python

Scroll pHAT Tetris  raspberry-pi

The Scroll pHAT is a little 11x5 (55) white LED matrix pHAT (pi-HAT extension board) which you can control easily from a Raspberry Pi. In this project we’ll squeeze a tiny-yet-playable game of Tetris onto the original Scroll pHAT (HD coming soon). Continue reading



Create Simple GUI Applications with Python and Qt  gui

Create Simple GUI Applications with Python and Qt

Create Simple GUI Applications will show you how to use Python and Qt to do just that. This ebook was written to accompany the video tutorial course on Udemy, adding background and detail to the lectures, with more examples and reference documentation. However, it stands perfectly well alone as a ... Continue reading



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 ... Continue reading


Create Simple GUI Applications with Python and Qt  gui

Create Simple GUI Applications with Python and Qt

If you want to learn to build GUI applications with Python the learning curve is pretty steep. There is a lot you need to know just to get something to work. Many tutorials offer only screen casts and miss the simple concepts that actually matter. Like writing any code, successfully ... Continue reading


Wooey  web

Wooey

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 ... Continue reading


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 ... Continue reading


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 ... Continue reading


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 ... Continue reading



PyQtConfig

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. Continue reading


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 ... Continue reading


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. Continue reading


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! Continue reading





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 Continue reading


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 Continue reading


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