genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 45)

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[Genex-cvs-commit] genex-server/Genex/ContactOwner .cvsignore,1.2,NONE

From: <jas...@us...> - 2002-10-20 13:30:41

Update of /cvsroot/genex/genex-server/Genex/ContactOwner
In directory usw-pr-cvs1:/tmp/cvs-serv5580/Genex/ContactOwner

Removed Files:
	.cvsignore 
Log Message:
cruft


--- .cvsignore DELETED ---

[Genex-cvs-commit] genex-server/Genex/ArrayMeasurement .cvsignore,1.2,NONE Makefile.PL,1.4,NONE

From: <jas...@us...> - 2002-10-20 13:29:40

Update of /cvsroot/genex/genex-server/Genex/ArrayMeasurement
In directory usw-pr-cvs1:/tmp/cvs-serv4890/Genex/ArrayMeasurement

Removed Files:
	.cvsignore Makefile.PL 
Log Message:
cruft


--- .cvsignore DELETED ---

--- Makefile.PL DELETED ---

[Genex-cvs-commit] genex-server/Genex/ArrayLayout .cvsignore,1.2,NONE

From: <jas...@us...> - 2002-10-20 13:29:40

Update of /cvsroot/genex/genex-server/Genex/ArrayLayout
In directory usw-pr-cvs1:/tmp/cvs-serv4890/Genex/ArrayLayout

Removed Files:
	.cvsignore 
Log Message:
cruft


--- .cvsignore DELETED ---

[Genex-cvs-commit] genex-server Install,1.6,1.7

From: <jas...@us...> - 2002-10-20 13:07:36

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv26576

Modified Files:
	Install 
Log Message:
db.pl fix

Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Install	15 Oct 2002 19:24:50 -0000	1.6
--- Install	20 Oct 2002 13:07:33 -0000	1.7
***************
*** 549,552 ****
--- 549,553 ----
  }
  
+ chdir($MOTHERDIR);
  slow() if ($SLOW);
  
***************
*** 574,577 ****
--- 575,579 ----
  
  my $db_init = 'db.pl';
+ my $command = "su -c '$^X $MOTHERDIR/$db_init' postgres";
  
  my $run_installer;
***************
*** 581,585 ****
  
  Hmmm - you are not running this as root. I\'m going to execute the
! command "su -c '$^X $db_init' postgres", and since you\'re
  not root, 'su' will prompt you for a password, which is likely to fail
  since the postgres account rarely has it\'s own password.
--- 583,587 ----
  
  Hmmm - you are not running this as root. I\'m going to execute the
! command "$command", and since you\'re
  not root, 'su' will prompt you for a password, which is likely to fail
  since the postgres account rarely has it\'s own password.
***************
*** 599,606 ****
  
  If I encounter trouble, you can run the DB installer yourself using:
!     '$^X $db_init'.
  
  EOM
! genex_system("su -c '$^X ./$db_init' postgres");
  die(<<EOE) if $?;
  
--- 601,608 ----
  
  If I encounter trouble, you can run the DB installer yourself using:
!     '$command'.
  
  EOM
! genex_system("$command");
  die(<<EOE) if $?;

[Genex-cvs-commit] genex-server/html/graphics GeneX101602_1.jpg,NONE,1.1.2.1 GeneX101602_2.jpg,NONE,1.1.2.1 GeneX101602_3.jpg,NONE,1.1.2.1 GeneX101602_4.jpg,NONE,1.1.2.1

From: <tw...@us...> - 2002-10-18 19:42:07

Update of /cvsroot/genex/genex-server/html/graphics
In directory usw-pr-cvs1:/tmp/cvs-serv21708

Added Files:
      Tag: Rel-1_0_1-branch
	GeneX101602_1.jpg GeneX101602_2.jpg GeneX101602_3.jpg 
	GeneX101602_4.jpg 
Log Message:
Jodi's new schema images.


--- NEW FILE: GeneX101602_1.jpg ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: GeneX101602_2.jpg ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: GeneX101602_3.jpg ---
(This appears to be a binary file; contents omitted.)

--- NEW FILE: GeneX101602_4.jpg ---
(This appears to be a binary file; contents omitted.)

[Genex-cvs-commit] genex-server/html schema.html,1.1.2.1,1.1.2.2

From: <tw...@us...> - 2002-10-18 19:41:08

Update of /cvsroot/genex/genex-server/html
In directory usw-pr-cvs1:/tmp/cvs-serv21331

Modified Files:
      Tag: Rel-1_0_1-branch
	schema.html 
Log Message:
Updated with Jodi's new schema images.


Index: schema.html
===================================================================
RCS file: /cvsroot/genex/genex-server/html/Attic/schema.html,v
retrieving revision 1.1.2.1
retrieving revision 1.1.2.2
diff -C2 -d -r1.1.2.1 -r1.1.2.2
*** schema.html	14 Aug 2002 20:56:48 -0000	1.1.2.1
--- schema.html	18 Oct 2002 19:41:05 -0000	1.1.2.2
***************
*** 20,44 ****
      <td width="240">&nbsp; </td>
      <td width="530"> 
!     These images are not complete, not annotated, and missing details. However, they should
!     give you a good overview of the most important tables, and how they relate.
!     <br>
!     <br>
!     More documentation is being prepared.
!         <br><br>
      </td>
    </tr>
  </table>
  <br>
! <p><img src="graphics/study_exp_spots.jpg" width="1017" height="778"><br>
  </p>
! 
! <p><img src="graphics/order_sample_qc.jpg" width="971" height="567"><br>
  </p>
! 
! <p><img src="graphics/layout_spots.jpg" width="921" height="670"><br>
  </p>
! 
! 
! 
  </BODY>
  </HTML>
--- 20,45 ----
      <td width="240">&nbsp; </td>
      <td width="530"> 
!     These images are not complete, not annotated, and missing details. However, they should
!     give you a good overview of the most important tables, and how they relate.
!     <br>
!     <br>
!     More documentation is being prepared.
!         <br><br>
      </td>
    </tr>
  </table>
  <br>
! <p><img src="graphics/GeneX101602_2.jpg" width="971" height="556"><br>
!   <img src="graphics/GeneX101602_1.jpg" width="1020" height="780"><br>
  </p>
! 
! <p><img src="graphics/GeneX101602_3.jpg" width="921" height="670"><br>
  </p>
! 
! <p><img src="graphics/GeneX101602_4.jpg" width="850" height="582"><br>
  </p>
! 
! 
! 
  </BODY>
  </HTML>

[Genex-cvs-commit] genex-www/genex-2 AM_Spots.html,1.2,1.3 BlastHits.html,1.2,1.3 ExperimentSet.html,1.2,1.3 ExternalDatabase.html,1.2,1.3 Feature.html,1.2,1.3 HotSpots.html,1.2,1.3 PhysicalBioAssay.html,1.1,1.2 QuantitationLink.html,1.1,1.2 QuantitationType.html,1.1,1.2 SF_ExternalDBLink.html,1.2,1.3

From: <jas...@us...> - 2002-10-17 16:57:46

Update of /cvsroot/genex/genex-www/genex-2
In directory usw-pr-cvs1:/tmp/cvs-serv8950

Modified Files:
	AM_Spots.html BlastHits.html ExperimentSet.html 
	ExternalDatabase.html Feature.html HotSpots.html 
	PhysicalBioAssay.html QuantitationLink.html 
	QuantitationType.html SF_ExternalDBLink.html 
Log Message:
new


Index: AM_Spots.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/AM_Spots.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** AM_Spots.html	29 Aug 2002 13:58:07 -0000	1.2
--- AM_Spots.html	17 Oct 2002 16:57:43 -0000	1.3
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: AM_Spots Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The AM_Spots table provides the expression level for     each spot on an PhysicalBioAssay. It is directly linked to the     SequenceFeature whose expression level has been     measured. Additionally,  it may be linked directly to an AL_Spot     row through the SpotLink table in order to deal with spots that     are not represented by a  SequenceFeature (e.g. control spots) or     with SequenceFeatures that are replicated on a given     ArrayDesign.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td>Array Layout Spot</td><td>int4</td><td>true</td><td>maps 1-to-1 with the layout</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td>Array Measurement</td><td>int4</td><td>true</td><td>the PhysicalBioAssay to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>spot_value</td><td>Spot Value</td><td>float</td><td>true</td><td>the actual expression level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td><a href="Feature.html">Feature</a></td><td>feature_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td><a href="PhysicalBioAssay.html">PhysicalBioAssay</a></td><td>pba_pk</td><td>LOOKUP_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk pba_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
\ No newline at end of file
--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: AM_Spots Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The AM_Spots table provides the expression level for     each spot on an PhysicalBioAssay. It is directly linked to the     Reporter whose expression level has been     measured. Additionally,  it may be linked directly to an AL_Spot     row through the SpotLink table in order to deal with spots that     are not represented by a  Reporter (e.g. control spots) or     with Reporters that are replicated on a given     ArrayDesign.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td>Array Layout Spot</td><td>int4</td><td>true</td><td>maps 1-to-1 with the layout</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td>Array Measurement</td><td>int4</td><td>true</td><td>the PhysicalBioAssay to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>spot_value</td><td>Spot Value</td><td>float</td><td>true</td><td>the actual expression level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ams_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk</td><td><a href="Feature.html">Feature</a></td><td>feature_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>pba_fk</td><td><a href="PhysicalBioAssay.html">PhysicalBioAssay</a></td><td>pba_pk</td><td>LOOKUP_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_fk pba_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
\ No newline at end of file

