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awesome-science

A currated list of awesome scientific software, libraries and services.
https://github.com/deverte/awesome-science

Last synced: 3 days ago
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  • Writing

    • ONLYOFFICE - Office almost fully compatible with *Microsoft Office* (**Open Source**).
    • LaTeX - Markup language with math expressions.
    • OpenOffice Math - A tool for creating and editing mathematical formulae (**Open Source**).
    • LibreOffice Math - An application designed for creating and editing mathematical formulae based on *Apache OpenOffice Math* (**Open Source**).
    • AsciiDoc - Text document format for writing articles, books. Supports AsciiMath, MathML and LaTeX formulas.
    • Markdown - Lightweight markup language and text-to-HTML conversion tool. Some converters are supporting LaTeX math, diagrams and so on.
    • R Markdown - Dynamic documents for R language and more.
    • reStructuredText - Plaintext markup syntax and parser system (natively supports LaTeX math).
    • KaTeX - The fastest math typesetting library for the web.
    • MathJax - A JavaScript display engine for mathematics that works in all browsers.
    • MathML - Mathematical markup language, an application of XML for describing mathematical notations and capturing both its structure and content.
    • Asciidoctor - A fast, open source text processor and publishing toolchain for converting AsciiDoc content to HTML5, DocBook, PDF, and other formats.
    • Docutils - Plaintext processor.
    • Pandoc - Markup formats converter.
    • LyX - A document processor that encourages an approach to writing based on the structure of your documents (WYSIWYM) and not simply their appearance (WYSIWYG) (**Open Source**).
    • Microsoft Word - WYSWYG text processor (**EULA / Commercial**).
    • Overleaf - Online LaTeX Editor (**Open Source / Freemium**).
    • CodeSandbox - Online Code Editor and IDE for Rapid Web Development (**Open Source**, **Proprietary** (server)).
    • Codespaces - Online development environment, hosted by GitHub and powered by Visual Studio Code, that allows you to develop entirely in the cloud (**EULA / Free**).
    • Visual Studio Code - High extensible text editor (**Open Source**).
    • VSCodium - High extensible text editor based on *Visual Studio Code* (**Open Source**).
    • StackEdit - In-browser Markdown editor (**Open Source**).
    • Jupyter Notebook - Interactive documents with live code, equations and visualization for [many languages](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).

  • Archives

    • PsyArXiv - Preprint service for the psychological sciences.
    • arXiv.org - E-Print archive for physics, mathematics, computer science, economics and engineering.
    • bioRxiv - Preprint server for biology.
    • medRxiv - Preprint server for health sciences.
    • SocArXiv - Preprint service for the social sciences.
    • viXra.org - Unorthodox and fringe science e-print archive ([warning](https://webspace.science.uu.nl/~hooft101/fringe-oct-2017.pdf)).
    • IEEE Xplore - IEEE archive.
    • Library Genesis - Shadow library for scientific and general-interest books ([warning](https://en.wikipedia.org/wiki/Shadow_library)).
    • @libgen_book_bot - Telegram - Unofficial Libgen bot for Telegram Messenger.
    • PeerJ - Open access peer-reviewed scientific mega journal covering research in the biological and medical sciences.
    • Z-Library - Shadow library project for file-sharing access to pirated scholarly journal articles, academic texts, and general-interest books without the permission of authors or payment to them ([warning](https://en.wikipedia.org/wiki/Shadow_library)).
    • КиберЛенинка - Open science Russian library.
    • Google Scholar - Web search engine for scholarly literature.
    • PeerLibrary - Search engine for academic publications and people.
    • PubMed - Citations for biomedical literature.
    • Sci-Hub - Shadow library website with access to research papers ([warning](https://en.wikipedia.org/wiki/Shadow_library)).
    • @scihubot - Telegram - Official Sci-Hub bot for Telegram Messenger.
    • Semantic Scholar - Scientific literature search engine.
    • PsyArXiv - Preprint service for the psychological sciences.

  • MOOCs

  • Services

  • Literature Management

    • JabRef - Reference manager (**Open Source**).
    • BibTeX - Reference management software for formatting lists of references (**Open Source**).
    • EndNote - Bibliography information and reference manager (**EULA / Commercial**).
    • Mendeley - Reference and literature collection manager with PDFs annotation (**EULA / Free**).
    • Zotero - Program for collecting, orginizing, synchronizing and citing scientific literature (**Open Source**).

