Multiobjective Analyzer for Genetic Marker Acquisition

A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a col- lection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype.

MAGMA is a project which employ's a multiobjective evolutionary algorithm to solve this problem. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2.

Hubley R., Zitzler E., Siegel A.F., Roach J., Multiobjective
Genetic Marker Selection
, Parallel Problem Solving
from Nature 2002 PDF

This software uses ECJ8: A Java-based Evolutionary Computation and Genetic Programming Research System by Sean Luke. In addition MAGMA uses ECJ enhancements which perform the SPEA2 multiobjective evolutionary algorithm (currently included in the MAGMA distiribution). With ECJ version 9 the SPEA2 enhancments should be part of the distribution.

  • After downloading the EC package (listed above), you must set the java CLASSPATH. If you downloaded EC to /users/joe/tools/ec/ and MAGMA to /users/joe/tools/MAGMA-1.1/ then you would set your classpath as:

    setenv CLASSPATH /users/joe/tools:/users/joe/tools/MAGMA-1.1/MAGMA.jar

  • Edit the example.params file and set the parameters for your run. Particularly you should look at the parameters with the "#->" comments above them.
  • Create the snp data file ( currently called snpdata.txt in the example.params file )
  • Run MAGMA:

    java ec.Evolve -file ./example.params

    MAGMA Project Page

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    Robert M. Hubley - <>