The following procedure has been tested on an RedHat Linux system.  
Please make necessary modifications for your platform.

PART I: Data Load

NOTE: Order of execution of these commands is important. 

  (a) Make sure you that Oracle is installed and you are able to execute 
      SQL*Plus and SQL*Loader. 

  shell> which sqlplus sqlldr
   /opt/oracle/product/10.2.0/db_1/bin/sqlplus
   /opt/oracle/product/10.2.0/db_1/bin/sqlldr

  (b) Create Oracle user (e.g. snp), and execute SNP_Tables_102507.sql 
      and SNP_Package_102507.sql to create the user's schema.
    
   shell> cd sql
   shell> sqlplus snp/pass@SID
   SQL> @SNP_Tables_102507.sql
   SQL> @SNP_Package_102507.sql
   SQL> exit;
   shell> cd ..

  (c) Load data 

  shell> cd ctl
  shell> sqlldr userid=snp/pass@SID control=population.ctl
  shell> sqlldr userid=snp/pass@SID control=technology.ctl
  shell> sqlldr userid=snp/pass@SID control=omim.ctl
  shell> sqlldr userid=snp/pass@SID control=snp_omim_map.ctl
  shell> sqlldr userid=snp/pass@SID control=single_omim_map.ctl
  shell> sqlldr userid=snp/pass@SID control=double_omim_map.ctl

  (d) Check that the data was loaded properly.  Log on to the database
      and check the number of rows in each of 6 tables below. For example:

  shell> sqlplus snp/pass@SID
  SQL> select count(*) from Population;

  Commands and table names are NOT case-sensitive. 
  Row counts should be as follows:

  1) Population 3
  2) Technology 6
  3) OMIM 18003
  4) SNP_OMIM_Map 187
  5) Single_OMIM_Map 905
  6) Double_OMIM_Map 396
      
  If there are fewer rows in any of the tables, check the file
  data/<Table Name>.log for any errors.

PART II: Using the System 

We provide a Java program that demonstrates how an individual's 
genetic data may be loaded into the database, and how to invoke
MutaGeneSys on this data to generate disease susceptibility hypotheses.
You may choose to write your own load mechanisms, this program is just
and example.

The program accepts the following arguments.  Please 
see http://www.cs.columbia.edu/~jds1/MutaGeneSys/ for
format information.

db connect string -- user/pass@database, e.g. snp/snp@SID
input_file -- name of a file that stores snp ids and alleles
output_file -- file into which MutaGeneSys will write its output
population -- can be one of 'any', 'CEU', 'JPT+CHB', 'YRI'
technology -- genotyping technology, can be one of: 'any', 'Illumina', 'Affymetrix'
coefficient -- coefficient of determination, a number between 0 and 1
 
In order to execute the program, you must have an JDBC library in your
classpath, or supply the path to this library to java when you invoke the
program.  JDBC drivers are available for download from Orace:
http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/index.html
They should already be installed in $ORACLE_HOME/jdbc/lib.

For example:
java MutaGeneSys snp/pass@SID snpSample.txt snpSample.out JPT+CHB any 0.3