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

Epidemiological Data Visualisation

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

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

mSCAPE kubernetes orchestration module for downstream pathogen pipelines

An application for NCBI taxonomy wrangling

Removal of reference sequence data from metagenomic datasets

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

Nextflow workflow for mSCAPE sample processing through the Orange Box.

Nextflow pipeline for characterisation of Streptococcus pneumoniae in metagenomic samples

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

TICLR is a Timeline for Infection Clusters tool.

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.

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

UKHSA Conference Website 2023

A metagenomics report detailing the per sample QC metrics, species contents, HCID presence and hopefully fungal contents. Designed for mSCAPE.

UKHSA Cloud Engineering Standards

Template for standards documentation repositories

UKHSA Standards for Quality Assurance Testing

Development standards for engineering teams

UKHSA Ways of Working Standards

UKHSA development technology radar

A tool that generates basic statistics given a fastq.gz as input

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

Pipeline to analyse clinical metagenomic samples

A reverse proxy designed for Prometheus exporters

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

Dockerfile and SPIs for the Better Health Auth Keycloak service. Repo managed by devops-github-repos

Static site containing OHID Technical Guidance for OHID Mobile Apps. 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).

testing the use of git-repo-filter

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

Plotting Library

Back end application for processing requests and results for lab tests

A fork of taxaplease using the PlusPF inspect.txt file

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.

Application to confirm the presence of species specific loci in fastq data

A nextflow pipeline wrapping a tool that generates basic statistics given a fastq.gz as input

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.