Maltcms Files

Maui 1.0 Beta2 Release Notes, May 18th 2012

The Modular Application Toolkit for Chromatography Mass Spectrometry User Interface project is a framework mainly for programmers and power-users for data preprocessing tasks, such as filtering, baseline correction, peak finding, alignment, and visualization of high-throughput data. It provides a visual frontend for manual inspection of results and raw data, database-driven identification of mass spectra and statistical features like Anova and PCA.

Please note: This is work in progress and as such may or may not work as expected in its current state. Furthermore, there is no documentation available yet. If you need further assistance, please contact the author at http://maltcms.sf.net/contact

Requirements:
 - Java Runtime Environment >1.6 (http://www.java.com/en/)
 - GNU R >2.14
 - Rserve (Please follow installation instructions at http://www.rforge.net/Rserve/files/)
 - The 3D-Views require a working setup of drivers for your graphics card that are compatible to OpenGL

Installation Instructions:
 - Download the installer appropriate for your Operating System and run it
 - Follow the on-screen instructions and install the application
 - Download the example data (1D and 2D GC-MS) from http://sourceforge.net/projects/maltcms/files/maltcms/example-data/
   and extract it to a location of your choice
Usage:
 - After successful installation, startup Maui and create a new project using the new Project wizard. 
 - Select the files from one of the subdirectories of the extracted sample data and continue with the wizard.
 - Define experimental groups (e.g. for the 1D dataset: groups MAN, SUC and GLU) and assign each sample to a group
 - On the final wizard page, you can optionally define an external normalization quantity for each sample
 - Finish the wizard and wait until the project is initialized and opened
 - To test the installation, go to Preferences => Rserve and Test your setup. On success, a plot for the Iris dataset will be shown. 
 - Browse the data by selecting multiple chromatograms and right-click to see possible options

Known Issues:
 - Currently only netcdf compatible files are supported (.cdf). In the final release there will be support for other formats like mzML as well.
 - In order to run and execute Maltcms pipelines you need to download and unzip Maltcms to a custom location and set the path to it in the preferences tab.
 - A complete user guide will be published along with the final version of Maui.
 - Some menu items do not have a final position in the menus. These are subject to change.