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 Awesome Research Tools
 Awesome Research Tools
!Awesome (https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg) (https://github.com/sindresorhus/awesome)
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Version Control System
▐ First things first, everyone should know version control system, aka VCS. VCS helps us track changes in our documents as well as collaborations on the documents. Needless to say, version 
▐ control is one of the most useful tools for scientists.
▐ First things first, everyone should know version control system, aka VCS. VCS helps us track changes in our documents as well as collaborations on the documents. Needless to say, version control is one of the most useful tools for 
▐ scientists.
⟡ git
⟡ svn
@@ -88,8 +88,7 @@
⟡ GitHub (https://github.com/): 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 (https://jekyllrb.com) built websites.
⟡ GitLab (https://about.gitlab.com/): 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 (https://about.gitlab.com/): 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 than GitHub Actions.
⟡ BitBucket (https://bitbucket.org): Alternative to GitHub and GitLab with free private repositories.
@@ -109,8 +108,7 @@
Pomodoro
▐ Pomodoro Technique
▐  (https://en.wikipedia.org/wiki/Pomodoro_Technique) can be used to boost your productivity and probably improve your health. There are almost infinite choices for the tools.
▐ Pomodoro Technique (https://en.wikipedia.org/wiki/Pomodoro_Technique) can be used to boost your productivity and probably improve your health. There are almost infinite choices for the tools.
⟡ Pomotodo (https://pomotodo.com/) (Cloud,Mac,Win,Android,iOS,Chrome): A mix of todo list and pomodoro timer, with sync across devices and weekly report Free .
⟡ Tadam (https://tadamapp.com/) (Mac): Simple and elegant pomodoro timer USD$ 4.99 .
@@ -119,15 +117,14 @@
GTD-Task Manager
▐ The GTD (Getting Things Done) method unloads the todo lists off the mind by recording them using external tools. It allows one to focus on one active task instead of on all of them (
▐ Wikipedia (https://en.wikipedia.org/wiki/Getting_Things_Done)).
▐ Tasks can be classified in contexts (@home, @computer, @office, etc), time of action (now, next actions, scheduled or someday) and projects. Here (https://hamberg.no/gtd/) we have a good 
▐ pragmatic guide to GTD and here (https://gettingthingsdone.com/pdfs/tt_workflow_chart.pdf) is a flowchart.
▐ The GTD (Getting Things Done) method unloads the todo lists off the mind by recording them using external tools. It allows one to focus on one active task instead of on all of them (Wikipedia 
▐ (https://en.wikipedia.org/wiki/Getting_Things_Done)).
▐ Tasks can be classified in contexts (@home, @computer, @office, etc), time of action (now, next actions, scheduled or someday) and projects. Here (https://hamberg.no/gtd/) we have a good pragmatic guide to GTD and here 
▐ (https://gettingthingsdone.com/pdfs/tt_workflow_chart.pdf) is a flowchart.
⟡ Microsoft To Do (https://todo.microsoft.com/tasks) (Cloud,Mac,Win,Android,iOS,Win Store,Chrome OS): Almost perfect todo lists with cooperation and sharing.
⟡ Google Keep (https://keep.google.com/)(Cloud,Android,iOS,Chrome OS)
⟡ Evernote (https://evernote.com/) (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.
⟡ Evernote (https://evernote.com/) (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 (https://www.any.do/) (Cloud,Mac,Android,iOS): Good because it has a very good daily review which can help users remember what to do.
⟡ Todoist (https://todoist.com/) (Cloud,Mac,Win,Android,iOS): Todoist invented the karma system which keeps track of the tasks done.
⟡ Taskade (https://taskade.com/) (Cloud,Mac,Win,Chrome OS,Firefox,Android,iOS): Taskade is a collaborative task list and outliner for team projects.
@@ -155,8 +152,7 @@
⟡ Azure Notebooks (https://notebooks.azure.com/): online jupyter notebooks.
⟡ Datalore (https://datalore.io/): online jupyter notebook by JetBrains.
⟡ CoCalc (SageMathCloud) (https://cocalc.com/): LaTeX, R, iPython Notebook, etc.
⟡ SageMaker (https://aws.amazon.com/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.
⟡ SageMaker (https://aws.amazon.com/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 (https://www.wolframalpha.com/): Excellent engine to do mathematical derivation online and search.
⟡ Mathematica Online (https://www.wolfram.com/mathematica/online/): Bring Mathematica to life in the cloud.
@@ -233,8 +229,7 @@
Make use of these programs for publishing:
⟡ Sphinx (http://sphinx-doc.org): RestructuredText as source files, powerful, flexible and modularized.
⟡ Gitbook
 (https://www.gitbook.com/): 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.
