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 iancas [at] cyllene.uwa.edu.au.
Go to IDAlign on the Web
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.
New! You can now have IDAlign on your computer
much
better for very large data sets, no need to be connected to the internet.
mz2mgfmz2mgf is a small program to convert mzData files to MGF (current version is 1.2.0) 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! mz2tsvA variation for Josh: . Convert MS mzxml files to simple "  This work is licenced under a Creative Commons Licence. |
|
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. |
|
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 0.8.10
A plugin ( This work is licenced under a Creative Commons Licence. |
| ||||
RatioDiffRatioDiff computes the same p-values as this statistics page. More info is here. This work is licenced under a Creative Commons Licence. |
|
dat2mgf
A small enhancement to Mascot to convert the search files back into Mascot Generic Format.
Download Zip file. Instructions are in theREADME file.
