Research ToolBoX (RTBX)

This is an ongoing collection of tools and resources, gathered for research throughout my personal journey. Feel free to use and share if you find something helpful!

Table of Contents

• Literature
• Documentation
• Computing
• Storage
• Learning
• Communities
• Miscellaneous

Literature

• Search engine
  • Google Scholar
  • Semantic Scholar
  • Bielefeld Academic Search Engine
  • Open Research Knowledge Graph (ORKG)
  • Open Knowledge Maps
  • Connected Papers
  • Litmaps
• Reference manager
  • Zotero

Documentation

• Note-taking
  • Markdown
    • HackMD
  • LaTeX
    • Overleaf
  • Computational notebooks
    • Jupyter
    • Org-Mode
  • Flashcards
    • RemNote
• Convertor
  • FFmpeg
  • ImageMagick
  • Pandoc
• Whiteboard/Canvas
  • Mural
  • Miro
  • Excalidraw
  • Draw.io
  • Inkscape

Computing

• Command-Line Interface (CLI)
  • Vim
  • GNU Emacs
  • Git
• Environment
  • Docker
  • Singularity
  • Apptainer
  • GNU Guix
  • Conda
  • Mamba
  • uv
  • Pixi
• Workflow
  • GNU Make
  • Snakemake
• Quality
  • IDE/ADE
  • Test suite
  • Linter
  • CI/CD

Storage

• Repositories
  • Github
  • Gitlab
  • Codeberg
  • Software Heritage
  • Zenodo
  • Figshare
  • Open Science Framework
  • ArXiv
  • HAL
  • Protocols.io
  • Huggingface
  • Internet Archive
• Data formats
  • Flexible Image Transport System (FITS)
  • Hierarchical Data Format (HDF)
• Data managment
  • RAID levels
  • Rsync
  • Rclone
  • Git-Annex
  • DataLad

Learning

• MIT OpenCourseWare
• FUN MOOC
• edX
• Coursera
• Udacity
• Codecademy
• Cognitive Class
• The Carpentries Lessons
• UNIVERSE-HPC training materials
• CodeRefinery lessons
• ARCHER2 Online Training
• Digital Research Academy

Communities

• Open Science & Open Research
  • The Turing Way
  • Center for Open Science
  • Open Research Europe
  • EU Open Research Repository
  • Nationale Forschungsdateninfrastruktur
• Research Software Engineering
  • Software Sustainability Institute
  • Research Software Engineers International
  • The Society of Research Software Engineering
  • Nordic-RSE
  • Learning and teaching RSE
  • Research Software Alliance
  • INTERSECT

Miscellaneous

• Glossary
• Templates
• Tips
• Notes