Biodefense Bioinformatics Blog

Thursday, June 23, 2005

MDR 0.4 Released

The Dartmouth Computational Genetics Laboratory is pleased to announce the release of version 0.4 of our open-source multifactor dimensionality reduction (MDR) software package.

MDR 0.4 has been posted to sourceforge.net which can be accessed from here.

New features in MDR 0.4 include:

1) Threading to take advantage of multi-processor computers. MDR will now automatically detect if your computer has multiple processors and will parallelize the algorithm accordingly. Thus, if you have two processors with threading turned on, MDR will run 4x faster.

2) Batch/command line mode to allow MDR to be run from scripts. This new feature allows MDR to be run from the command line with a Perl script, for example. This makes it possible to run MDR on a grid or parallel computer for simulation studies.

3) Visualization of the fitness landscape. This new feature plots the training accuracy for every model evaluated by MDR. Line plots or histograms can be selected. A zoom feature permits 'drilling down' on a particular region of the landscape. At a fine resolution, mousing over points reveals the model and the training accuracy of that model.

4) Odds ratios. This statistic and its 95% confidence interval have been added to the MDR output to facilitate an epidemiological interpretation of MDR models.

The next major additions to the MDR software will include computation search or wrapper algorithms for variable or attribute selection when the number of combinations to be evaluated is not computationally feasible. Random, greedy, and stochastic search algorithms will be added. These are necessary for genome-wide association studies. This feature will be available later in the summer.

Is there something you would like to see added to MDR? Request it here.

Note that MDR will be in beta testing for another 2-3 months. Please send us your feedback so we can roll out a polished MDR 1.0 later this summer.

The MDR project is funded by NIH grant AI59694.

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