Scroll pHAT Tetris  raspberry-pi

The Scroll pHAT is a little 11x5 (55) white LED matrix pHAT which you can control easily from a Raspberry Pi. In this project we'll squeeze a tiny-yet-playable game of Tetris onto the Scroll pHAT. More

Safari Sam  retro

Safari Sam is a platform game I developed for the Sam Coupé, sometime in 1994 — I didn't have the optional system clock for the Coupé so there are no timestamps on all except one file, but the copyright message says a year earlier — The game is a standard platformer ... More

Early T Cell Recognition of B Cells following Epstein-Barr Virus Infection: Identifying Potential Targets for Prophylactic Vaccination

Epstein-Barr virus, a B-lymphotropic herpesvirus, is the cause of infectious mononucleosis, has strong aetiologic links with several malignancies and has been implicated in certain autoimmune diseases. Efforts to develop a prophylactic vaccine to prevent or reduce EBV-associated disease have, to date, focused on the induction of neutralising antibody responses. However ... More

Changes in urinary metabolomic profile during relapsing renal vasculitis.

Current biomarkers of renal disease in systemic vasculitis lack predictive value and are insensitive to early damage. To identify novel biomarkers of renal vasculitis flare, we analysed the longitudinal urinary metabolomic profile of a rat model of anti-neutrophil cytoplasmic antibody (ANCA) vasculitis. Wistar-Kyoto (WKY) rats were immunised with human myeloperoxidase ... More

Partial Least Squares Discriminant Analysis (PLS-DA)  data-science

Partial least squares discriminant analysis (PLS-DA) is an adaptation of PLS regression methods to the problem of supervised1 clustering. It has seen extensive use in the analysis of multivariate datasets, such as that derived from NMR-based metabolomics. In this method the groups within the samples are already known (e ... More

1D 1H NMR data processing  science

1D 1H NMR is a common technique applied to metabolomic studies, being well suited to untargeted analysis of complex biofluids. It has been successfully applied to the classification and diagnosis of a number of diseases including [ref]. There are a number of important steps that must be applied prior ... More

Metabolomics in rheumatology

The omic with the potential to provide a holistic view of patients and their disease. Metabolomics studies have been reported for virtually all of the main rheumatologic diseases, although notably none yet for SSc [5]. Our own group has demonstrated the use of urinary metabolic fingerprint analysis to predict responses ... More

Wooey  web

Wooey is a simple web interface to run command line Python scripts. Think of it as an easy way to get your scripts up on the web for routine data analysis, file processing, or anything else. The project was inspired by how simply and powerfully sandman could expose users to ... More

Live Demo - Wooey: Web UIs for Python scripts

A new live demo of Wooey is now up and running with a few simple example scripts. Features: Web UIs for Python scripts generated automatically from argparse An automated background worker to run scripts and collect outputs Run Queue to schedule (and prioritise) jobs Automatic rendering of viewable outputs, downloadable ... More

Pathomx Linux Developer Release

A developer release of Pathomx (Python3) is now available. This release can be installed by using the ./ script from the cloned Github repository. This script installs all dependencies (via apt-get and pip) that are required for Pathomx to run. This developer release is an important first step to ... More

Pathomx: an interactive workflow-based tool for the analysis of metabolomic data

Background Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility. However, the development of robust methods for the analysis of metabolomic data is a work-in-progress. The tools that do exist are often not ... More

Getting Started with Pathomx  data-science

This is quick start-up guide for new users of Pathomx. Following it should give you everything that you need to know to start using Pathomx right away. Once you've been through the basics you might like to see some of the demos to see what Pathomx is capable of ... More


PyQtConfig: a simple API for handling, persisting and synchronising configuration within PyQt applications. This module was built initially as part of the Pathomx data analysis platform but spun out into a standalone module when it became clear it was quite useful. More

Pathomx v3.0.2 released

Pathomx v3.0.2 has been released for both Windows and MacOS X. This marks the first stable, bug-fixed release for the v3.0 line featuring the new IPython-kernel with cluster support for parallel processing of tools. More

Pathomx v3.0.0 Release Candidate 2

The final release candidate for Pathomx v3.0.0 is available for both Mac and Windows. This latest version features the new IPython backend providing parallel processing (via IPython ipcluster support), numerous bugfixes and improvements to the UI and figure outputs. While a development version it is considered stable enough for regular use. If you're a current user of Pathomx, please download and test with your own hardware and data, see how it holds up and then report any problems! More

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