UK Public Sector Code by Organisation

ODE modelling in Python

Animal welfare assessment grid

Infrastructure for UKHSA data dashboard

UKHSA organisation standards

Front end for UKHSA data dashboard

Public API and backend services for the UKHSA data dashboard

UKHSA API design guidelines.

Exploring how to quickly and easily design/prototype/deploy high quality digital forms for UK Gov. Based on the excellent work by DEFRA. Currently maintained by [email protected] at Caution Your Blast and a community collaboration between FCDO, HO, GDS, DfE, DIT, Version 1

Epidemiological Data Visualisation

One-function R package for adding a y-axis break symbol to a ggplot object

Removal of reference sequence data from metagenomic datasets

Terraform module providing standard alarms that can be deployed to services. Repo managed by devops-github-repos

Implementation and operational documentation for the relay and central Lambda components for alerting. Repo managed by devops-github-repos

Data sync API for the Active 10 service. Repo managed by devops-github-repos

An application for NCBI taxonomy wrangling

intreeactive is a tool to create a single, portable interactive phylogeny using Python and a handful of libraries, with no need for other software or online tools.

This repository contains the R scripts, Stan scripts and Excel data sheets used in the publication "Robustly Quantifying Uncertainty in International Avian Influenza A(H5N1) Infection Fatality Ratios" by Gada et al. (2026).

Repo containing Github Reusable Workflows. Repo managed by devops-github-repos

UKHSA Conference Website 2023

Collection of reusable workflows used to build, test and deploy applications. Repo managed by devops-github-repos

ClasPar: the friendly classification parser that parses, filters and publishes analysis tables using various microbial classifier results. This tool is specifically developed for use in mSCAPE (Orange Box).

Profiler: assign profiles to classified taxa. For use in the Orange Box.

A repository containing helper functions to interact with onyx analysis functionality.

UKHSA Cloud Engineering Standards

Template for standards documentation repositories

UKHSA Standards for Quality Assurance Testing

UKHSA Ways of Working Standards

UKHSA development technology radar

Development standards for engineering teams

Static site containing OHID Technical Guidance for OHID Mobile Apps. Repo managed by devops-github-repos

Plotting Library

Back end application for processing requests and results for lab tests

TICLR is a Timeline for Infection Clusters tool.

Provides in-app content (e.g., articles) for the Active 10 mobile app. Written using Django framework. Repo managed by devops-github-repos

mSCAPE kubernetes orchestration module for downstream pathogen pipelines

A fork of taxaplease using the PlusPF inspect.txt file

Pipeline to analyse clinical metagenomic samples

testing the use of git-repo-filter

Nextflow pipeline for characterisation of Streptococcus pneumoniae in metagenomic samples

Nextflow workflow for mSCAPE sample processing through the Orange Box.

A script that generates a HTML report with synteny plots, given CLIMB IDs as input

Slurm Exporter is a Prometheus exporter designed to scrape and expose a comprehensive range of performance and scheduling metrics from Slurm-managed clusters. It supports both CPU and GPU resource accounting, node and partition state monitoring, job tracking, and scheduler statistics.

Template repository containing key files required for mSCAPE projects

Fork of PneumoKITy - Fast sensitive Pneumococcal Capsular Serotype screening from WGS data

References for HCID check competitive mapping

Frontend component of the DevOps example project. Repo managed by devops-github-repos

Repo containing reusable Github Actions. Repo managed by devops-github-repos

Evaluation code for the PubHealthBench benchmark.

Container image used to run CI pipelines. Repo managed by devops-github-repos

Public mirror of the UKPID Backend application currently in development by Juicy Media.

OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker, plus shared extension packages

Send POST request to trigger a webhook with GitHub Actions.