Index: BlastHits.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/BlastHits.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** BlastHits.html	29 Aug 2002 13:58:07 -0000	1.2
--- BlastHits.html	17 Oct 2002 16:57:43 -0000	1.3
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: BlastHits Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The BlastHits table allows any number of blast results to be associated with a given SequenceFeature.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>expect_value</td><td>Expectation Value</td><td>float</td><td>true</td><td>??will probably have to be based on log(E), since these       values can be very tiny...</td></tr><tr bgcolor="#D8E4F7"><td>match_accession</td><td>Match Accession</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>Sequence Feature</td><td>int4</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td><a href="SequenceFeature.html">SequenceFeature</a></td><td>sf_pk</td><td>MANY_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>match_accession sf_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>blasthits_sf_fk</td></tr></table><br></body></html>
\ No newline at end of file
--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: BlastHits Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The BlastHits table allows any number of blast results to be associated with a given Reporter.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>expect_value</td><td>Expectation Value</td><td>float</td><td>true</td><td>??will probably have to be based on log(E), since these       values can be very tiny...</td></tr><tr bgcolor="#D8E4F7"><td>match_accession</td><td>Match Accession</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>Sequence Feature</td><td>int4</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>bh_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td><a href="Reporter.html">Reporter</a></td><td>rep_pk</td><td>MANY_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>match_accession rep_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>blasthits_rep_fk</td></tr></table><br></body></html>
\ No newline at end of file

