Downloads/Software/Databases available at this centre.
Most of this software uses Java WebStart as a delivery mechanism. Some of the software has been packaged with a windows Installer. And there are equivalent Application Packages for Mac here
If you would prefer a Windows Installer/Mac Application for some of the software but can't find it here or if - heaven forbid! - you find a bug in any of the software then just send us a email at ian.castleden [at] uwa.edu.au.
"Debugging is twice as hard as writing the code in the first place. Therefore, if you write the code as cleverly as possible, you are, by definition, not smart enough to debug it." - Brian W. Kernighan
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GC/MS based metabolomics has been used for many aspects of biological studies, but data processing has been problematic due to the frame shifting among chromatograms. We developed a web based program using the jython scripting language to process GC/MS metabolomics data. This program, IDAlgin, can align metabolite peaks by their identifications, thus overcome retention time shifting caused misalignment. This program is useful for both targeted and non-targeted metabolite profiling analysis. GC/MS data is first processed using AMDIS (Automated mass spectral deconvolution and identification system) for deconvolution and identification with existing or custom made libraries. The peak area or integrated signal of each metabolite from all chromatograms identified by AMDIS is then aligned regardless of retention time. The identification of metabolites can be precisely controlled by using AMDIS algorithm incorporating retention index in the deconvolution process. Unknown metabolites are included in the library by assigning them defined identifiers. Alignment quality is controlled by user defined parameters including signal to noise ratio (S/N), difference of retention time or difference of retention index. Alignment can utilize either TIC or integrated signal of metabolite aligning to metabolite name, ID or CAS number. The aligned result can be normalized to a defined internal standard or any metabolite presented in the analysis and can be exported as an Excel spreadsheet for chemometric analysis. This program has potential to be used as a tool to perform large online metabolomics data analysis.
More Info...
mz2mgfmz2mgf is a small program to convert mzData files to MGF (current version is 1.3.5). NEW! will convert BioTools xml files too! Application notes: mz2mgf was choking on our 1.5Gb mzData files so we junked the internally provided java XML parser in favour of an XML PullParser kindly written by Aleksander Slominski (see also here). It's much faster and does not choke on even 3Gb files... oh yes! mz2tsv
A variation for Josh: Convert MS mzxml files to simple "  This work is licenced under a Creative Commons Licence. |
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AtmatchAtmatch matches At numbers from Mascot with peptide fragments from GeneSpring.This is currently in beta development. This work is licenced under a Creative Commons Licence. |
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Uniform Sampling of Metabolic Reaction RatesThis is currently in *alpha* development. You'll need one of these metabolism reaction files as input to the program:
CHECK THAT THE BUILD NUMBER (top right corner) IS 0.8.16
A plugin ( This work is licenced under a Creative Commons Licence. |
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Coming soon...
ce4csb Bandicoot
RatioDiffRatioDiff computes the same p-values as this statistics page. More info is here. This work is licenced under a Creative Commons Licence. |
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dat2mgf
A small enhancement to Mascot to convert the search files back into Mascot Generic Format.
Download Zip file. Instructions are in theREADME file.
BrukerBuster
A small program to copy a directory tree generated by Bruker into a layout more suitable for reading by... Windows installer: download(Windows only - and you'll still need a Java virtual machine 1.5 or better installed). Web Start FAQ
This work is licenced under a Creative Commons Licence.
Web Equations
Insert equations into your webpages simply and easily! Simple step-by-step instructions on how to add an equation to your website (no downloads required... and you can even be javascript free!) Test your LaTeX skills hereCentre Researcher Sota Fujii part of Rhizanthella Team
Western Australia's Mysterious Underground Orchid Revealed
Rhizanthella gardneri is a cute, quirky and critically endangered orchid that lives all its life underground. It even blooms underground, making it virtually unique amongst plants. Last year, using radioactive tracers, scientists at The University of Western Australia showed that the orchid gets all its nutrients by parasitising fungi associated with the roots of broom bush, a woody shrub of the WA outback. Now, with less than 50 individuals left in the wild, Plant Energy Biology scientists have made a timely and remarkable discovery about its genome.
Read our story in
Link to the UWA media release
Publication:
Centre Researcher Sota Fujii awarded by the JSPS 独立行政法人日本学術振興会
Sota Fujii Awarded:
Plant Energy Biology Research Associate Dr Sota Fujii is off to a terrific start in 2011. Following on from his recent publication (Full Text) in the Proceedings of the National Academy of Sciences (PNAS), he has won both a Japanese research award and a fellowship to continue his valuable work in plant genetics.
Dr Fujii was selected from 300 agricultural scientists for the position of "Super Postdoctoral Fellow" by the Japan Society for the Promotion of Science (JSPS). The fellowship is funded by the Japanese Ministry of Education, Science, Sports and Culture.
I will do my best to use this precious money from Japanese Taxpayers to contribute to the advancement of life science at global level, like my hero Dr. Barbara McClintock,
pledged Dr Fujii.Dr Fujii's research on restorer to fertility genes in plants has also earned him a Inoue Research Award for Young Scientists. This prize for early career scientists highlights the great work being done by this promising young researcher.
