Awesome Research ✨

As PhD students and researchers, we find ourselves navigating a complex landscape, and the right software can make all the difference. I have compiled a list of software tools that have proven invaluable to myself and my friends who are pursuing their PhDs. These tools have enhanced our research process, and boosted productivity.

Disclaimer: The installation instructions for the listed software are tailored for Ubuntu/Debian. Users of other Linux distributions can adapt accordingly, and good luck to Windows users.

Tools

Editors

Vim: A simple editor which runs in your terminal. If you what a more graphical approach you can try gvim. And vim has famous fork called neovim which emphasises more on customizability as it uses a programming language called lua for customizaition. while vim relies on Vimscript for its customization

sudo apt install gvim
sudo apt install neovim

VScode: The preferred editor for most developers, owned by Microsoft. Its popularity is attributed to a broad user base and the availability of plugins. For an open-source version, refer to this link. If you have Snap installed, use the following command:

sudo snap install code --classic

Jupyter Notebooks: A twist to the popular IPython format, Jupyter Notebooks is named after Julia, Python, and R, the three languages it supports. It can also be configured for languages such as Haskell, Ruby, Sage, etc.

pip install jupyterlab

Sublime Text: Renowned for its exceptional speed as an editor, Sublime Text is favored for its efficiency and sleek design. Although the application is not available in APT, you can manually add the repository to APT and install it.
PyCharm: A robust integrated development environment (IDE) tailored for Python, PyCharm is developed by JetBrains. By beware as the application is proprietary and doesn't have an opensource counterpart.
Google Colab: A cloud-based platform offered by Google, Google Colab is a free, interactive, and collaborative environment tailored for data science and machine learning. Utilizing Google's infrastructure, it enables users to write and execute Python code directly in a browser, eliminating the need for local installations. It excels in scenarios where sharing code with others is crucial or when local system resources are limited.

Figures/Mindmaps

Inkscape: Inkscape is a Free and open source vector graphics editor for GNU/Linux, Windows and macOS. It offers a rich set of features and is widely used for both artistic and technical illustrations such as cartoons, clip art, logos, typography, diagramming and flowcharting.
```
sudo apt install inkscape
```
Reference: Latex inkscape workflow
Geogebra:GeoGebra is a dynamic mathematics software for all levels of education that brings together geometry, algebra, spreadsheets, graphing, statistics and calculus in one engine. In addition, we can generate also use it to generate graphs and geometric shapes.
```
sudo apt install geogebra
```
Gimp: It is a freely distributed program for such tasks as photo retouching, image composition and image authoring.
```
sudo apt install gimp
```
draw.io: Used to create diagrams such as flowcharts, wireframes, organizational charts, and network diagrams. But at the end it's just a website which has lot of templates.
Biorender
Prism

Versioning

Git: A awesome versioning system. A word of advice, if you code spend some time to learn git. Some interestion trivia
svn:

Rss reader

Researcher (android)
Aggregator (rss)

ai tools

Citation Manager

Endnote
Mendeley
Zotero

Communication

Slack
Telegram
Discord

Notetaking

Evernote
Markdown
Notion
Obsidian
LaTeX

Latex

latexdiff
latexpand
arara

Plotting

Prism
Origin
Desmos
Inkscape
Geogebra

dhancodes / awesome-research