TIGR MeV 3.0 Release

Braisted, John braisted at tigr.org
Mon Aug 9 04:11:41 EST 2004


The MeV software team is pleased to announce the release of MeV 3.0. 
This is a major release including many graphical and functional
improvements and many user requested features. 

The most significant new features include:

*  Analysis Saving; This option allows you to save the state of the 
   analysis to file so that analysis results can be accumulated over 
   several analysis sessions.  Reloading the analysis restores all 
   analysis results and automatically restores the loaded data set.

*  Analysis Scripting; The scripting option enables multiple algorithms 
   to run successively without user interaction between algorithms.  
   Branching of processing is supported to permit the results from one 
   algorithm to be used as input for additional algorithms.  Scripting  
   makes it convenient to share analysis techniques between you and your 
   colleagues working on a shared data set.

*  Improved Cluster Table Viewers; These new tables provide the ability 
   sort and search the element lists for annotation terms.  Subsets of 
   elements can be used to create custom clusters based on information
   in the table such as reported statistics or annotation.  The new tables
   also enable you to link to web resources related to the clustered genes. 


Four major analysis modules have been added: 

*  Expression Analysis Systematic Explorer (EASE); EASE is used to find 
   significant biological themes within expression based gene clusters.
   The MeV implementation can also be used to survey the input data for 
   represented biological themes which can be tracked during cluster analysis.

*  Two Factor ANOVA;  This module can be used to find genes that have significant
   effects across two independent variables (factors) and their interaction.

*  K-nearest neighbors classifier (KNNC); This supervised multi-class classifier
   is MeV's first classification module to produce multi-class partitions of the data.
   Many features are rolled into this module to permit filtering of input data to
   find the features that best partition data and there is a leave one out cross 
   validation option. 

*  Gene Distance Matrix (GDM); GDM is the first module to provide a basic similarity 
   matrix viewer in which the similarity of each element (gene or experiment) can 
   be easily assessed relative to any other gene in the input data set.  Sorting 
   on nearest neighbor and imposing cluster partitions on the view are two of the 
   many options in the GDM.

A full list of new features for 3.0 is in the MeV_3_0_release_notes.pdf in the 
'documentation' directory.  This folder also includes MeV_Manual_3_0.pdf that 
describes all of MeV's features and analysis modules. 

This version of MeV replaces all previous versions and we recommend upgrading as soon 
as possible.  Visit TM4 Software's MeV page, http://www.tigr.org/software/tm4/mev.html, 
select the appropriate download package, either with or without source code for
developers, and follow the prompts to download MeV 3.0. After unzipping the file, 
Windows users can hit the 'TMEV.bat' icon to start the program. A Mac OSX application 
bundle and a Linux/Unix command-line script are also in the download. 

**Please register on the TM4 website during download by supplying your email 
if you have not registered yet.  This private MeV user list is only used 2-3 times 
per year on average to notify users of MeV software releases.  Registration is optional 
but we strongly recommend registration since it will allow us to keep you informed 
about useful new features and releases.

Please forward any comments or questions to mev at tigr.org. 

Thank you, 

TM4 MeV Development Team

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