Index: ExperimentSet.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/ExperimentSet.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ExperimentSet.html	29 Aug 2002 13:58:07 -0000	1.2
--- ExperimentSet.html	17 Oct 2002 16:57:43 -0000	1.3
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: ExperimentSet Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExperimentSet table groups a set of       PhysicalBioAssay rows into a coherent collection representing a       conceptually related set of treatments (e.g. time series or       quantity series) of the same genetic elements.  In its standard       use, all PhysicalBioAssays belonging to a single  ExperimentSet       will derive from the same ArrayDesign and will have been assayed       by the same group. However, there may be cases in which virtual       ExperimentSets may be created to link PhysicalBioAssays that       illustrate some interesting relationship, even though they do       not meet these criteria.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>analysis_description</td><td>Analysis Description</td><td>text</td><td>false</td><td> high level description of how experiment was       analyzed</td></tr><tr bgcolor="#D8E4F7"><td>archive_bundle_ref</td><td>Archive Bundle Reference</td><td>varchar(128)</td><td>false</td><td> path to image files etc. the linking of particular       files in the bundle with specific PhysicalBioAssays is going to       be done through some convention, as yet to be determined...</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>biology_description</td><td>Biology Description</td><td>text</td><td>false</td><td> gives the intended purpose of the experiment</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td>Primary Citation</td><td>int4</td><td>false</td><td> publication in which experiment was described</td></tr><tr bgcolor="#D8E4F7"><td>es_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>local_accession</td><td>Local Accession Number</td><td>varchar(128)</td><td>false</td><td> id of experiment in submitter's database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Experiment Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the experiment info it is       important to destinquish between this and the rw_groupname because if       data is imported from another DB then the owner of the data will       not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>quantity_series_type</td><td>Quantity Series Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab, only appropriate for quantity       series</td></tr><tr bgcolor="#D8E4F7"><td>release_date</td><td>Release Date</td><td>datetime</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr><tr bgcolor="#D8E4F7"><td>submission_date</td><td>Submission Date</td><td>datetime</td><td>true</td><td> indicates when XML was uploaded to NCGR</td></tr><tr bgcolor="#D8E4F7"><td>treatment_type</td><td>Treatment Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td><a href="Citation.html">Citation</a></td><td>cit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: ExperimentSet Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExperimentSet table groups a set of       PhysicalBioAssay rows into a coherent collection representing a       conceptually related set of treatments (e.g. time series or       quantity series) of the same genetic elements.  In its standard       use, all PhysicalBioAssays belonging to a single  ExperimentSet       will derive from the same ArrayDesign and will have been assayed       by the same group. However, there may be cases in which virtual       ExperimentSets may be created to link PhysicalBioAssays that       illustrate some interesting relationship, even though they do       not meet these criteria.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>analysis_description</td><td>Analysis Description</td><td>text</td><td>false</td><td> high level description of how experiment was       analyzed</td></tr><tr bgcolor="#D8E4F7"><td>archive_bundle_ref</td><td>Archive Bundle Reference</td><td>varchar(128)</td><td>false</td><td> path to image files etc. the linking of particular       files in the bundle with specific PhysicalBioAssays is going to       be done through some convention, as yet to be determined...</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>biology_description</td><td>Biology Description</td><td>text</td><td>false</td><td> gives the intended purpose of the experiment</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td>Primary Citation</td><td>int4</td><td>false</td><td> publication in which experiment was described</td></tr><tr bgcolor="#D8E4F7"><td>creation_date</td><td>Creation Date</td><td>datetime</td><td>true</td><td> indicates when the experiment was created</td></tr><tr bgcolor="#D8E4F7"><td>es_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>local_accession</td><td>Local Accession Number</td><td>varchar(128)</td><td>false</td><td> id of experiment in submitter's database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Experiment Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the experiment info it is       important to destinquish between this and the rw_groupname because if       data is imported from another DB then the owner of the data will       not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>quantity_series_type</td><td>Quantity Series Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab, only appropriate for quantity       series</td></tr><tr bgcolor="#D8E4F7"><td>release_date</td><td>Release Date</td><td>datetime</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr><tr bgcolor="#D8E4F7"><td>treatment_type</td><td>Treatment Type</td><td>varchar(128)</td><td>false</td><td>controlled vocab</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>cit_fk</td><td><a href="Citation.html">Citation</a></td><td>cit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: ExternalDatabase.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/ExternalDatabase.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ExternalDatabase.html	29 Aug 2002 13:58:07 -0000	1.2
--- ExternalDatabase.html	17 Oct 2002 16:57:43 -0000	1.3
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: ExternalDatabase Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExternalDatabase table gives information that may be used to access databases outside of GeneX for information about SequenceFeatures. The information stored here is used to create hyperlinks in HTML output of various routines.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>main_url</td><td>Main DB URL</td><td>varchar(128)</td><td>true</td><td> the primary url for the database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Database Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>parameterized_url</td><td>Parameterized URL</td><td>varchar(128)</td><td>false</td><td> if present this url contains the pattern %%ID%%, which can be replaced by the DB accession number in order to retrieve a dynamic WWW page for the sequence feature</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: ExternalDatabase Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The ExternalDatabase table gives information that may be used to access databases outside of GeneX for information about Reporters. The information stored here is used to create hyperlinks in HTML output of various routines.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>main_url</td><td>Main DB URL</td><td>varchar(128)</td><td>true</td><td> the primary url for the database</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Database Name</td><td>varchar(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>parameterized_url</td><td>Parameterized URL</td><td>varchar(128)</td><td>false</td><td> if present this url contains the pattern %%ID%%, which can be replaced by the DB accession number in order to retrieve a dynamic WWW page for the sequence feature</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>ed_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>name</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: Feature.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/Feature.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Feature.html	29 Aug 2002 13:58:07 -0000	1.2
--- Feature.html	17 Oct 2002 16:57:43 -0000	1.3
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: Feature Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Feature table gives detail information concerning     each individual element (spot) of a given ArrayDesign. In     particular, it indicates the location of the spot on the Array and     characterizes the genetic material that will be bound to an     instance of the ArrayDesign at the given location.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td>Array Layout</td><td>int4</td><td>true</td><td>the ArrayDesign to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>feature_concentration</td><td>Feature Concentration</td><td>float</td><td>false</td><td>used to indicate the concentration of the probe on the       array (may differ from the default value in the referenced       ArrayDesign, but will be measured in the same units)</td></tr><tr bgcolor="#D8E4F7"><td>feature_description</td><td>Feature Description</td><td>varchar(128)</td><td>false</td><td>a meaningful description of the       genetic material that will be placed on an instance at this       position; in some cases, e.g. foreign DNA used as a control, the       sf_fk will be left null, and this field will provide the only       description of what material has been used, and hence the       significance of expression levels observed at these positions in       an instance of the ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_identifier</td><td>Feature Identifier</td><td>varchar(128)</td><td>false</td><td>the GOD file identifier for the position on the       ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_type</td><td>Feature Type</td><td>varchar(128)</td><td>true</td><td>distinguishes various kinds of control spot from those       linked to SequenceFeatures iff type = seqfeat then sf_fk must be       supplied</td></tr><tr bgcolor="#D8E4F7"><td>grid_image_location</td><td>Grid Image Location</td><td>varchar(128)</td><td>false</td><td>these fields specify the position of the spot with       respect to the entire Array; their purpose is to allow our       software to generate a virtual image that can be compared to the       actual image for an PhysicalBioAssay instance. The x and y are       specified relative to the origin of distinct blocks of spots;       the location of the block is given by the       grid_image_location. They may be left null for data without       images.        the current specification seems problematic, in that       unless we know how to translate a grid location into an x-y       coordinate for the block, we don't know how to lay out the       blocks. Further, it would seem to make more sense to translate       at insert time into a simple x-y spec for each spot, since       this makes the virtual image easier to calculate, and the       latter will be done many times, while the insert will only       occur once...         JES: Mon Oct  9 15:59:26 MST 2000  Changed to type varchar to       support 'Field1', 'A15', etc</td></tr><tr bgcolor="#D8E4F7"><td>pin_identifier</td><td>Pin</td><td>varchar(128)</td><td>false</td><td>Indicates which pin of the spotter is used to print       this spot.</td></tr><tr bgcolor="#D8E4F7"><td>print_sequence</td><td>Print Sequence</td><td>int4</td><td>false</td><td>Indicates the order of printing of spots on a single       visit of a pin to a source well. Used in replicate resolution       coupled with sf_fk and source_visit, and tracking systematic       variation in spot data. A value of 0 represents a virtual spot       that represents the result of resolving replicates across       print_sequence.</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>Sequence Feature</td><td>int4</td><td>false</td><td>indicates what genetic element will be placed on an       instance at this location; may be null, in the case of controls       which are not characterized to the level of detail required by       SequenceFeature</td></tr><tr bgcolor="#D8E4F7"><td>source_visit</td><td>Source Visit</td><td>int4</td><td>false</td><td>Distinguishes the visits to a source well that is       represented by the sf_fk relationship to the sequence       feature. If used, assumes that a sequence feature entry       represents a unique source well. Used coupled with       print_sequence and sf_fk to resolve replicates. A value of 0       represents a virtual spot that represents the value resulting       from resolving replicates across source visits.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_end</td><td>Sub-sequence End</td><td>int4</td><td>false</td><td>these fields indicate the subsequence of the       SequenceFeature actually used on the Array. When these are left       null, the  entire SequenceFeature is implied. These may be       useful when a PCR product or oligonucleotide is used on the       array.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_start</td><td>Sub-sequence Start</td><td>int4</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>x_image_location</td><td>X Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>y_image_location</td><td>Y Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td><a href="ArrayDesign.html">ArrayDesign</a></td><td>ad_pk</td><td>LOOKUP_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td><a href="SequenceFeature.html">SequenceFeature</a></td><td>sf_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_identifier ad_fk</td></tr><tr bgcolor="#D8E4F7"><td>x_image_location y_image_location grid_image_location ad_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
\ No newline at end of file
