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!
A new developer release of Pathomx (v3.0.0a) is out today via Github and PyPi. This release brings an IPython backend and support for IPython-notebook based plugins.
Today I’ve released Python module BioCyc that provides an 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.
Today sees the release of a little utility: QtIPy: The data automator! a simple GUI-based run-automator for IPython notebooks. It allows you to attach triggers to files, folders or timers to automatically run notebooks.
I’ve just released a simple API for managing matplotlib line and marker styles for plots. It’s called mplstyler and you can get it from Github or PyPi. This code is based on the style manager in Pathomx, extracted for more general use.
Below is a short snippet to implement a color-picker attached to a button in Qt. Clicking on the button pops up a dialog (native) to select a color. The color is shown by the color of the button face. A right-click option is included to allow clearing of the color ...
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 ...
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Convert Accuri .c6 files to .fcs standard
Python interface to the BioCyc Web API
A command-line/Python GPML to SVG pathway renderer
A Python implmentation of the Icoshift algorithm
An API for assigning consistent marker styles to Matplotlib plots.
Freely available lab protocols under a CC license
A Python interface to the MetaboHunter 1D NMR metabolite identification service
Algorithmically score and select pathways/reactions from compound, protein or gene data