python

Can I use setup.py to pack an app that requires PyQt5? 19.05.2016

Can I require PyQt5 via setup.py? In a word yes, as long as you restrict your support to PyQt5 and Python3. The requirements specified in setup.py are typically provided by requesting packages from the Python Package Index (PyPi). Until recently these packages were source only, meaning that an ...


How to know the enabled features of a matplotlib installation? 29.04.2016

The optional dependency output you see when installing matplotlib is generated by a set of environment-testers defined in setupext.py. There is a list of these, in the order they are displayed, in setup.py: mpl_packages = [ 'Building Matplotlib', setupext.Matplotlib(), setupext.Python(), setupext.Platform(), 'Required dependencies and extensions', setupext.Numpy ...


Why are numpy calculations not affected by the global interpreter lock? 07.04.2016

Many numpy calculations are unaffected by the GIL, but not all. While in code that does not require the Python interpreter (e.g. C libraries) it is possible to specifically release the GIL - allowing other code that depends on the interpreter to continue running. In the Numpy C codebase the ...


How to create a HTML-dialog window in Python with Internet Explorer control? 01.04.2016

You can embed a Internet Explorer window within a Python GUI application by using the wxWidgets WebView component (via wxPython). Unlike e.g. Qt that includes a standardised browser component across all platforms, wxWidgets uses the native browser on the host platform by default. You can also force IE (ignoring ...



Why do Ipython cells stop executing? 06.01.2016

The asterisk next to a cell [*] indicates that the cell is currently executing. While IPython provides each notebook with it’s own kernel, there is only one kernel per notebook. When that kernel is busy executing code (either a cell, or a series of cells) it cannot accept or run ...


Fail during installation of Pillow (Python module) in Linux 06.01.2016

There is a bug reported for Pillow here, which indicates that libjpeg and zlib are now required as of Pillow 3.0.0. The installation instructions for Pillow on Linux give advice of how to install these packages. Note that not all of the following packages may be missing on ...


Partial Least Squares Discriminant Analysis (PLS-DA) 18.10.2015

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 ...


1D 1H NMR data processing 17.10.2015

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 ...



Wooey

Wooey

How do I open an image from the internet in PIL? 29.03.2015

This pull-request adds support for stream-handling native to Pillow (the friendly PIL fork) and should be available from version 2.8.0. This allows the simpler opening remote files with urllib: from PIL import Image import urllib2 Image.open(urllib2.urlopen(url)) …or using requests: from PIL import Image import ...


Live Demo - Wooey: Web UIs for Python scripts 24.03.2015

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 ...


Pathomx Linux Developer Release 04.01.2015

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 ...



Getting Started with Pathomx 08.12.2014

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 ...


PyQtConfig

PyQtConfig


Pathomx v3.0.2 released 26.10.2014

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.


Pathomx v3.0.0 Release Candidate 2 07.10.2014

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!


Pathomx v3.0.0alpha4 for Mac 15.07.2014

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.


PyQt5 support in Matplotlib 27.06.2014

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.



Automatic phase correction of NMR spectra 01.06.2014

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


NMRLab 1D NMR processing (MATLAB) 28.05.2014

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


Snippets (MATLAB) 28.05.2014

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


MetaboHunter (API) 25.05.2014

MetaboHunter (API)

MetaboHunter is a Python module for accessing the MetaboHunter web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra.


MetaboHunter 1D NMR Identification (Python Interface) Demo 25.05.2014

MetaboHunter is a web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra. Identification is performed in comparison to two publicly available databases (HMDB, MMCD) of NMR standard measurements. More information about the algorithm is available in the published paper: Tulpan, D., Leger, S., Belliveau, L., Culf, A., Cuperlovic-Culf, M. (2011). MetaboHunter: semi-automatic identification of 1H-NMR metabolite spectra in complex mixtures


BioCyc (API) 24.05.2014

BioCyc (API)

BioCyc is a Python interface to the BioCyc Web API. Acting as a wrapper it queries the database and then presents the XML returned in a pythonic object-based interface. Support for IPython views is included offering nice summary tables of object attributes.


