KropBot: Multiplayer Internet-controlled robot raspberry-pi
KropBot is a little multiplayer robot you can control over the internet. Co-operate with random internet strangers to drive around in circles and into walls. More
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
Multithreading PyQt applications with QThreadPool gui
A common problem when building GUI applications is "locking up" of the interface when attempting to perform long-running background tasks. In this tutorial I'll cover one of the simplest way to achieve concurrent execution in PyQt. More
Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons
Because of the low stoichiometry of protein phosphorylation, targeted enrichment prior to LC–MS/MS analysis is still essential. The trend in phosphoproteome analysis is shifting toward an increasing number of biological replicates per experiment, ideally starting from very low sample amounts, placing new demands on enrichment protocols to make ... 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
Differential proteomics reveals the hallmarks of seed development in common bean (Phaseolus vulgaris L.)
Common bean (Phaseolus vulgaris L.) is one of the most consumed staple foods worldwide. Little is known about the molecular mechanisms controlling seed development. This study aims to comprehensively describe proteome dynamics during seed development of common bean. A high-throughput gel-free proteomics approach (LC–MS/MS) was conducted on seeds ... 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
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 ./developer_release_linux_python3.sh 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
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
Gremlins in the Machine: Creating custom tools for the Pathomx data analysis platform data-science
Pathomx is a workflow-based data analysis tool built on IPython. It began as a metabolomic-analysis toolkit, but has extended to support general data analysis workflows. It aims to be simple to use for non-experts while powerful enough for complex analysis tasks. Key to both of these goals is the ability ... 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