  • Social

  • Project Management

    • Element.io - Cross-platform messenger based on Matrix protocol (**Open Source**).
    • Discord - Instant messaging and VoIP (**EULA / Free**).
    • Telegram Messenger - Instant messaging application with a bots platform (**Open Source** (client), **Proprietary** (server)).
    • GitHub - Hosting for IT projects and version control. Can be used for general purpose projects (including scientific) (**EULA / Freemium**).
    • Yandex.Tracker - Project management and organizational tool (**EULA / Freemium**).
    • Confluence - Web-based corporate wiki (**EULA / Freemium**).
    • docsify - A magical documentation site generator (**Open Source**).
    • Gatsby - A framework based on ReactJS, Webpack, JavaScript and CSS that helps developers quickly build very fast static websites and apps (**Open Source**).
    • GitBook - A modern documentation platform where teams can document everything from products to internal knowledge-bases and APIs (**EULA / Freemium**).
    • Jira - Bug tracking and agile project management (**EULA / Freemium**).
    • Kanboard - Kanban project management software (**Open Source**).
    • Notion - Note taking, wiki and project management application (**EULA / Freemium**).
    • Org mode - GNU Emacs major mode for keeping notes, authoring documents, computational notebooks, literate programming, maintaining to-do lists, planning projects, and more — in a fast and effective plain text system (**Open Source**).
    • Redmine - Flexible project management web application (**Open Source**).
    • Restyaboard - Kanban board for task management (**Open Source**).
    • Trello - Project management with kanban boards (**EULA / Freemium**).
    • GitHub Pages - Websites for projects, hosted directly from GitHub repository (**EULA / Freemium**).
    • Jekyll - Simple, blog-aware, static sites (**Open Source**).
    • MkDocs - A fast, simple and downright gorgeous static site generator that's geared towards building project documentation (**Open Source**).
    • Obsidian - Powerful knowledge base that works on top of a local folder of plain text Markdown files (**EULA / Freemium**).
    • VuePress - Vue-powered Static Site Generator (**Open Source**).
    • Read the Docs - Read the Docs hosts documentation for the open source community (**Open Source**).

  • Engineering

    • eBay - Auction-style sales web site (including electrical equipment and etc.).
    • KiCad - Suite for electronic design automation (EDA) (**Open Source**).
    • SOLIDWORKS - Solid modeling computer-aided design (CAD) and computer-aided engineering (CAE) computer program (**EULA / Commercial**).
    • AutoCAD - Computer-aided design (CAD) and drafting software application (**EULA / Commercial**).
    • Intel Quartus Prime - Programmable logic device design software (**EULA / Freemium**).

  • Data Visualization

    • Microsoft Visio - Diagramming and vector graphics application (**EULA / Commercial**).
    • flowchart.js - Draws simple SVG flow chart diagrams from textual representation of the diagram (**Open Source**).
    • Bokeh - An interactive visualization library for modern web browsers (**Open Source**).
    • gnuplot - Portable command-line driven graphing utility (**Open Source**).
    • Grafana - Multi-platform open source analytics and interactive visualization web application (**Open Source**).
    • Manim - Engine for precise programmatic animations, designed for creating explanatory math videos (**Open Source**).
    • Matplotlib - Visualization library for Python (**Open Source**).
    • seaborn - Library for making statistical graphics in Python (**Open Source**).
    • ParaView - Open-source, multi-platform data analysis and visualization application (**Open Source**).
    • Plotly - Library for data visualization and dashboards (**Open Source**).
    • Dash - A productive Python framework for building web analytic applications (**Open Source**).
    • QCustomPlot - Qt C++ widget for plotting and data visualization (**Open Source**).

  • Instruments

    • Blender - 3D computer graphics software toolset with ability to simulate physical, chemical, biological, ... systems with game engines (**Open Source**).
    • Armory - 3D game engine with full *Blender* integration (**Open Source**).
    • Godot Engine - 2D and 3D game engine (**Open Source**).
    • Quantum ESPRESSO - Suite for first-principles electronic-structure calculations and materials modeling (**Open Source**).
    • Cirq - An open source framework for programming quantum computers (**Open Source**).
    • Strawberry Fields - Python library for simulating and executing programs on quantum photonic hardware (**Open Source**).
    • Xcos - Dynamic systems modeler and simulator in discrete and continuous time domains (**Open Source**).
    • PennyLane - Python library for differentiable programming of quantum computers (**Open Source**).
    • Simulink - Simulation and Model-Based Design (**EULA / Commercial**).

