Pathomx is a workflow-based analysis tool featuring a NMR toolkit allowing rapid, reproducible and adaptable analysis of metabolomics data. It was developed as part of my PhD in metabolomics of inflammatory diseases, where I found a need for a tool to enable higher-throughput reproducible analysis and aid interpretation of findings in biological context.
Workflows as constructed by a drag-drop interface from the toolkit. Each tool can be independently configured, and outputs are recalculated on the fly. Input is supported from pre-processed or raw Bruker NMR (other formats can be added on request), spectra can be processed for baseline correction, alignment (including icoshift) and normalisation (TSA, PQN). Peak assignments can be performed using online services or manual peak-match files (e.g. exported from Chenomx) and identified metabolites mapped to database entities using BioCyc, HMDB or other identifiers. Pathomx includes a pathway mining and automated visualisation tool to visualised most-regulated pathways, as well as support for more traditional views using GPML/WikiPathways or KEGG pathways.
Pathomx is fully extendible with the ability to create custom tools to perform new tasks, and allows manual editing of tool scripts to customise processing if needed. Workflows can be saved, shared and re-used, and all outputs/figures can be saved as high-resolution TIF for publication.
If you have any questions, comments or suggestions please let me know!
MA Fitzpatrick et al. Pathomx: an interactive workflow-based tool for the analysis of metabolomic data BMC Bioinformatics 2014 doi:10.1186/s12859-014-0396-9