⟡ Gitbook (https://www.gitbook.com/): 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 (https://github.com/schacon/git-scribe): Good for writing ebooks.
⟡ Static Site Generator (#static-site-generator): For more please refer to Static Site Generator (#static-site-generator).
@@ -275,8 +270,8 @@
⟡ ReadtheDocs (http://readthedocs.org/): Turn your reStructuredText source to HTML, PDF, and epub, all done online.
⟡ GitHub pages (https://pages.github.com/): Integrated with Jekyll and turns markdown posts automatically. Jekyll is a tool for blogging.
⟡ GitHub (http://github.com): 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.
⟡ GitHub (http://github.com): 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.
⟡ Surge (https://surge.sh/): One command upload your static website to make it live. Surge also integrates GitHub hooks.
⟡ Heroku (https://www.heroku.com/): The one that needs no explanation.
⟡ AWS (https://aws.amazon.com/): Amazon AWS provide student perks.
@@ -309,14 +304,12 @@
▐ Here is a nice website (https://staticsitegenerators.net/) that tells you all the static site generators. Nonetheless here is a list of the most popular ones.
⟡ Jekyll (http://jekyllrb.com/) (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.
⟡ Jekyll (http://jekyllrb.com/) (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 (http://octopress.org/) (Written in Ruby)(Markdown): Octopress is easier to use compared with Jekyll while being somewhat compatible with Jekyll.
⟡ Hexo (https://hexo.io/) (Written in Node.js)(Markdown): "A fast, simple & powerful blog framework" as they say on their website. It supports GFM.
⟡ Pelican (http://getpelican.com) (Written in Python)(reStructuredText,Markdown,AsciiDoc): Pelican is a modularized framework and is perfect for blogging.
  ⟡ Pelican Svbtle Theme (https://github.com/wting/pelican-svbtle)
⟡ Nikola (https://getnikola.com/) (Written in Python)(reStructuredText,Markdown,IPython Notebook/Jupyter,PHP, etc): It takes in multiple input formats including reStructuredText and many 
others.
⟡ Nikola (https://getnikola.com/) (Written in Python)(reStructuredText,Markdown,IPython Notebook/Jupyter,PHP, etc): It takes in multiple input formats including reStructuredText and many others.
⟡ Hugo (http://gohugo.io/)(Written in Go)(Markdown): Easy to use and really fast. It also supports more input formats through plugins.
⟡ Hyperdraft (https://hyperdraft.rosano.ca)(Written in JavaScript)(Markdown): Automatically generate a website as you type plaintext or Markdown.
@@ -333,8 +326,7 @@
Editors
▐ Markdown, LaTeX, and reStructuredText are the three useful languages.
▐ In most cases, a tweakable text editor such as Visual Studio Code, aka vscode (https://code.visualstudio.com) is good enough. In fact vscode comes with a enormous amount of extensions which
▐ can be used to build your own IDE.
▐ In most cases, a tweakable text editor such as Visual Studio Code, aka vscode (https://code.visualstudio.com) is good enough. In fact vscode comes with a enormous amount of extensions which can be used to build your own IDE.
Markdown
@@ -346,10 +338,9 @@
⟡ Authorea (https://www.authorea.com/)(Cloud): A much more powerful Markdown and LaTeX online editor that can be used to produce nice academic papers.
⟡ Dillinger (http://dillinger.io/)(Cloud): Markdown editor but no math mode.
⟡ Pandoc Markdown (http://pandoc.herokuapp.com/)(Cloud): Just another Markdown editor with math (MathJax) support.
⟡ Marxico (http://marxi.co/)(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。
⟡ Madoko (https://www.madoko.net/)(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.
⟡ Marxico (http://marxi.co/)(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。
⟡ Madoko (https://www.madoko.net/)(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 (http://markx.herokuapp.com/)(Cloud): Markdown editor for scientific writing. Batteries included.
⟡ typora (https://www.typora.io/)(Mac,Win): Beautiful UI and in-situ live preview.
⟡ Haroopad (http://pad.haroopress.com/)(Mac,Win,Linux): A powerful github flavored markdown editor with useful extensions. Math (mathjax) is supported.
@@ -509,8 +500,7 @@
LaTeX Beamer
⟡ Beamer (https://bitbucket.org/rivanvx/beamer/wiki/Home): Shipped with standard LaTeX installations. A lot of themes has been invented. Start editing with one click on Overleaf 
(https://www.overleaf.com/)
⟡ Beamer (https://bitbucket.org/rivanvx/beamer/wiki/Home): Shipped with standard LaTeX installations. A lot of themes has been invented. Start editing with one click on Overleaf (https://www.overleaf.com/)
Mathematica
@@ -541,8 +531,8 @@
⟡ Visual Studio Code, aka VS Code (https://code.visualstudio.com/)(Free,Cross-platform,Plugins): same technology as atom but faster than atom, and Microsoft made.