BioCyc Interface Demo 24.05.2014

This notebook is a quick demo of a BioCyc Web API I’ve released for Python. While incomplete the API offers access to most basic attributes for metabolites, proteins, reactions, pathways and organisms in the database. The Python interface comes with an disk-based caching mechanism under ~/.biocyc that greatly reduces the delay (and load) for BioCyc servers.



QtIPy

QtIPy

mplstyler



Pathomx does MATLAB, R, Python 19.02.2014

The development version of Pathomx now supports custom scripting in Python, MATLAB and R. Integration with existing omics workflows is a key goal of Pathomx, and to do this requires interoperability with other platforms. In the upcoming release you’ll now get access to custom scripting in MATLAB, R or ...


Pathomx (née MetaPath) v2.2.0 released 07.02.2014

MetaPath is now named Pathomx, reflecting the focus on analysis of multi-omics data within pathway contexts. Pathomx v2.2.0 has also been released for both Windows and MacOS X.


MetaPath is now Pathomx 04.02.2014

MetaPath has now been renamed Pathomx. The name change was neccessary due to a name clash with another piece of published bioinformatics software, but it also better reflects the focus on analysis of multi-omics data in a pathway context.


MetaPath v2: Visual analysis for metabolomics [Released] 13.01.2014

MetaPath v2.0.0 has been released today! This latest version features a new visual editor for construction fo analysis workflows, new analysis plugins, graphing powered by Matplotlib and all sorts of other goodness. Downloads are available for Windows and MacOS X.


Pathomx: Analysis of public GEO datasets 09.01.2014

This short demo shows analysis of a publically available GEO dataset using Pathomx, with a workflow build using the new visual editor (available in the next release).


MetaPath v1.0.0 released 17.12.2013

MetaPath v1.0.0 has been released today for both Windows and MacOS X. In addition, MetaPath now has its own website for updates, demos, plugins and more.


MetaPath v0.9.9-beta released 29.11.2013

An up-to-date build of MetaPath for Mac OS X is available for download today. This is the first public build supporting the interactive workflow, automated processing, NMR spectra processing, gene expression analysis, PCA, PLS-DA, and the rest.


NCBI Gene Expression Omnibus (GEO) support added to MetaPath 18.11.2013

The NCBI Gene Expression Omnibus (GEO) is ‘is a public functional genomics data repository supporting MIAME-compliant data submissions.’ In other words, its a online database of freely available experimental gene-expression data. Quite useful. To make this resource available to users of MetaPath I’ve today released a simple GEO ...


Pathomx: Example Analysis 13.11.2013

Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service. The video shows an example analysis from processed data through ...



Icoshift

Icoshift

MetaPath v0.7.0 Released 03.07.2013

An update has been released today for MetaPath, a metabolic pathway visualisation and analysis tool. It is available via PyPi and github. A Mac .app bundle is also available.


MetaPath v0.6.0 Released 20.06.2013

An update has been released today for MetaPath, a metabolic pathway visualisation and analysis tool. It is available via PyPi and github. A Mac .app bundle is also available.


cx_Freeze and PySide on Mac 18.04.2013

I’d had success using py2app for building Mac binaries for distribution but wanted to give cx_Freeze a go since it’s cross platform - allowing builds for Windows, Linux, and more. Unfortunately, attempting to build using cx_Freeze was resulting in errors: libpyside-python2.7.1.1.dylib: No such file or ...



Pelicans on Webfaction 07.04.2013

As mentioned in the previous post, I recently migrated this site over to the very clever Pelican. Setting it up was relatively straightforward using a combination of the official docs, this post and linked github repo from Dominic Rodger. That said, there were a few things that I stumbled at and non-obvious decisions that I’ve documented below.