Welcome to the UKDRI Bioinformatics Toolkit

A practical starting point for onboarding, reproducibility, and bioinformatics project organisation

About This Toolkit

This toolkit is designed to help new and continuing researchers get started with bioinformatics work in a way that is organised, reproducible, and easy to hand over. It is especially aimed at people working in institutional research settings, where projects need to remain understandable and usable beyond the person who first set them up.

The core idea running through the site is simple: reproducibility and onboarding are the same problem. If a new person cannot understand how to start, the work is not truly reproducible.

Start Here

If you are beginning a new piece of work, start with Start Here, then set up a consistent layout on Reproducible Project Structure, and review Institutional GitHub before you begin sharing or collaborating.

What You’ll Find Here

This site is organised around a simple idea: start well, organise work consistently, document decisions, and use GitHub intentionally.

Start Here

A simple pathway for beginning a new project: decide where the work belongs, create the repository, add a README, define the structure, document the data, and make the first commit.

Tools & Setup

Essential software and environment setup for day-to-day bioinformatics work.

Reproducible Project Structure

A practical guide to organising folders, scripts, data, results, documentation, and environment information using a consistent structure influenced by the same principles covered in our GitHub reproducibility session.

Best Practices

Core habits that keep work understandable and maintainable:

Maintaining an analysis catalogue (with downloadable template)
Documentation best practices
Referencing and citation management

Institutional GitHub

How and when to use the institutional GitHub, what belongs there, and what minimum standards make shared repositories useful for collaboration and continuity.

Tutorials & Workshops

Curated learning resources when you need to build specific technical skills.

Resources

Databases, communities, and reference material for ongoing work.

Key Principles for Success

Documentation is Everything

From day one, document your analyses thoroughly. Your future self (and collaborators) will thank you. See our Best Practices page for templates and tips.

Essential Habits

📝 Keep an Analysis Catalogue Track every analysis you run - parameters, data sources, results, and interpretations. We provide a template in the Best Practices section.

📁 Consistent Folder Structure Use the same basic layout for every project so collaborators can immediately tell where scripts, data, results, and documentation live. See Reproducible Project Structure.

🚪 Treat the README as the front door The first file in a repository should tell someone what the project is, how to start, where the data lives, and who maintains it.

🔄 Version Control Everything Use Git for code, documentation, and lightweight configuration. Decide early whether the work should live on a personal repository or on the Institutional GitHub.

📊 Reproducibility First Write code that others (including future you) can run and understand. Use workflow management tools, document dependencies, and create clear README files.

🧪 Validate Your Results Always sanity-check your results. Use positive/negative controls, compare methods, and understand the biology behind your findings.

A Practical Starting Sequence

If you are unsure where to begin, use this order:

Use This as a Working Reference

This toolkit is intended to be revisited during real projects, not just read once. Use it when you start new work, when you need to tidy a repository, or when you are handing work over to someone else.

A Useful Final Check

Before you call a repository “done enough”, ask:

Could someone who does not know this project find the right place to start quickly, with no help from me?

If not, the repository usually needs one of three things: a clearer README, a clearer structure, or better onboarding notes.

Support and Community

Getting Help

Consult this toolkit first
Check tool documentation and GitHub issues
Ask colleagues and local bioinformatics support
Engage with online communities (Biostars, Stack Overflow, etc.)

Contributing

If you find broken links, have suggestions for additional resources, or want to contribute content, please reach out to the toolkit maintainers.

Ready to Begin?

Start with Start Here if you are setting up a new project, or go to Tools & Setup if you need to configure your working environment first.

