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Web pyms: An interactive web based gas chromatography - mass spectrometry data processing tool

Dayalan, S., O'Callaghan, S., Power, B., Macgregor, A., Wellington, C., Szabo, T., Hunter, A., Bellgard, M., de Souza, D., Tull, D., Roessner, U., Bacic, A., McConville, M.J. and Likic, V. (2011) Web pyms: An interactive web based gas chromatography - mass spectrometry data processing tool. In: Seventh International Conference of the Metabolomics Society, 27 - 30 June, Cairns, Qld, Australia.


Web PyMS is a web based interactive tool for processing gas chromatography –mass spectrometry (GC-MS) data. Web PyMS allows the processing of complete pipeline of GC-MS data, starting from reading of instrument generated files in standard data formats to creating data matrices ready to be analysed through statistical methods. Web PyMS provides access to reading ANDI-MS/NetCDF and JCAMP-DX files, noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration and peak alignment through dynamic programming. Web PyMS is composed of two technologies -YABI for user interface, workflow construction, and compute pipelining, and the PyMS library for data processing. YABI is a web-facing workflow and high-performance computing interface developed by the Centre for Comparative Genomics, with Web PyMS customisations by the Australian Bioinformatics Facility. PyMS is a suite of data processing tools, and is implemented in Python. Future work on Web PyMS will include (a) the ability of users to interactively query data at the various stages of the pipeline to assist the user to make better informed decisions in setting values to the different parameters of the various modules and (b) the ability to perform targeted analysis of GC-MS data. PyMS is built as an open-source solution under the GPL licence and is available at

Publication Type: Conference Item
Murdoch Affiliation: Centre for Comparative Genomics
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