--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: Feature Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Feature table gives detail information concerning     each individual element (spot) of a given ArrayDesign. In     particular, it indicates the location of the spot on the Array and     characterizes the genetic material that will be bound to an     instance of the ArrayDesign at the given location.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td>Array Layout</td><td>int4</td><td>true</td><td>the ArrayDesign to which the spot belongs</td></tr><tr bgcolor="#D8E4F7"><td>feature_concentration</td><td>Feature Concentration</td><td>float</td><td>false</td><td>used to indicate the concentration of the probe on the       array (may differ from the default value in the referenced       ArrayDesign, but will be measured in the same units)</td></tr><tr bgcolor="#D8E4F7"><td>feature_description</td><td>Feature Description</td><td>varchar(128)</td><td>false</td><td>a meaningful description of the       genetic material that will be placed on an instance at this       position; in some cases, e.g. foreign DNA used as a control, the       rep_fk will be left null, and this field will provide the only       description of what material has been used, and hence the       significance of expression levels observed at these positions in       an instance of the ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_identifier</td><td>Feature Identifier</td><td>varchar(128)</td><td>false</td><td>the GOD file identifier for the position on the       ArrayDesign</td></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>feature_type</td><td>Feature Type</td><td>varchar(128)</td><td>true</td><td>distinguishes various kinds of control spot from those       linked to Reporters iff type = seqfeat then rep_fk must be       supplied</td></tr><tr bgcolor="#D8E4F7"><td>grid_col_image_location</td><td>Grid Column Number</td><td>varchar(128)</td><td>false</td><td>This field supports designs that track the       grids in a row,column format</td></tr><tr bgcolor="#D8E4F7"><td>grid_image_location</td><td>Grid Image Location</td><td>varchar(128)</td><td>false</td><td>these fields specify the position of the spot with       respect to the entire Array; their purpose is to allow our       software to generate a virtual image that can be compared to the       actual image for an PhysicalBioAssay instance. The x and y are       specified relative to the origin of distinct blocks of spots;       the location of the block is given by the       grid_image_location. They may be left null for data without       images.        the current specification seems problematic, in that       unless we know how to translate a grid location into an x-y       coordinate for the block, we don't know how to lay out the       blocks. Further, it would seem to make more sense to translate       at insert time into a simple x-y spec for each spot, since       this makes the virtual image easier to calculate, and the       latter will be done many times, while the insert will only       occur once...         JES: Mon Oct  9 15:59:26 MST 2000  Changed to type varchar to       support 'Field1', 'A15', etc</td></tr><tr bgcolor="#D8E4F7"><td>grid_row_image_location</td><td>Grid Row Number</td><td>varchar(128)</td><td>false</td><td>This field supports designs that track the       grids in a row,column format</td></tr><tr bgcolor="#D8E4F7"><td>pin_identifier</td><td>Pin</td><td>varchar(128)</td><td>false</td><td>Indicates which pin of the spotter is used to print       this spot.</td></tr><tr bgcolor="#D8E4F7"><td>print_sequence</td><td>Print Sequence</td><td>int4</td><td>false</td><td>Indicates the order of printing of spots on a single       visit of a pin to a source well. Used in replicate resolution       coupled with rep_fk and source_visit, and tracking systematic       variation in spot data. A value of 0 represents a virtual spot       that represents the result of resolving replicates across       print_sequence.</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>Sequence Feature</td><td>int4</td><td>false</td><td>indicates what genetic element will be placed on an       instance at this location; may be null, in the case of controls       which are not characterized to the level of detail required by       Reporter</td></tr><tr bgcolor="#D8E4F7"><td>source_visit</td><td>Source Visit</td><td>int4</td><td>false</td><td>Distinguishes the visits to a source well that is       represented by the rep_fk relationship to the sequence       feature. If used, assumes that a sequence feature entry       represents a unique source well. Used coupled with       print_sequence and rep_fk to resolve replicates. A value of 0       represents a virtual spot that represents the value resulting       from resolving replicates across source visits.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_end</td><td>Sub-sequence End</td><td>int4</td><td>false</td><td>these fields indicate the subsequence of the       Reporter actually used on the Array. When these are left       null, the  entire Reporter is implied. These may be       useful when a PCR product or oligonucleotide is used on the       array.</td></tr><tr bgcolor="#D8E4F7"><td>sub_sequence_start</td><td>Sub-sequence Start</td><td>int4</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>x_image_location</td><td>X Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>y_image_location</td><td>Y Image Location</td><td>varchar(128)</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>feature_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>ad_fk</td><td><a href="ArrayDesign.html">ArrayDesign</a></td><td>ad_pk</td><td>LOOKUP_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td><a href="Reporter.html">Reporter</a></td><td>rep_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>feature_identifier ad_fk</td></tr><tr bgcolor="#D8E4F7"><td>x_image_location y_image_location grid_row_image_location grid_col_image_location grid_image_location ad_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
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Index: HotSpots.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/HotSpots.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** HotSpots.html	29 Aug 2002 13:58:07 -0000	1.2
--- HotSpots.html	17 Oct 2002 16:57:43 -0000	1.3
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: HotSpots Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>LINKING</th><th> The HotSpots table indicates a subset of SequenceFeatures whose expression levels changed above a given threshold during the course of an experiment. It can be used to quickly access experiments in which genes of interest seemed to be important. It applies to the processed ratio values derived by comparing levels of expression under treatments to those under control conditions. ??It remains to be seen if this wouldn't better be done as a view. Not doing ??so introduces consistency problems if PhysicalBioAssays are added to ??experiments or values are changed.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>es_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>sf_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>threshold_type</td><td>threshold_type</td><td>varchar(128)</td><td>false</td><td> controlled vocab, specifies the threshold used to       select the interesting genes, may further specify if the sense       is up-regulation down-regulation or an absolute change above the       threshold level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>LINKING_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td><a href="SequenceFeature.html">SequenceFeature</a></td><td>sf_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>sf_fk es_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>hotspots_es_fk</td></tr><tr bgcolor="#D8E4F7"><td>sf_fk</td><td>hotspots_sf_fk</td></tr></table><br></body></html>
\ No newline at end of file
--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: HotSpots Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>LINKING</th><th> The HotSpots table indicates a subset of Reporters whose expression levels changed above a given threshold during the course of an experiment. It can be used to quickly access experiments in which genes of interest seemed to be important. It applies to the processed ratio values derived by comparing levels of expression under treatments to those under control conditions. ??It remains to be seen if this wouldn't better be done as a view. Not doing ??so introduces consistency problems if PhysicalBioAssays are added to ??experiments or values are changed.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>es_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>rep_fk</td><td>int4</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>threshold_type</td><td>threshold_type</td><td>varchar(128)</td><td>false</td><td> controlled vocab, specifies the threshold used to       select the interesting genes, may further specify if the sense       is up-regulation down-regulation or an absolute change above the       threshold level</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>LINKING_TABLE</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td><a href="Reporter.html">Reporter</a></td><td>rep_pk</td><td>LINKING_TABLE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>rep_fk es_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>hotspots_es_fk</td></tr><tr bgcolor="#D8E4F7"><td>rep_fk</td><td>hotspots_rep_fk</td></tr></table><br></body></html>
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Index: PhysicalBioAssay.html
===================================================================
RCS file: /cvsroot/genex/genex-www/genex-2/PhysicalBioAssay.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** PhysicalBioAssay.html	29 Aug 2002 13:57:18 -0000	1.1
--- PhysicalBioAssay.html	17 Oct 2002 16:57:43 -0000	1.2
***************
*** 3,5 ****
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: PhysicalBioAssay Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The PhysicalBioAssay table is used in two related, but       distinct fashions: to represent the primary data for gene       expression experiments and to represent processed data such as       averaged values across replicates or ratio values for treatment       vs. controls.   In representing the primary data, it describes       an instance of an ArrayDesign  that has been used to assay gene       expression levels in a preparation of the mRNA from a sample       that has been subjected to a specific treatment in the context       of an experiment.   It contains detailed information as to the       treatment and protocols used on this ArrayDesign instance. The       actual expression levels for each spot are stored in the       PhysicalBioAssaySpots table. In general, the PhysicalBioAssay       table has the same relationship to the PhysicalBioAssaySpots       table as the ArrayDesign table has to the  ArrayDesignSpots       table. However, there several cases in which the  relationship       breaks down to some extent.   First, there may be       PhysicalBioAssays for which no ArrayDesign is given. Second, for       spots that represent controls on a given ArrayDesign, we may       choose not to store expression levels for the control spots.       Finally, in cases of ArrayDesigns with replicate spots (i.e. the       same SequenceFeature is used in different locations on the       ArrayDesign), replicates will be broken out into separate       PhysicalBioAssay rows. For example, an ArrayDesign with 1000       distinct SequenceFeatures, each of which has been replicated 2       times on the ArrayDesign will have 3000 corresponding       ArrayDesignSpot rows, while a given instance of the ArrayDesign       will be represented by three distinct PhysicalBioAssay rows,       each of which has 1000 corresponding PhysicalBioAssaySpots       rows. A related example is when mutiple channels are used to       detect the signal of the expression level for each spot. In this       case, an ArrayDesign that has 1000 distinct SequenceFeatures may       be represented by two or more PhysicalBioAssay rows, each with       1000 PhysicalBioAssaySpot rows representing the expression level       reported by one channel.  PhysicalBioAssays that represent       primary data will be grouped into  sets around the ReplicateDef       table. This set of primary data may then be used to define       derived PhysicalBioAssays representing the averaged values       across members of the replicate set. Further, these       ReplicateDefs can be used to describe TreatmentDefs which define       the levels of the treatment and associated control       ReplicateDefs. The TreatmentDef may reference a third type of       PhysicalBioAssay that is derived from the ratio between the       averaged values for the treatment replicates and the averaged       values of the control replicates.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td>Array</td><td>int4</td><td>true</td><td>The chip or array used with this assay</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td> a more verbose description of the purpose of this       PhysicalBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Primary Experiment Set</td><td>int4</td><td>true</td><td> the primary experiment in which the PhysicalBioAssay       was taken (the ExperimentSet in which it was submitted)</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Array Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the array info it is       important to destinquish between this and the rw_groupname       because if data is imported from another DB then the owner of       the data will not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td><a href="Array.html">Array</a></td><td>array_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>MANY_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
\ No newline at end of file
--- 3,5 ----
      </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
        GeneX-2.0 DB: PhysicalBioAssay Table
!     </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The PhysicalBioAssay table is used in two related, but       distinct fashions: to represent the primary data for gene       expression experiments and to represent processed data such as       averaged values across replicates or ratio values for treatment       vs. controls.   In representing the primary data, it describes       an instance of an ArrayDesign  that has been used to assay gene       expression levels in a preparation of the mRNA from a sample       that has been subjected to a specific treatment in the context       of an experiment.   It contains detailed information as to the       treatment and protocols used on this ArrayDesign instance. The       actual expression levels for each spot are stored in the       PhysicalBioAssaySpots table. In general, the PhysicalBioAssay       table has the same relationship to the PhysicalBioAssaySpots       table as the ArrayDesign table has to the  ArrayDesignSpots       table. However, there several cases in which the  relationship       breaks down to some extent.   First, there may be       PhysicalBioAssays for which no ArrayDesign is given. Second, for       spots that represent controls on a given ArrayDesign, we may       choose not to store expression levels for the control spots.       Finally, in cases of ArrayDesigns with replicate spots (i.e. the       same Reporter is used in different locations on the       ArrayDesign), replicates will be broken out into separate       PhysicalBioAssay rows. For example, an ArrayDesign with 1000       distinct Reporters, each of which has been replicated 2       times on the ArrayDesign will have 3000 corresponding       ArrayDesignSpot rows, while a given instance of the ArrayDesign       will be represented by three distinct PhysicalBioAssay rows,       each of which has 1000 corresponding PhysicalBioAssaySpots       rows. A related example is when mutiple channels are used to       detect the signal of the expression level for each spot. In this       case, an ArrayDesign that has 1000 distinct Reporters may       be represented by two or more PhysicalBioAssay rows, each with       1000 PhysicalBioAssaySpot rows representing the expression level       reported by one channel.  PhysicalBioAssays that represent       primary data will be grouped into  sets around the ReplicateDef       table. This set of primary data may then be used to define       derived PhysicalBioAssays representing the averaged values       across members of the replicate set. Further, these       ReplicateDefs can be used to describe TreatmentDefs which define       the levels of the treatment and associated control       ReplicateDefs. The TreatmentDef may reference a third type of       PhysicalBioAssay that is derived from the ratio between the       averaged values for the treatment replicates and the averaged       values of the control replicates.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td>Array</td><td>int4</td><td>true</td><td>The chip or array used with this assay</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td> a more verbose description of the purpose of this       PhysicalBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Primary Experiment Set</td><td>int4</td><td>true</td><td> the primary experiment in which the PhysicalBioAssay       was taken (the ExperimentSet in which it was submitted)</td></tr><tr bgcolor="#D8E4F7"><td>name</td><td>Array Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Data Provider</td><td>int4</td><td>false</td><td> the researcher that provided the array info it is       important to destinquish between this and the rw_groupname       because if data is imported from another DB then the owner of       the data will not be the individual that submitted it.</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>pba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>array_fk</td><td><a href="Array.html">Array</a></td><td>array_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>MANY_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BF...
 