--- title: "Welcome to the UKDRI Bioinformatics Toolkit" subtitle: "A practical starting point for onboarding, reproducibility, and bioinformatics project organisation" format: html: toc: true --- ## About This Toolkit This toolkit is designed to help new and continuing researchers get started with bioinformatics work in a way that is organised, reproducible, and easy to hand over. It is especially aimed at people working in institutional research settings, where projects need to remain understandable and usable beyond the person who first set them up. The core idea running through the site is simple: reproducibility and onboarding are the same problem. If a new person cannot understand how to start, the work is not truly reproducible. ::: {.callout-tip} ## Start Here If you are beginning a new piece of work, start with [Start Here](start-here.qmd), then set up a consistent layout on [Reproducible Project Structure](reproducible-project-structure.qmd), and review [Institutional GitHub](institutional-github.qmd) before you begin sharing or collaborating. ::: ## What You'll Find Here This site is organised around a simple idea: start well, organise work consistently, document decisions, and use GitHub intentionally. ### [Start Here](start-here.qmd) A simple pathway for beginning a new project: decide where the work belongs, create the repository, add a README, define the structure, document the data, and make the first commit. ### [Tools & Setup](tools-setup.qmd) Essential software and environment setup for day-to-day bioinformatics work. ### [Reproducible Project Structure](reproducible-project-structure.qmd) A practical guide to organising folders, scripts, data, results, documentation, and environment information using a consistent structure influenced by the same principles covered in our GitHub reproducibility session. ### [Best Practices](best-practices.qmd) Core habits that keep work understandable and maintainable: - Maintaining an analysis catalogue (with downloadable template) - Documentation best practices - Referencing and citation management ### [Institutional GitHub](institutional-github.qmd) How and when to use the institutional GitHub, what belongs there, and what minimum standards make shared repositories useful for collaboration and continuity. ### [Tutorials & Workshops](tutorials-workshops.qmd) Curated learning resources when you need to build specific technical skills. ### [Resources](resources.qmd) Databases, communities, and reference material for ongoing work. --- ## Key Principles for Success ::: {.callout-important} ## Documentation is Everything From day one, document your analyses thoroughly. Your future self (and collaborators) will thank you. See our [Best Practices](best-practices.qmd) page for templates and tips. ::: ### Essential Habits **📝 Keep an Analysis Catalogue** Track every analysis you run - parameters, data sources, results, and interpretations. We provide a template in the [Best Practices](best-practices.qmd) section. **📁 Consistent Folder Structure** Use the same basic layout for every project so collaborators can immediately tell where scripts, data, results, and documentation live. See [Reproducible Project Structure](reproducible-project-structure.qmd). **🚪 Treat the README as the front door** The first file in a repository should tell someone what the project is, how to start, where the data lives, and who maintains it. **🔄 Version Control Everything** Use Git for code, documentation, and lightweight configuration. Decide early whether the work should live on a personal repository or on the [Institutional GitHub](institutional-github.qmd). **📊 Reproducibility First** Write code that others (including future you) can run and understand. Use workflow management tools, document dependencies, and create clear README files. **🧪 Validate Your Results** Always sanity-check your results. Use positive/negative controls, compare methods, and understand the biology behind your findings. --- ## A Practical Starting Sequence If you are unsure where to begin, use this order: 1. [Start Here](start-here.qmd) 2. [Tools & Setup](tools-setup.qmd) 3. [Reproducible Project Structure](reproducible-project-structure.qmd) 4. [Best Practices](best-practices.qmd) 5. [Institutional GitHub](institutional-github.qmd) 6. [Tutorials & Workshops](tutorials-workshops.qmd) ::: {.callout-note} ## Use This as a Working Reference This toolkit is intended to be revisited during real projects, not just read once. Use it when you start new work, when you need to tidy a repository, or when you are handing work over to someone else. ::: ## A Useful Final Check Before you call a repository "done enough", ask: > Could someone who does not know this project find the right place to start quickly, with no help from me? If not, the repository usually needs one of three things: a clearer README, a clearer structure, or better onboarding notes. --- ## Support and Community ### Getting Help - Consult this toolkit first - Check tool documentation and GitHub issues - Ask colleagues and local bioinformatics support - Engage with online communities (Biostars, Stack Overflow, etc.) ### Contributing If you find broken links, have suggestions for additional resources, or want to contribute content, please reach out to the toolkit maintainers. --- ## Ready to Begin? Start with [Start Here](start-here.qmd) if you are setting up a new project, or go to [Tools & Setup](tools-setup.qmd) if you need to configure your working environment first.