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
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 )
java ec.Evolve -file ./example.params
MAGMA Project Page
Robert M. Hubley -