⟡ Atom (https://atom.io/)(Free,Cross-platform,Plugins): electron based editor with numerous plugins and easy modifications. Cross-platform with settings and plugins synchronized through the 
sync-settings (https://atom.io/packages/sync-settings) plugin.
⟡ Atom (https://atom.io/)(Free,Cross-platform,Plugins): electron based editor with numerous plugins and easy modifications. Cross-platform with settings and plugins synchronized through the sync-settings 
(https://atom.io/packages/sync-settings) plugin.
⟡ Sublime Text (https://www.sublimetext.com/)(Free Evaluation,Cross-platform,Plugins): cross-platform, fast, and with plugins. Not free but can be freely used forever.
⟡ JetBrains (https://www.jetbrains.com/)(Free for Students, Cross-platform,Plugins): beautiful IDE's with many debugging and editing modes integrated.
⟡ vim (https://github.com/vim/vim)(Free,Cross-platform,Plugins): no words can describe the almighty vim.
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Investigate Papers
⟡ Synthical (https://synthical.com): 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.
⟡ Synthical (https://synthical.com): 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 (http://paperscape.org/): Finding interesting papers.
⟡ Peerus (https://peer.us/): Monitor specific topics or journal for new and relevant papers.
⟡ SciRate (https://scirate.com/): An front-end for arXiv with rates from readers.
⟡ ArXiv Sanity Preserver (http://arxiv-sanity.com/): Accelerate research through arXiv specific for many things machine learning by Andrej Karpathy.
⟡ Iris.ai (https://the.iris.ai/): Explore scientific papers and how they connect to a paper of your choice.
⟡ Publish or Perish (https://harzing.com/resources/publish-or-perish): Retrieves and analyzes academic citations designed to empower individual academics to present their case for research 
impact to its best advantage.
⟡ Publish or Perish (https://harzing.com/resources/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 (http://pubchase.com/): Life sciences and medical literature recommendation engine.
⟡ Connected Papers
 (https://www.connectedpapers.com/): 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.
⟡ Connected Papers (https://www.connectedpapers.com/): 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.
Get Yourself A Citable Code for Anything
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Tips for Researchers
⟡ Ten Simple Rules by PLoS One (http://collections.plos.org/ten-simple-rules): 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.
⟡ Check the Academic Resources and Grey Literature List (https://github.com/jivoi/awesome-osint#-academic-resources-and-grey-literature) of the Awesome Open-Source Intelligence List 
(https://github.com/jivoi/awesome-osint) for search engines to search for papers.
⟡ Ten Simple Rules by PLoS One (http://collections.plos.org/ten-simple-rules): 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.
⟡ Check the Academic Resources and Grey Literature List (https://github.com/jivoi/awesome-osint#-academic-resources-and-grey-literature) of the Awesome Open-Source Intelligence List (https://github.com/jivoi/awesome-osint) for search 
engines to search for papers.
Pacifier
▐ Rainy Mood (http://www.rainymood.com/), Coffitivity (https://coffitivity.com/) and Noisli (http://www.noisli.com/) are the recommended ones.
⟡ Rainy Mood (http://www.rainymood.com/)(iOS, Android, Web): rainy day rainy mood, simple but with excellent white noise; a new beautiful soundtrack each day
⟡ Coffitivity (http://coffitivity.com/)(iOS, Android, Web, Mac): a rather simple but useful coffee shop noise library; premium has more three more soundtracks; elegant UI; scientific research
powered
⟡ Coffitivity (http://coffitivity.com/)(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 (https://www.brain.fm/)(Web): Improve Focus, Relaxation & Sleep with audio brainwave training. Not free but worth every penny.
⟡ Noizio (http://noiz.io/)(iOS, Mac): a handy white noise tool that stays in your Mac status bar.
⟡ Noisli (http://www.noisli.com/) (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.
⟡ Noisli (http://www.noisli.com/) (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 (http://soundrown.com/)(Web): free mixing of multiple tracks
⟡ Muji Sleep (http://sleep.muji.net/)(iOS, Android)
⟡ A Soft Murmur (http://asoftmurmur.com/)(Web): free mixing of multiple tracks; simple UI; Timer provided; Meander available
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⟡ MapInSeconds.com (http://www.mapinseconds.com/): Create maps with corresponding data quickly by copy-pasting from a spreadsheet.
⟡ Unpay Wall (http://unpaywall.org/): legally download research papers for free.
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This is a CC BY-SA licensed project. Use the source! Keep the source open!