS,Chrome OS)

Evernote

(Cloud,Mac,Win,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

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

Todoist

(Cloud,Mac,Win,Android,iOS): Todoist invented the karma system which keeps track of the tasks done.

Taskade

(Cloud,Mac,Win,Chrome OS,Firefox,Android,iOS): Taskade is a collaborative task list and outliner for team projects.

Agenda

(Mac): Date-focused note taking.

Google Colab

free 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 or Google Drive.

NextJournal

the notebook for reproducible research.; Basically, NextJournal runs almost anything.; Focusing on reproducibility.

Kaggle

kaggle has built-in free jupyter notebook.; One can also connect to Google BigQuery to access big data.

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.

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.

SankeyDiagram.net

Web-based tool for creating & sharing Sankey Diagrams from data (open-source)

DRYAD

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

Figshare

(Storage, Lookup): Data sharing and storage

Data.gov

(Lookup): Data by US Federal Government

GenBank

(Lookup): Genetic sequence database

National Centers for Environmental Information

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

GEOSS Portal

(Lookup): Earth science data

US Virtual Astronomical Observatory

(Lookup)

MAST: Barbara A. Mikulski Archive for Space Telescopes

(Lookup)

Mikulski Archive for Space Telescopes

(Lookup)

Archaeology Data Service

(Lookup): Certified repository

Open Energy Information (OpenEI)

(Lookup): Wiki of collections of energy information

Inter-university Consortium for Political and Social Research (ICPSR)

(Lookup)

Institute for Quantitative Social Science (IQSS)

(Lookup)

Voidly Censorship Index

(Lookup, API): Open dataset of global internet censorship — 19.6M live OONI samples, 1.6M historical records across 119+ countries, 5,356 citable incidents with 16,822 evidence items. CC BY 4.0, REST/MCP API, HuggingFace parquet exports.

ColorBrewer

Multi-hue and single-hue palettes for heat maps and data visualization.

Paletton

A designer tool for creating color combinations that work together well.

Color Calculator

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

Good for writing ebooks.

rtd theme

Developed by ReadtheDocs.org

Alabaster

Clean and simple

Bootstrap theme

Theoretical Physics

Statistical Physics

Neutrino Physics

Hemingway App

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

proselint

A linter for English prose using advice from Garner's Modern American Usage 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).

cut_the_crap.py

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.

De-Jargonizer

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

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

the most popular platform for git with social and collaborations built-in.; GitHub also provides GitHub Actions. With Actions one could automate processes.; GitHub provides GitHub Pages. With GitHub Pages, on could host static files as well as Jekyll built websites.

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.

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.

Ghost

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

Pico

(PHP): Lightweight cms, open source, no database.

Dropplets

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

Wordpress

(PHP): Very popular but requires a lot of maintenance.

Here is a nice website

that tells you all the static site generators. Nonetheless here is a list of the most popular ones.

Jekyll

(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.

Octopress

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

Hexo

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

Pelican

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

Pelican Svbtle Theme

Nikola

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

Hugo

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

Hyperdraft

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

Findings

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

Learnly AI

AI-powered academic assistant for students, featuring smart note-taking from lectures, PDFs and videos, essay writing with literature review, and AI presentation generator.

Hackmd.io

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

StackEdit

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

CMD markdown

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

Penflip

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

Authorea

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

Dillinger

(Cloud): Markdown editor but no math mode.

Pandoc Markdown

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

Marxico

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

Madoko

(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.

Markx

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

typora

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

Haroopad

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

jbt/markdown-editor

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

MarkdownPad

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

ReText

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

eme

(Win,Mac,Linux): Math support.

Moeditor

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

boostnote

(Win,Mac,Linux): Math + Markdown, with snippet note support.

Quiver

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

Findings

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

Notion

(Win,Mac,iOS,Android): Notetaking with kanban, math, calendar, table, etc.

Agenda

(Mac): Date-focused note taking.

Overleaf

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

Papeeria

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

JaxEdit

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

SpicyChai LaTeX

(Cloud): Online LaTeX editor with AI-powered template population, real-time PDF preview, and pre-built templates for resumes, papers, and more. Free anonymous renders without signup.

Overleaf Source Code

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.

Scientific Python Lectures

Lectures on scientific computing with python, as IPython notebooks by Robert Johansson.

Reproduced Papers

More

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

KityMinder By Baidu

Chinese Interface

my-mind

repo here.

beautiful Mind

repo here

Mindmup

repo here

mindmaps

repo here

gojs

jsmind

a mind mapping library built by javascript

jsmind

mindmaps

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

Gliffy

all kinds of diagrams

ProcessOn

all kinds of diagrams

Draw.io

all kinds of diagrams

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.

Caffeine

(Mac): As simple as a single click.

Amphetamine

(Mac): More configurations involved and more intelligent.

