AN OPEN NOTEBOOK FOR BIOINFORMATICS

A gentle beginning

Where would you like to start?

You do not need every prerequisite before you begin. Choose the route closest to your background, then learn through one small project.

I come from biology.

Keep a biological question in view while you learn to work with data.

  • Start with either Python or R and basic file handling.
  • Learn sample metadata and experimental design.
  • Try a small structure or RNA-seq project.
Begin with practical foundations →

I come from computing.

Build the experimental context that makes an analysis meaningful.

  • Learn the assay, biological units, and data formats.
  • Study controls, replication, and confounding.
  • Reproduce a published tutorial before extending it.
Begin with biological data →

I am exploring.

You can get a feel for the work before choosing a specialization.

  • Inspect a protein structure or try a Galaxy tutorial.
  • Note the questions and methods that interest you.
  • Choose a track and a concrete next activity.
Find a first project →

A map, with room to wander.

Two scientific tracks share a practical foundation. Workflow engineering and AI connect across them.

Your bioinformatics learning map Start with a question and shared foundations. Choose structural bioinformatics or omics, apply your learning in a project, and connect workflows and AI across both paths. START HEREAsk a biological question Shared foundationsCode · Data · Statistics Structures & designPrediction · Binders · Simulation Omics & single-cellRNA · Multimodal · Perturbations Make a projectPractice · Explain · Share Tools that connect the pathsReproducible workflows · Nextflow · Snakemake · AI for research Choose a starting point. Learn the next thing your question needs.

From curiosity to a first result.

  1. Choose a question.

    What would you like to understand: a protein structure, a treatment response, or a reproducible analysis?

  2. Learn the next necessary skill.

    Use each topic’s prerequisites and outcome to choose a resource. Start with one; the library is a menu, not a completion checklist.

  3. Reproduce a small example.

    Inspect the data and run the analysis from the beginning. Keep notes about decisions and things you cannot yet explain.

  4. Explain and share what you found.

    Record your dataset, versions, parameters, results, and limitations. A clear explanation is part of the result.

How to read the difficulty labels

Beginner means an accessible entry point. Intermediate assumes some coding or analysis experience. Advanced assumes the preceding scientific and statistical context. You can revisit the foundations whenever you need them.

Prefer Arabic for your first programming steps? Explore Arabic-language resources. Most specialist material in this collection is currently in English; suggestions for strong Arabic resources are welcome.