  • Data Storage

  • Data Processing

    • ROOT - Data analysis framework for C++ (**Open Source**).
    • TensorFlow - Platform for machine learning (**Open Source**).
    • Xframe - C++ library meant for numerical analysis with multi-dimensional labeled array expressions (also referred as variable expressions) and data frame expressions (**Open Source**).
    • C++ - General purpose language with high performance.
    • Julia - Language for mathematical computations with high performance.
    • Python - General purpose language with many scientific libraries.
    • Numba - JIT compiler that translates a subset of Python and NumPy code into fast machine code (**Open Source**).
    • R - Statistical computing and graphics.
    • Apache Arrow - Cross-language development platform for in-memory analytics (**Open Source**).
    • Boost C++ Libraries - Free peer-reviewed portable C++ source libraries (**Open Source**).
    • OpenCL - Open, royalty-free standard for cross-platform, parallel programming of diverse accelerators found in supercomputers, cloud servers, personal computers, mobile devices and embedded platforms (**EULA**).
    • PyTorch - Machine learning framework (**Open Source**).
    • Xtensor - C++ library meant for numerical analysis with multi-dimensional array expressions (**Open Source**).
    • Gonum - A set of packages designed to make writing numerical and scientific algorithms productive, performant, and scalable (**Open Source**).
    • Astropy - Community effort to develop a common core package for Astronomy in Python (**Open Source**).
    • Diofant - Python library for symbolic mathematics (fork of the _SymPy_).
    • Gensim - An open-source library for unsupervised topic modeling and natural language processing, using modern statistical machine learning (**Open Source**).
    • NetworkX - A Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks (**Open Source**).
    • Natural Language Toolkit (NLTK) - A suite of libraries and programs for symbolic and statistical natural language processing (NLP) for English written in the Python programming language (**Open Source**).
    • Open Neural Network Exchange (ONNX) - An open format built to represent machine learning models (**Open Source**).
    • scikit-learn - Machine learning library (**Open Source**).
    • Xeus Cling - Jupyter kernel for C++ based on the C++ interpreter cling and the native implementation of the Jupyter protocol xeus (**Open Source**).
    • Axiom - General-purpose computer algebra system (**Open Source**).
    • Deepnote - Data science notebook for teams (**EULA / Freemium**).
    • NumPy - Base N-dimensional array package (**Open Source**).
    • pandas - Data structures & analysis (**Open Source**).
    • SciPy library - Fundamental library for scientific computing (**Open Source**).
    • SymPy - Symbolic mathematics (**Open Source**).
    • statsmodels - Python module for statistical models (**Open Source**).
    • Anaconda - Python and R distribution with many scientific libraries (**Open Source / Freemium**).
    • Conda - Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more (**Open Source**).
    • Mamba - Fast, robust, and cross-platform package manager (**Open Source**).
    • Google Colaboratory - Python code in browser with access to GPU and TPU (**EULA / Free**).
    • Juno - Julia IDE based on Atom text editor (**Open Source**).
    • Magma - a computer algebra system designed to solve problems in algebra, number theory, geometry and combinatorics (**EULA / Free**).
    • Maple - A symbolic and numeric computing environment as well as a multi-paradigm programming language (**EULA / Commercial**).
    • Mathcad - Math software for engineering (**EULA / Commercial**).
    • SMath Studio - Tiny, powerful, free mathematical program with WYSIWYG editor and complete units of measurements support (**EULA / Free**).
    • Spyder - Scientific Python IDE (**Open Source**).
    • Wolfram Mathematica - Technical calculations (**EULA / Commercial**).
    • MATLAB - Mathematics and graphics for engineers and scientists (**EULA / Commercial**).
    • Maxima - A system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series and etc (**Open Source**).
    • Microsoft Excel - Spreadsheet with calculations, graphing and macro programming (**EULA / Commercial**).
    • OriginLab - Graphing and data analysis (**EULA / Commercial**).
    • PAST (Paleontological Statistics) - Software for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy (**EULA / Free**).
    • PyCharm - The Python IDE for Professional Developers (includes scientific tools) (**Open Source** or **EULA / Commercial**).
    • SageMath - Mathematics software system (**Open Source**).
    • SciDAVis - Scientific data analysis and visualization (**Open Source**).
    • SciLab - Software for numerical computation (**Open Source**).

  • Presentation

    • beamer - LaTeX class for producting slides (**Open Source**).
    • Microsoft PowerPoint - WYSWYG text processor (**EULA / Commercial**).
    • reveal.js - The HTML presentation framework (**Open Source**).
Categories
Data Processing 49 Writing 23 Project Management 22 Archives 19 Data Visualization 12 Instruments 9 MOOCs 7 Data Storage 5 Engineering 5 Literature Management 5 Presentation 3 Services 2 Social 2
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