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

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

Impressionist

hovercraft

Impress.js

more about it impress wiki page.

Jimpress

A jQuery version of impress.js

Reveal.js

A framework for easily creating beautiful presentations using HTML.

Beckpoke.js

DIY Presentation Micro-Framework

CSSS

Scrolldeck

Deck.js

markdown based presentation on your browser

Shower

Flowtime.js

Slides

remark

A simple, in-browser, Markdown-driven slideshow tool targeted at people who know their way around HTML and CSS.

Beamer

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

Mathematica slides

can be made interactive.

ext-sozi

Inkscape

(Mac,Win,Linux)

GIMP

(Mac,Win,Linux)

GitHub pages

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

Speaker Deck

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

Visual Studio Code, aka VS Code

(Free,Cross-platform,Plugins): same technology as atom but faster than atom, and Microsoft made.

Atom

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

Sublime Text

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

JetBrains

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

vim

(Free,Cross-platform,Plugins): no words can describe the almighty vim.

Vundle

the vim plugin manager

vimrc from amix

"The ultimate Vim configuration: vimrc"

Synthical

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

Mathematica

One Software to Rule Them All

iPython Notebook

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

wakari.io

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.

Matlab

An industry standard for modeling and numerical optimization in economics. Free alternatives:

Maple

RStudio

(R)

Python

is by far the most popular language in science, due in no small part to the ease at which it can be used and the vibrant ecosystem of user-generated packages. To install packages, there are two main methods: Pip (invoked as pip install), the package manager that comes bundled with Python, and…

scipy

scientific computing made easy

SnakeViz

A nice tool for python debugging and performance improvement.

Julia

R

R is a free software environment for statistical computing and graphics.

Rust

dna-claude-analysis

Personal genome analysis toolkit with Python scripts analyzing raw DNA data across 17 categories and generating terminal-style HTML visualization for scientific research.

Code Fights

Practice programming and land a job.

wikipedia:Plagiarism#Self-plagiarism

.

Synthical

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

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.

Uncited

Keeping up with the literature.

ODataMap

Interactive map of global scientific research. Visualizes 250M+ papers across 7 knowledge continents with AI research assistant. Demo

citracer

Trace citation chains for any concept across research papers. Given a source PDF (or arXiv/DOI), recursively walks the citation graph and produces an interactive HTML visualization. Supports forward and reverse tracing.

BGPT MCP API

Search scientific papers with structured full-text experimental data (methods, results, conclusions, sample sizes, limitations, quality scores — 25+ fields per paper). Works via the Model Context Protocol with Claude, Cursor, and other AI tools. Free tier: 50 searches without authentication.…

Zenodo

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

orcid

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.

Open Science Framework

A open science tool with a lot of integrations.

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.

CiteMe

AI-powered citation generator that searches 11+ academic databases and formats references in 43+ styles including APA, Harvard, Chicago, Vancouver, and IEEE.

org-ref

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

ScholarRef

Convert citation styles (APA 7, Harvard, Vancouver) directly inside Word .docx files.

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.

Rainy Mood

, Coffitivity and Noisli are the recommended ones.

Coffitivity

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

Brain.fm

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

Noizio

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

Noisli

(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.

Soundrown

(Web): free mixing of multiple tracks

Muji Sleep

(iOS, Android)

A Soft Murmur

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

mynoise

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

Rainy Cafe

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

Sleep Pillow

(iOS, Mac): 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

(Android): sound mixings to concentrate

Calm

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

Raining

(iOS, Android, Web): raining and thunder

focus@will

(iOS, Android, Web): 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

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.

Open Definition

Read the license here and pick the one you like.

Choose a License

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

Guokr Badge

Green CC License badges. (Documentation is in Chinese.)

D3 js

(js)

Highcharts

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

Flot

(jQuery)

Raphaël

(js)

JavaScript InfoVis Toolkit

(js)

Paper.js

(js)

matplotlib

seaborn

statistical data visualization

Plotnine

A Grammar of Graphics for Python

ggplot for python

plot.ly

Internet required, interactive plotting.

bokeh

Internet required, interactive plotting.

itermplot

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

GeoGebra

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

LaTeXDraw

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

TikZ

(LaTeX)

BoxPlotR

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

Graphviz

(Linux,Win,Max,Solaris,FreeBSD): Open source graph visualization software.

colorcet

can be used to investigate colormaps.

wikibooks - LaTeX

A good manual.

Detexify

find out what the symbol is by drawing online

TeX Example

(Tikz/PGF)

Font Catalogue

LaTeX Templates

plot in terminal

asciinema

Command line recording.

fuck

correct the command by typing in fuck.

CC Search

Search engine for images under CC License.

Unsplash

Free high resolution images.

Academicons

Phylopic

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? TitleCap 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.