Practical Tools

We are always on the lookout for tools that make life easier and more enjoyable, but we are not collectors. We seek out well-designed, practical tools that we can actually use, prioritising functionality over quantity. We prefer tools that provide genuine value without requiring a subscription, and we are willing to invest in quality when it makes sense. This list is not meant to be comprehensive. It is simply an honest attempt to share the tools we have found genuinely useful in our work.

General Tools

fman is a dual-pane file manager. We have long been fans of Midnight Commander, a console-based file manager with a text user interface, though it lacks mouse support. With fman, we found a similar solution that offers a sleek interface, powerful functionality, and some welcome extras.

Zettlr is an open source Markdown editor with built-in reference management via Zotero integration and support for LaTeX. It is particularly useful for writing scientific papers, keeping lab notes, or organising research. A great lightweight alternative to more complex writing tools.

Zotero is an open source tool for managing and organising research papers and bibliographies. It integrates with word processors and web browsers, making it easy to collect and cite references without a paywall.

Joplin is an open source note-taking and task management tool. It supports Markdown for formatting, allows you to organise notebooks, synchronise notes across devices, and optionally encrypt your data. While Zettlr is better suited for long-form scientific writing with citations, Joplin shines as a lightweight, fast, and cross-device notebook for capturing quick thoughts, meeting notes, and task lists.

Git and GitHub are the standard tools for version control and code sharing. Git tracks changes to your files over time, making it easy to go back to earlier versions and collaborate without overwriting each other's work. GitHub provides a home for your repositories online and is widely used in the scientific community for sharing code and analysis workflows. For a course that emphasises reproducibility, version control is not optional.

bioicons offers a collection of open source, high-quality icons for the life sciences. We find it invaluable when preparing professional presentations and visual content. It is free and saves a lot of time when we need ready-to-use scientific illustrations.

BioRender is an online tool for creating professional scientific figures and illustrations. It offers a drag-and-drop interface and a large library of pre-built components. Although not fully open source, it offers a free tier and is a quick solution for creating biology-related visuals.

wizard zines by Julia Evans are compact, focused tech publications. We have all bought large IT books, only to find them outdated or filled with irrelevant content. Julia Evans' zines focus on essential, evergreen knowledge in an approachable format. Perfect when you want just the knowledge you need, without the fluff.

Spurious Correlations by Tyler Vigen is a website that humorously showcases unrelated datasets with high statistical correlations, highlighting how correlation does not imply causation. Worth a visit.

Bioinformatics Tools

Seaview is a user-friendly sequence alignment editor that supports various alignment and tree-building methods. It is a good alternative to more complex software for users who want quick results.

Jalview is an interactive tool for the analysis and visualisation of sequence alignments. It supports alignment editing, annotation, and secondary structure visualisation, making it well suited for sequence comparison.

Galaxy (European Server) is a web-based platform that provides free and open access to a wide array of bioinformatics tools, workflows, and computational resources. Hosted by the Freiburg Galaxy Team, it supports genomics, transcriptomics, and metagenomics analyses without requiring any local installation, with a strong focus on reproducibility and accessibility.

MEGA (Molecular Evolutionary Genetics Analysis) is a widely used tool for sequence alignment, molecular evolution analysis, and phylogenetic tree construction. It is commonly used in evolutionary biology and genetics research.

IGV (Integrative Genomics Viewer) enables the exploration of large-scale genomic datasets, allowing users to browse and visualise variants, alignments, and annotations across different genomes.

UCSC Genome Browser is one of the most widely used genome browsers in the field. It provides interactive visualisation of genome assemblies, gene annotations, regulatory elements, and comparative genomics tracks across a large number of species.

Ensembl is a genome browser and annotation database maintained by EMBL-EBI. It provides detailed gene annotation, variation data, and comparative genomics, and is particularly strong for vertebrate genomes. A valuable complement to the UCSC Genome Browser.

Snakemake is a workflow management system that allows you to define reproducible and scalable data analysis pipelines in a readable, Python-based syntax. It is widely used in bioinformatics for automating multi-step workflows and is well suited for running analyses on HPC clusters.

Nextflow is another workflow manager designed for scalable and reproducible scientific pipelines. It is particularly popular in the genomics community and integrates well with container systems like Docker and Singularity, making pipelines highly portable across different computing environments.