python

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

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

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 ./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

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

Pathomx v3.0.0alpha4 for Mac

A development version of Pathomx v3.0.0-alpha4 is now available as a installable app for Mac. This latest version showcases the new IPython backend, with notebooks and reports. More

PyQt5 support in Matplotlib

My pull-request for matplotlib to add PyQt5 support has been accepted and merged, meaning PyQt5 support will be available in the upcoming v1.4.0 release of matplotlib. More

Automatic phase correction of NMR spectra  science

This notebook demonstrates automatic phase correction algorithms implemented for nmrglue. Two standard algorithms are implemented: ACME algorithm by Chen Li et al. Journal of Magnetic Resonance 158 (2002) 164-168 Naive peak minima minimisation The outputs for the two algorithms are shown below. Automatic phase correction can be used through the addition of an autops More

NMRLab 1D NMR processing (MATLAB)  science

This notebook uses a subset of the available processing features in NMRLab (+Metabolab) to process 1D NMR spectra. The output is saved as a CSV file that can be imported into pandas, PLS_Toolbox or any other package for subsequent analysis. To use this workbook you will need an installation of MATLAB More

Snippets (MATLAB)  data-science

This notebook contains snippets of code that are useful when working with MATLAB in IPython Notebooks. Displaying images from MATLAB¶Passing variables into cells using the %%matlab magic requires h5py which is tricky to install. If you only need to pass in simple variables (strings) you can instead pass it in using Python string formatting and mlab.run_code More

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