Software
Software
We write open-source software for clinical genetics, for analysing biological rhythms and for teaching. All of it is free to use.
All our code on GitHubClinical genetics
Pedigree Studio
Draw clinical genetics pedigrees in a web browser. Pedigree Studio is a single HTML file that works offline, and no data leaves the device, so it can be used where online tools can’t: in prisons, rural clinics and home visits, and wherever patient data mustn’t go to an outside server.
It is also useful for teaching, as students can practise drawing pedigrees without accounts or any setup.
Python packages for Pedigree Studio files
Convert pedigrees between Pedigree Studio, PED files, the GA4GH Pedigree standard and Phenopackets, and standardise their disease and phenotype terms. Each package installs with pip.
Time-course data
nugap
A Python package that finds which genes, or which relationships between them, change their dynamics between two conditions, such as wild type and mutant. It uses the Vinnicombe ν-gap, a distance between dynamical systems from control theory, and its results have been checked against MATLAB’s implementation.
$ pip install nugap
Teaching
Bioinformatics workbench
A workbench in the browser for bioinformatics practicals: Python and R notebooks, a Linux terminal with real bioinformatics programs, Galaxy, public databases, a genome browser, a 3D structure viewer and a network viewer.
Everything runs in the student’s browser. There is nothing to install and no server, and students’ files stay on their own computer.
Teaching
Software in teaching
We write software for teaching genomics and bioinformatics, and share it so that others can use it too. Most of it runs entirely in the browser, so students don’t need to install anything and their work stays on their own computer.
www.genomics.tel Our website for teaching genomics. Visit ›More code
Other software we are working on, and the analysis code behind our papers.