bioinformatics

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



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




MetaboHunter (API)

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. Continue reading


BioCyc (API)

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. Continue reading


mplstyler

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. Continue reading




MetaPath is now Pathomx

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. Continue reading



Cytoscape v3.0.2 on Mac OS X  science

Cytoscape 3.0.2 was released on 1st August, a bugfix release for the 3.x series. However, there is a compatibility issue with the latest Java update from Apple resulting in Cytoscape hanging on startup. I’d followed advice found elsewhere to update to the latest Java version with ... Continue reading




gpml2svg

Gpml2svg, a command-line/Python API for rendering GPML (GenMAPP Pathway Markup Language) to SVG, has been released today via github and PyPi. Continue reading