[truncated message content]

[Genex-cvs-commit] genex-www/genex-2 MeasuredBioAssay.html,NONE,1.1

From: <jas...@us...> - 2002-10-17 16:57:36

Update of /cvsroot/genex/genex-www/genex-2
In directory usw-pr-cvs1:/tmp/cvs-serv8874

Added Files:
	MeasuredBioAssay.html 
Log Message:
new


--- NEW FILE: MeasuredBioAssay.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
      GeneX-2.0 DB: MeasuredBioAssay Table
    </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
      GeneX-2.0 DB: MeasuredBioAssay Table
    </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The MeasuredBioAssay table holds the meta-data       associated with a data matrix stored in a MeasuredBioAssayData       table</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>text</td><td>false</td><td> a more verbose description of the purpose of this       MeasuredBioAssay</td></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td>Primary Experiment Set</td><td>int4</td><td>true</td><td> the primary experiment in which the MeasuredBioAssay       was taken (the ExperimentSet in which it was submitted)</td></tr><tr bgcolor="#D8E4F7"><td>fesw_fk</td><td>Feature Extraction Software</td><td>int4</td><td>true</td><td>The feature extraction software used to extract the       numerical data from the image</td></tr><tr bgcolor="#D8E4F7"><td>mba_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>mba_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>es_fk</td><td><a href="ExperimentSet.html">ExperimentSet</a></td><td>es_pk</td><td>MANY_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>fesw_fk</td><td><a href="FeatureExtractionSoftware.html">FeatureExtractionSoftware</a></td><td>fesw_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>

[Genex-cvs-commit] genex-www/genex-2 AL_Spots.html,1.2,1.3 ArrayLayout.html,1.2,1.3 ArrayMeasurement.html,1.2,1.3 ContactOwner.html,1.2,1.3 FeatureExtractionSoftware.html,NONE,1.1 G2G.html,NONE,1.1 QuantitationTypeDimension.html,NONE,1.1 Reporter.html,NONE,1.1 Security.html,1.2,1.3 Sessions.html,NONE,1.1

From: <jas...@us...> - 2002-10-17 16:57:17

Update of /cvsroot/genex/genex-www/genex-2
In directory usw-pr-cvs1:/tmp/cvs-serv8723

Added Files:
	AL_Spots.html ArrayLayout.html ArrayMeasurement.html 
	ContactOwner.html FeatureExtractionSoftware.html G2G.html 
	QuantitationTypeDimension.html Reporter.html Security.html 
	Sessions.html 
Log Message:
new






--- NEW FILE: FeatureExtractionSoftware.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
      GeneX-2.0 DB: FeatureExtractionSoftware Table
    </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
      GeneX-2.0 DB: FeatureExtractionSoftware Table
    </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The FeatureExtractionSoftware table holds information       specific to feature extraction software packages</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>data_end_regex</td><td>Data End Regular Expression</td><td>varchar(128)</td><td>false</td><td>This string locates the end of the data block in the       input file.</td></tr><tr bgcolor="#D8E4F7"><td>data_start_regex1</td><td>Data Start Regular Expression 1</td><td>varchar(128)</td><td>false</td><td>This string locates the start of the data block in the       input file</td></tr><tr bgcolor="#D8E4F7"><td>data_start_regex2</td><td>Data Start Regular Expression 2</td><td>varchar(128)</td><td>false</td><td>This string locates the start of the data block in the       input file if the first regex alone is not sufficient</td></tr><tr bgcolor="#D8E4F7"><td>feature_identifier_string</td><td>Feature Identifier String</td><td>varchar(128)</td><td>true</td><td>This string documents what columns in the data are used       to constructor the feature identifier</td></tr><tr bgcolor="#D8E4F7"><td>fesw_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>qd_fk</td><td>Quantitation Type Dimension</td><td>int4</td><td>true</td><td>The quantitation dimension that this software package       outputs its data as</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>fesw_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>qd_fk</td><td><a href="QuantitationTypeDimension.html">QuantitationTypeDimension</a></td><td>qd_pk</td><td>ONE_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: G2G.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
      GeneX-2.0 DB: G2G Table
    </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
      GeneX-2.0 DB: G2G Table
    </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The G2G table supports distributed queries amongst Genex DB's</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>URL</td><td>URL</td><td>character(128)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>g2g_pk</td><td>Accession Number</td><td>serial</td><td>true</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>g2g_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: QuantitationTypeDimension.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
      GeneX-2.0 DB: QuantitationTypeDimension Table
    </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
      GeneX-2.0 DB: QuantitationTypeDimension Table
    </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The QuantitationTypeDimension table stores        the ordered lists of QuantitationTypes that define the spot tables</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>data_table_name</td><td>Data Table Name</td><td>varchar(128)</td><td>true</td><td>Every QuantitationTypeDimension stores its data in its own    unique data table</td></tr><tr bgcolor="#D8E4F7"><td>qd_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>qd_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>
--- NEW FILE: Reporter.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
      GeneX-2.0 DB: Reporter Table
    </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
      GeneX-2.0 DB: Reporter Table
    </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th> The Reporter table describes the genetic elements that are used as probes in gene expression experiments (e.g. the cDNA elements that are immobilized on a glass slide). They can be cloned genes, ESTs, etc.</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td>Audit</td><td>int4</td><td>true</td><td>The audit entry when this data was last modified</td></tr><tr bgcolor="#D8E4F7"><td>chromosome</td><td>Chromosome Location</td><td>varchar(128)</td><td>false</td><td> the chromosome on which the Reporter resides</td></tr><tr bgcolor="#D8E4F7"><td>clone_name</td><td>Clone Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>clone_provider_con_fk</td><td>Clone Provider Contact</td><td>int4</td><td>false</td><td> useful for tracking where the sequence feature came from if the clone was provided by another source ??an untested feature at best, shouldn't this be handled ??by the smp_fk</td></tr><tr bgcolor="#D8E4F7"><td>description</td><td>Description</td><td>varchar(128)</td><td>false</td><td> a short description of the Reporter</td></tr><tr bgcolor="#D8E4F7"><td>end_position</td><td>End Position</td><td>int4</td><td>false</td><td> the location with respect to the origin of the chromosome</td></tr><tr bgcolor="#D8E4F7"><td>other_name</td><td>Other Name</td><td>varchar(128)</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>other_type</td><td>Other Type</td><td>varchar(128)</td><td>false</td><td> an alternative name by which the entity is known ??doesn't this want to be a restricted vocab</td></tr><tr bgcolor="#D8E4F7"><td>plate_column</td><td>Plate Column</td><td>varchar(128)</td><td>false</td><td> column reference to indentify the well on the plate this sequence feature came from.</td></tr><tr bgcolor="#D8E4F7"><td>plate_identifier</td><td>Plate</td><td>varchar(128)</td><td>false</td><td> Used to identify a source plate for this sequence feature This could be a reference to the spotting plate, or it could refer to the  original clone library plate.</td></tr><tr bgcolor="#D8E4F7"><td>plate_row</td><td>Plate Row</td><td>varchar(128)</td><td>false</td><td> Row reference to indentify the well on the plate this sequence feature came from.</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td>Provider Contact</td><td>int4</td><td>false</td><td> the researcher that provided the reporter info</td></tr><tr bgcolor="#D8E4F7"><td>rep_name</td><td>Sequence Feature Name</td><td>varchar(128)</td><td>true</td><td> an identifier such as EST or ORF name, by which the entity is known in the lab using it is expression experiments</td></tr><tr bgcolor="#D8E4F7"><td>rep_pk</td><td>Accession Number</td><td>serial</td><td>false</td><td></td></tr><tr bgcolor="#D8E4F7"><td>rep_type</td><td>Sequence Feature Type</td><td>varchar(128)</td><td>true</td><td>conrolled vocab</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td>Read-Only Group Name</td><td>name</td><td>true</td><td>The group with permission to view this data</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td>Read/Write Group Name</td><td>name</td><td>true</td><td>The group with permission to modify this data</td></tr><tr bgcolor="#D8E4F7"><td>sequence</td><td>Sequence</td><td>text</td><td>false</td><td> may be used when dealing with ESTs that have not been submitted to a public database (won't be used for public version, but may be useful for local installations)</td></tr><tr bgcolor="#D8E4F7"><td>smp_fk</td><td>Sample</td><td>int4</td><td>false</td><td> sample information for the Reporter this may be useful for identifying the state of the organism from which the sequence feature was obtained</td></tr><tr bgcolor="#D8E4F7"><td>spc_fk</td><td>Species</td><td>int4</td><td>false</td><td> the species to which the Reporter belongs</td></tr><tr bgcolor="#D8E4F7"><td>start_position</td><td>Start Position</td><td>int4</td><td>false</td><td> the location with respect to the origin of the chromosome</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr><tr bgcolor="#D8E4F7"><td>rep_pk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr><tr bgcolor="#D8E4F7"><td>audit_fk</td><td><a href="Audit.html">Audit</a></td><td>audit_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>clone_provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>provider_con_fk</td><td><a href="Contact.html">Contact</a></td><td>con_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>ro_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>rw_groupname</td><td><a href="GroupSec.html">GroupSec</a></td><td>name</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>smp_fk</td><td><a href="Sample.html">Sample</a></td><td>smp_pk</td><td>ONE_TO_ONE</td></tr><tr bgcolor="#D8E4F7"><td>spc_fk</td><td><a href="Species.html">Species</a></td><td>spc_pk</td><td>MANY_TO_ONE</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr><tr bgcolor="#D8E4F7"><td>rep_name provider_con_fk spc_fk</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>

