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ORNASEQ: Ontology for RNA sequencing.

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Documentation outlining our RNA-Seq schema.

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PIVOT released (replacing IDV); an extensive R-based GUI for the visualization and analysis of RNASeq data.

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PESS has been released and is available for download with source code.

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Download Oracle data dump: Oracle Dump (29 GB)

The dump was successfully loaded into the following Oracle database:
   Oracle Database 11g Enterprise Edition Release - 64bit Production
   With the Partitioning, OLAP, Data Mining and Real Application Testing options


  • The data dump needs to be extracted from the tar file. This will create a directory called "oracle.dump". The data files (*.dmp) are compressed with bzip2. You must uncompress them prior to loading them into Oracle, using bunzip2. The uncompressed data files will take about 2 TB of disk space. You will need another 2 TB of disk space for the data within the Oracle database. Once loaded into Orace, the oracle.dump directory can be deleted.
  • [oracle@o1 ~]$ tar xvf oracle.dump.tar; cd oracle.dump; bunzip2 *.bz2


  • Set DB_CREATE_FILE_DEST, if necessary, specifying where data will go
  • SQL> alter system set DB_CREATE_FILE_DEST = '{location for Oracle managed datafiles}' scope=both;
  • See the result with:
  • SQL> show parameters db_create;
  • Load the create_cipress_tablespace.sql file to create the CIPRES tablespaces. Since the sizes were not specified, they are 100MB each, autoextend on, no max limit.
  • SQL> start create_cipress_tablespace;
  • Specify the location of the data dump
  • SQL> create directory imp_dir as '{directory with data dump}';
  • Load READONLY dataset
  • oracle@o1 ~]$ impdp DIRECTORY=imp_dir DUMPFILE=export_srb3_READONLY_CIPRES_12-01-2009_22935.dmp LOGFILE=import-readonly.log
  • Load CIPRES dataset
  • oracle@o1 ~]$ impdp DIRECTORY=imp_dir DUMPFILE=export_srb3_cipres_11-18-2009_15511_1_01.dmp, export_srb3_cipres_11-18-2009_15511_2_01.dmp, export_srb3_cipres_11-18-2009_15511_3_01.dmp, export_srb3_cipres_11-18-2009_15511_4_01.dmp, export_srb3_cipres_11-18-2009_15511_5_01.dmp, export_srb3_cipres_11-18-2009_15511_6_01.dmp, export_srb3_cipres_11-18-2009_15511_7_01.dmp, export_srb3_cipres_11-18-2009_15511_8_01.dmp, export_srb3_cipres_11-18-2009_15511_9_01.dmp, export_srb3_cipres_11-18-2009_15511_10_01.dmp LOGFILE=import-cipres.log

Web Access

It is not necessary to use a web proxy to access the Oracle database. However if you wish to use a web proxy, one has been included below ("DatabaseProxy.php"). To open an Oracle database connection using a web proxy, include the proxy's URL as the database server (eg 'http://{your website}/DatabaseProxy.php'), with a blank username and password. From the Crimson command line, this can be done using the following commands:
      >>> setDBType("oracle")
      >>> openDatabase("", "", "http://{your website}/DatabaseProxy.php")
The following web proxy only allows for read-only access to the CIPRES database.

Web Proxy For Oracle Database (DatabaseProxy.php)

     * Created on March 28, 2006 Henry Jaime
     * Database proxy to return a list of specific values
     * NOTE: must modify results to return specific columns
    $OracleSID = '';
    $OracleReadOnlyUserID = '';
    $OracleReadOnlyPasswd = '';
    define('DB_SID', $OracleSID);
    $DB_USER = trim($_POST['user']);
    $DB_PASS = $_POST['passwd'];
    // if 'user' is empty, then use defaults above
    if (empty($DB_USER)) {
      $DB_USER = $OralceReadOnlyUserID;
      $DB_PASS = $OracleReadOnlyPasswd;
    $iDBConn = OCILogon($DB_USER, $DB_PASS, DB_SID) or die ("Could not connect.");
    executeSql("alter session set current_schema=cipres");
    //the sql statement must be the first statement to avoid compound statement sql injection
    define('DB_SQL', $_POST['sql']);
    list($sql, $other) = split(";", DB_SQL);
    //only execute SELECT statements; optionally you can limit to specific tables for insert/delete
    if (strpos(strtoupper($sql), 'SELECT') !== false) {
      //filter out malicious code here...
      //allow alpanumeric, space, - = * .
      $sql = preg_replace("/[^= .*a-zA-Z0-9'(,)_-]+/", "", $sql);
    function executeSql($sql) {
      global $iDBConn, $iStatement;
      $iStatement = @OCIParse($iDBConn, $sql);
      @OCIExecute($iStatement, OCI_DEFAULT);
      $arrError = OCIError($iStatement);
      if ($arrError['code']) {
    	print $arrError['message'];
      $nrows = ocifetchstatement($iStatement, $results,0,-1,OCI_FETCHSTATEMENT_BY_ROW);
      // this will return one row of values per line with either
      // column delimited by ';'.  It is assumed that the calling
      // function knows the order of the columns and the column IDs.
      foreach (array_values($results) as $data) {
    	while (list($key,$value) = each($data)) { echo "$value;"; }
    	echo "\n";
    	while (OCIFetchInto($iStatement, &$results, OCI_ASSOC+OCI_RETURN_NULLS))
          // returns ';' delimited string containing all keys and all values
          echo array_reduce(array_keys($results), "returnArray") . "\n";
    	  echo array_reduce($results, "returnArray") . "\n";
    // create a ';' delimited string containing all elements of the array
    function returnArray($val0, $val1) { return $val0 . ";" . $val1; }

HTML Test for Web Proxy

The following html code can be used to test the php proxy listed above.

    <FORM method=post action="DatabaseProxy.php">
    <INPUT ID=sql NAME=sql TYPE=TEXT SIZE=50 VALUE="select sysdate from dual;select again">
    <INPUT ID=user NAME=user TYPE=TEXT SIZE=25 VALUE=''>
    <INPUT ID=passwd NAME=passwd TYPE=PASSWORD SIZE=25 VALUE=''>