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 ...
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 ...
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 ...
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 ...
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) 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 ...
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 ...
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 ...
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 ...
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
PyQt5 support in Matplotlib 27.06.2014
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 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 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.
mplstyler StylesManager demo 24.05.2014
Pathomx v2.5.0 released 30.04.2014
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 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 v2.0.0 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
MetaPath v1.0.0 released 17.12.2013
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.
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 ...
MetaPath v0.7.0 Released 03.07.2013
MetaPath v0.6.0 Released 20.06.2013
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-python22.214.171.124.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.