--- NEW FILE: Sessions.html ---
<html><head><META http-equiv="Content-Type" content="text/html; charset=UTF-8"><title>
      GeneX-2.0 DB: Sessions Table
    </title></head><body bgcolor="#FFD78F"><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">
      GeneX-2.0 DB: Sessions Table
    </th></tr><tr bgcolor="#BFD8D8"><th>Table Type</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><th>DATA</th><th>The Session table supports storing WWW session data to     the DB</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="5">Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Full Name</th><th>Data Type</th><th>Not NULL</th><th>Comment</th></tr><tr bgcolor="#D8E4F7"><td>a_session</td><td>Session Data</td><td>text</td><td>false</td><td>the encrypted session data</td></tr><tr bgcolor="#D8E4F7"><td>id</td><td>Session Number</td><td>character(32)</td><td>true</td><td></td></tr><tr bgcolor="#D8E4F7"><td>modification_time</td><td>Modification Time</td><td>datetime</td><td>true</td><td>the encrypted session data</td></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Primary Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="4">Foreign Key Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Name</th><th>Foreign Table</th><th>Primary Key in Foreign Table</th><th>Foreign Key Type</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="1">Unique Column Information</th></tr><tr bgcolor="#BFD8D8"><th>Column Names</th></tr></table><br><table border="2"><tr bgcolor="#BFD8D8"><th colspan="2">Index Information</th></tr><tr bgcolor="#BFD8D8"><th>Name</th><th>Column Name</th></tr></table><br></body></html>

[Genex-cvs-commit] genex-server/G2G/mason add_user_to_group.html.in,NONE,1.1

From: <mwi...@us...> - 2002-10-17 00:52:23

Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv26371

Added Files:
	add_user_to_group.html.in 
Log Message:
modifies the group membership of a given user.  The code is not yet documented.  As soon as I get back from my job interview I will document all three of these HTMLMason files that I added.  I promise.

--- NEW FILE: add_user_to_group.html.in ---
% if (($response_page eq "NEW")) { 
        <center>
        <h1>Modify Group Assicoations of Genex Users</h1>
        <form action="add_user_to_group.html"><br>
        <br>    
        <table cellpadding="2" cellspacing="2" border="0"
         style="text-align: left; margin-left: auto; margin-right: auto;"
         title="Select the user to work with"
         summary="Choose User">
          <tbody>
            <tr>
              <td valign="top">Which User?<br>
              </td>
              <td valign="top">
                <select name="username">
% foreach my $user(@usernames) {        
                <option value="<% $user %>"><% $user %>
% }
                </select>        
              <td valign="top">
            </tr>
          </tbody>
        </table>
        <br><br>
        <input name="submitted" type="hidden" value="true">
        <input type="submit" name="submit" value="Modify This User"><br>
        </form>

% } else {  # session is initialized
        <center>
        <h1>Modify Group Assicoations of Genex Users</h1>
        <form action="add_user_to_group.html"><br>
        <input type="hidden" name="username" value="<% $username %>">
        <input type="hidden" name="modified" value=1>
% if ($response_page eq "DONE"){
        <div style="text-align: center;">
        <h1>Genex User-associations Updated</h1>
% }
        <br>
% if ($response_page eq "BadGroup"){
                <h3><font color="red">You chose an invalid group to associate this user with</font></h3>
% }
% if ($response_page eq "BadUsername"){
                <h3><font color="red">You chose an invalid User</font></h3>
% }
        <b>Check/Uncheck the Groups you wish this User to be associated with or dissociated from respectively.</b>
        <table cellpadding="5" cellspacing="2" border="0"
         style="text-align: left; margin-left: auto; margin-right: auto;"
         title="Enter the following information for your user"
         summary="information about the new genex user">
          <caption><br>
          </caption>  <tbody>
            <tr>
              <td valign="top">User <i><% $username %></i><br>is currently a member of<br>the groups shown here: <br>
              </td>
              <td valign="top">
% foreach my $groupname(@groupnames){           
                  <input type="checkbox" name="new_group_assoc" value="<% $groupname %>"
% if (grep (/^$groupname$/, @activegroups)){
                    checked
% }
              ><b><% $groupname %></b><br>
% }
            </td>
            </tr>
          </tbody>
        </table>
        <br>
        <input name="submitted" type="hidden" value="true">
        <input type="submit" name="submit" value="Modify This User"><br>
        <br>
        <br>
        last modified Oct 12, 2002<br>
        </center>
% }

<%attr>
  action=>'%%GENEX_WORKSPACE_URL%%/add_user_to_group.html'
  name=>'Associate Genex User With Group'
  path=>'%%GENEX_WORKSPACE_URL%%/add_user_to_group.html'
</%attr>
<%args>
    $username => ""
    $groupname => ""
    $SU_PASSWORD => ""
    $submitted => ""
    $modified => 0
    $debug => 0
    $new_group_assoc => []
</%args>
<%once>;
</%once>
<%init>;

use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::UserSec;
use Bio::Genex::GroupLink;

#my $ro_groupname = %%GENEX_RO_GROUPNAME%%;
#my $rw_groupname = %%GENEX_RW_GROUPNAME%%;
my $ro_groupname = "public";
my $rw_groupname = "superuser";
my $SU_USERNAME = "genex";  # this is now hard coded
my $dbname = "%%DB_NAME%%";
my $response_page;
my $db=Bio::Genex::Connect->new(USER=>$SU_USERNAME, PASSWORD=>$SU_PASSWORD, DBNAME=>$dbname);
my @activegroups;  # holds the names of the groups to which this user belongs

# get list of all valid users and groups for various purposes
my @groupnames;  # holds the names of all groups that exist
my @usernames;   # holds the names of all users that exist
my @allgroups = Bio::Genex::GroupSec->get_all_objects($db); #returns objects
foreach (@allgroups){
    push @groupnames, $_->name;
}
my @allusers = Bio::Genex::UserSec->get_all_objects($db);
foreach (@allusers){
    push @usernames, $_->username;
}
my $entered;
$rw_groupname = $rw_groupname?$rw_groupname:"superuser";  # set predictable default if this variable doesnt exist

if ($submitted ne "true"){  # this is a fresh load of the page
    $response_page="NEW";
} elsif (!$username || !(grep (/$username/, @usernames))){    # missing or invalid username
    $response_page="BadUsername";
} elsif ($groupname && !(grep (/$groupname/, @groupnames))) {
    $response_page="BadGroup";
} elsif (!$modified) {
    my @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
    @activegroups = map {if ($_->username eq $username){$_->groupname}} @grouplinks;
}else {
    my @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
    my @former_groups = map {if ($_->username eq $username){$_->groupname}} @grouplinks;
    foreach my $group(@{$new_group_assoc}){
        next if (grep {/^$group$/} @former_groups);
        $entered = "yes";
        my $sth = $db->prepare("insert into GroupLink (username, groupname) values ('$username', '$group')");
        $sth->execute;
    }
    
    foreach my $group(@former_groups){
        next if (grep {/^$group$/} @{$new_group_assoc});
        $db->do("delete from GroupLink where username='$username' and groupname='$group'");
    }
    $response_page="DONE";

