metabolomics

Changes in urinary metabolomic profile during relapsing renal vasculitis.

Current biomarkers of renal disease in systemic vasculitis lack predictive value and are insensitive to early damage. To identify novel biomarkers of renal vasculitis flare, we analysed the longitudinal urinary metabolomic profile of a rat model of anti-neutrophil cytoplasmic antibody (ANCA) vasculitis. Wistar-Kyoto (WKY) rats were immunised with human myeloperoxidase ... More

Metabolomics in rheumatology

The omic with the potential to provide a holistic view of patients and their disease. Metabolomics studies have been reported for virtually all of the main rheumatologic diseases, although notably none yet for SSc [5]. Our own group has demonstrated the use of urinary metabolic fingerprint analysis to predict responses ... More

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 ... More

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 ... More

Getting Started with Pathomx  data-science

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 ... More

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. More

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! More

Pathomx v3.0.0alpha4 for Mac

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. More

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. More

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. More

Pathomx does MATLAB, R, Python

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 ... More

Pathomx (née MetaPath) v2.2.0 released

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. More

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. More

MetaPath v2: Visual analysis for metabolomics [Released]

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. More

MetaPath v1.0.0 released

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. More

MetaPath v0.9.9-beta released

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. More

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