    @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
    @activegroups = map {if ($_->username eq $username){$_->groupname}} @grouplinks;
}

</%init>

[Genex-cvs-commit] genex-server/Genex MANIFEST,1.34,1.35

From: <jas...@us...> - 2002-10-16 16:46:54

Update of /cvsroot/genex/genex-server/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv29900

Modified Files:
	MANIFEST 
Log Message:
usual


Index: MANIFEST
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/MANIFEST,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** MANIFEST	18 Sep 2002 21:19:26 -0000	1.34
--- MANIFEST	16 Oct 2002 16:46:50 -0000	1.35
***************
*** 1,4 ****
! Feature/Feature.pm
! Feature/Makefile.PL
  AM_FactorValues/AM_FactorValues.pm
  AM_FactorValues/Makefile.PL
--- 1,31 ----
! Audit/Audit.pm
! Audit/Makefile.PL
! Channel/Channel.pm
! Channel/Makefile.PL
! ContactType/ContactType.pm
! FeatureExtractionSoftware/FeatureExtractionSoftware.pm
! FeatureExtractionSoftware/Makefile.PL
! G2G/G2G.pm
! Identifiable/Identifiable.pm
! Identifiable/Makefile.PL
! MeasuredBioAssay/Makefile.PL
! MeasuredBioAssay/MeasuredBioAssay.pm
! Provider/Makefile.PL
! Provider/Provider.pm
! QuantitationLink/Makefile.PL
! QuantitationLink/QuantitationLink.pm
! QuantitationType/Makefile.PL
! QuantitationType/QuantitationType.pm
! QuantitationTypeDimension/Makefile.PL
! QuantitationTypeDimension/QuantitationTypeDimension.pm
! Reporter/Makefile.PL
! Reporter/Reporter.pm
! SampleLink/Makefile.PL
! SampleLink/SampleLink.pm
! TableAdmin/Makefile.PL
! TableAdmin/TableAdmin.pm
! UserSec/Makefile.PL
! UserSec/UserSec.pm
! 
  AM_FactorValues/AM_FactorValues.pm
  AM_FactorValues/Makefile.PL
***************
*** 33,36 ****
--- 60,65 ----
  ExternalDatabase/ExternalDatabase.pm
  ExternalDatabase/Makefile.PL
+ Feature/Feature.pm
+ Feature/Makefile.PL
  Fkey/Fkey.pm
  Fkey/Makefile.PL
***************
*** 80,84 ****
  XMLUtils/Makefile.PL
  XMLUtils/XMLUtils.pm.in
! html/Feature.html
  html/AM_FactorValues.html
  html/AM_Spots.html
--- 109,113 ----
  XMLUtils/Makefile.PL
  XMLUtils/XMLUtils.pm.in
! 
  html/AM_FactorValues.html
  html/AM_Spots.html
***************
*** 97,102 ****
  html/ExperimentSet.html
  html/ExternalDatabase.html
  html/Genex.html
- html/Genex/Feature.html
  html/Genex/AM_FactorValues.html
  html/Genex/AM_Spots.html
--- 126,131 ----
  html/ExperimentSet.html
  html/ExternalDatabase.html
+ html/Feature.html
  html/Genex.html
  html/Genex/AM_FactorValues.html
  html/Genex/AM_Spots.html
***************
*** 112,118 ****
--- 141,149 ----
  html/Genex/ControlledVocab.html
  html/Genex/Connect.html
+ html/Genex/DBUtils.html
  html/Genex/ExperimentFactors.html
  html/Genex/ExperimentSet.html
  html/Genex/ExternalDatabase.html
+ html/Genex/Feature.html
  html/Genex/Genex.html
  html/Genex/GroupLink.html
***************
*** 131,134 ****
--- 162,166 ----
  html/Genex/TreatmentLevel.html
  html/Genex/Treatment_AMs.html
+ html/Genex/UserSec.html
  html/Genex/SF_ExternalDBLink.html
  html/Genex/SequenceFeature.html
***************
*** 154,157 ****
--- 186,190 ----
  html/TreatmentLevel.html
  html/Treatment_AMs.html
+ html/UserSec.html
  html/SF_ExternalDBLink.html
  html/SequenceFeature.html
***************
*** 197,200 ****
--- 230,234 ----
  pod/TreatmentLevel.pod
  pod/Treatment_AMs.pod
+ pod/UserSec.pod
  pod/SF_ExternalDBLink.pod
  pod/SequenceFeature.pod
***************
*** 203,206 ****
--- 237,245 ----
  pod/curation-tool-login.pl.pod
  pod/db2xml.pl.pod
+ 
+ samples/redirect-test.pl.in
+ samples/session-login.pl.in
+ samples/test.pl.in
+ samples/test2.pl.in
  samples/Makefile.PL.in
  samples/control-bundle.pl.in
***************
*** 215,218 ****
--- 254,277 ----
  samples/pass-mod.pl.in
  samples/status.pl.in
+ 
+ scripts/array-design-insert.pl.in
+ scripts/array-measurement-insert.pl.in
+ scripts/create-db-accounts.pl.in
+ scripts/create_genex_class.pl.in
+ scripts/create_genex_db.pl.in
+ scripts/dbxml2tab.pl.in
+ scripts/gendb.pl.in
+ scripts/generate_group.pl.in
+ scripts/generate_user.pl.in
+ scripts/genex1-to-genex2.pl.in
+ scripts/group-insert.pl.in
+ scripts/layout.pl.in
+ scripts/mbad-insert.pl.in
+ scripts/qtdim-insert.pl.in
+ scripts/reporter-insert.pl.in
+ scripts/substitute.pl.in
+ scripts/user-insert.pl.in
+ scripts/xml2form.pl.in
+ scripts/xml2sql.pl.in
  scripts/create_genex_class.pl
  scripts/cv-insert.pl.in
***************
*** 232,236 ****
  scripts/software-insert.pl.in
  scripts/species-insert.pl.in
! t/Feature.t
  t/AM_FactorValues.t
  t/AM_Spots.t
--- 291,295 ----
  scripts/software-insert.pl.in
  scripts/species-insert.pl.in
! 
  t/AM_FactorValues.t
  t/AM_Spots.t
***************
*** 238,244 ****
--- 297,308 ----
  t/ArrayDesign.t
  t/Array.t
+ t/Audit.t
  t/BlastHits.t
+ t/Channel.t
+ t/Chromosome-pre.xml
  t/Chromosome.t
  t/Citation.t
+ t/Contact-pre.xml
+ t/ContactType-pre.xml
  t/Contact.t
  t/ContactType.t
***************
*** 248,271 ****
  t/ExperimentSet.t
  t/ExternalDatabase.t
  t/Genex.t
  t/GenexAdmin.t
  t/GroupLink.t
  t/GroupSec.t
  t/HTMLUtils.t
  t/HotSpots.t
  t/PhysicalBioAssay.t
  t/Protocol.t
  t/Sample.t
  t/SampleProtocols.t
  t/Scanner.t
  t/Software.t
  t/Species.t
  t/Spotter.t
  t/TL_FactorValues.t
  t/TestDB.pm
  t/TreatmentLevel.t
  t/Treatment_AMs.t
! t/SF_ExternalDBLink.t
! t/SequenceFeature.t
  t/XMLUtils.t
  
--- 312,353 ----
  t/ExperimentSet.t
  t/ExternalDatabase.t
+ t/Feature.t
+ t/FeatureExtractionSoftware.t
  t/Genex.t
  t/GenexAdmin.t
  t/GroupLink.t
  t/GroupSec.t
+ t/GroupLink-pre.xml
+ t/GroupSec-pre.xml
  t/HTMLUtils.t
  t/HotSpots.t
+ t/Identifiable.t
+ t/MeasuredBioAssay.t
  t/PhysicalBioAssay.t
  t/Protocol.t
+ t/Provider.t
+ t/QuantitationLink.t
+ t/QuantitationType.t
+ t/QuantitationTypeDimension.t
+ t/Reporter.t
+ t/SampleLink.t
  t/Sample.t
  t/SampleProtocols.t
  t/Scanner.t
+ t/SF_ExternalDBLink.t
  t/Software.t
+ t/Software-pre.xml
+ t/Species-pre.xml
  t/Species.t
  t/Spotter.t
+ t/Spotter-pre.xml
+ t/TableAdmin-pre.xml
+ t/TableAdmin.t
  t/TL_FactorValues.t
  t/TestDB.pm
  t/TreatmentLevel.t
  t/Treatment_AMs.t
! t/UserSec-pre.xml
! t/UserSec.t
  t/XMLUtils.t

[Genex-cvs-commit] genex-server/Genex/t ArrayLayout.t,1.6,NONE ArrayMeasurement.t,1.6,NONE FeatureExtraction.t,1.2,NONE QuantitationDimension.t,1.2,NONE SequenceFeature.t,1.5,NONE

From: <jas...@us...> - 2002-10-16 16:46:27

Update of /cvsroot/genex/genex-server/Genex/t
In directory usw-pr-cvs1:/tmp/cvs-serv29650/t

Removed Files:
	ArrayLayout.t ArrayMeasurement.t FeatureExtraction.t 
	QuantitationDimension.t SequenceFeature.t 
Log Message:
cruft


--- ArrayLayout.t DELETED ---

--- ArrayMeasurement.t DELETED ---

--- FeatureExtraction.t DELETED ---

--- QuantitationDimension.t DELETED ---

--- SequenceFeature.t DELETED ---

[Genex-cvs-commit] genex-server/Genex/pod AL_Spots.pod,1.7,NONE ArrayLayout.pod,1.7,NONE ArrayMeasurement.pod,1.8,NONE CSF_ExternalDBLink.pod,1.7,NONE CanonicalSequenceFeature.pod,1.7,NONE RelatedCSF.pod,1.7,NONE SpotLink.pod,1.7,NONE USF_ExternalDBLink.pod,1.7,NONE UserCanonicalLink.pod,1.7,NONE UserSequenceFeature.pod,1.7,NONE

From: <jas...@us...> - 2002-10-16 16:46:26

Update of /cvsroot/genex/genex-server/Genex/pod
In directory usw-pr-cvs1:/tmp/cvs-serv29650/pod

Removed Files:
	AL_Spots.pod ArrayLayout.pod ArrayMeasurement.pod 
	CSF_ExternalDBLink.pod CanonicalSequenceFeature.pod 
	RelatedCSF.pod SpotLink.pod USF_ExternalDBLink.pod 
	UserCanonicalLink.pod UserSequenceFeature.pod 
Log Message:
cruft


--- AL_Spots.pod DELETED ---

--- ArrayLayout.pod DELETED ---

--- ArrayMeasurement.pod DELETED ---

--- CSF_ExternalDBLink.pod DELETED ---

--- CanonicalSequenceFeature.pod DELETED ---

--- RelatedCSF.pod DELETED ---

--- SpotLink.pod DELETED ---

--- USF_ExternalDBLink.pod DELETED ---

--- UserCanonicalLink.pod DELETED ---

--- UserSequenceFeature.pod DELETED ---

[Genex-cvs-commit] genex-server/Genex/html AL_Spots.html,1.7,NONE ArrayLayout.html,1.7,NONE ArrayMeasurement.html,1.8,NONE CSF_ExternalDBLink.html,1.7,NONE CanonicalSequenceFeature.html,1.7,NONE RelatedCSF.html,1.7,NONE SpotLink.html,1.7,NONE USF_ExternalDBLink.html,1.7,NONE UserCanonicalLink.html,1.7,NONE UserSequenceFeature.html,1.7,NONE

From: <jas...@us...> - 2002-10-16 16:46:24

Update of /cvsroot/genex/genex-server/Genex/html
In directory usw-pr-cvs1:/tmp/cvs-serv29650/html

Removed Files:
	AL_Spots.html ArrayLayout.html ArrayMeasurement.html 
	CSF_ExternalDBLink.html CanonicalSequenceFeature.html 
	RelatedCSF.html SpotLink.html USF_ExternalDBLink.html 
	UserCanonicalLink.html UserSequenceFeature.html 
Log Message:
cruft


--- AL_Spots.html DELETED ---

--- ArrayLayout.html DELETED ---

--- ArrayMeasurement.html DELETED ---

--- CSF_ExternalDBLink.html DELETED ---

--- CanonicalSequenceFeature.html DELETED ---

--- RelatedCSF.html DELETED ---

--- SpotLink.html DELETED ---

--- USF_ExternalDBLink.html DELETED ---

--- UserCanonicalLink.html DELETED ---

--- UserSequenceFeature.html DELETED ---

[Genex-cvs-commit] genex-server/Genex/SequenceFeature SequenceFeature.pm,1.12,NONE

From: <jas...@us...> - 2002-10-16 16:46:24

Update of /cvsroot/genex/genex-server/Genex/SequenceFeature
In directory usw-pr-cvs1:/tmp/cvs-serv29650/SequenceFeature

Removed Files:
	SequenceFeature.pm 
Log Message:
cruft


--- SequenceFeature.pm DELETED ---

[Genex-cvs-commit] genex-server/Genex/Security Makefile.PL,1.4,NONE

From: <jas...@us...> - 2002-10-16 16:46:22

Update of /cvsroot/genex/genex-server/Genex/Security
In directory usw-pr-cvs1:/tmp/cvs-serv29650/Security

Removed Files:
	Makefile.PL 
Log Message:
cruft


--- Makefile.PL DELETED ---

[Genex-cvs-commit] genex-server/Genex/ContactOwner Makefile.PL,1.4,NONE

From: <jas...@us...> - 2002-10-16 16:46:22

Update of /cvsroot/genex/genex-server/Genex/ContactOwner
In directory usw-pr-cvs1:/tmp/cvs-serv29650/ContactOwner

Removed Files:
	Makefile.PL 
Log Message:
cruft


--- Makefile.PL DELETED ---

[Genex-cvs-commit] genex-server/Genex/ArrayMeasurement ArrayMeasurement.pm,1.28,NONE

From: <jas...@us...> - 2002-10-16 16:46:22

Update of /cvsroot/genex/genex-server/Genex/ArrayMeasurement
In directory usw-pr-cvs1:/tmp/cvs-serv29650/ArrayMeasurement

Removed Files:
	ArrayMeasurement.pm 
Log Message:
cruft


--- ArrayMeasurement.pm DELETED ---

[Genex-cvs-commit] genex-server/Genex/ArrayLayout ArrayLayout.pm,1.27,NONE Makefile.PL,1.4,NONE

From: <jas...@us...> - 2002-10-16 16:46:21

Update of /cvsroot/genex/genex-server/Genex/ArrayLayout
In directory usw-pr-cvs1:/tmp/cvs-serv29650/ArrayLayout

Removed Files:
	ArrayLayout.pm Makefile.PL 
Log Message:
cruft


--- ArrayLayout.pm DELETED ---

--- Makefile.PL DELETED ---

[Genex-cvs-commit] genex-server ChangeLog,1.98,1.99

From: <jas...@us...> - 2002-10-15 19:25:14

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv27368

Modified Files:
	ChangeLog 
Log Message:
usual



Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.98
retrieving revision 1.99
diff -C2 -d -r1.98 -r1.99
*** ChangeLog	15 Oct 2002 14:58:03 -0000	1.98
--- ChangeLog	15 Oct 2002 19:25:10 -0000	1.99
***************
*** 1,4 ****
--- 1,7 ----
  2002-10-15  Jason E. Stewart  <ja...@op...>
  
+ 	* Install (Repository): 
+ 	Added making the mason data dir world writable
+ 
  	* DB/xml/QuantitationType.xml (Repository): 
  	added column_number column

[Genex-cvs-commit] genex-server Install,1.5,1.6

From: <jas...@us...> - 2002-10-15 19:24:53

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv27187

Modified Files:
	Install 
Log Message:
* Install (Repository): 
Added making the mason data dir world writable



Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Install	13 Oct 2002 07:25:55 -0000	1.5
--- Install	15 Oct 2002 19:24:50 -0000	1.6
***************
*** 183,186 ****
--- 183,191 ----
  genex_system("cd $MOTHERDIR/G2G/mason; cp -r * $DIR");
  
+ # the mason data dir needs to be world writable
+ $DIR = $VARS{GENEX_MASON_DIR};  # Brevity && Clarity!
+ genex_mkdir($DIR) unless -d $DIR;
+ genex_system("chmod 777 $DIR");
+ 
  if (0) {

[Genex-cvs-commit] genex-server/Genex/FeatureExtractionSoftware .cvsignore,NONE,1.1

From: <jas...@us...> - 2002-10-15 19:22:30

Update of /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware
In directory usw-pr-cvs1:/tmp/cvs-serv26016/Genex/FeatureExtractionSoftware

Added Files:
	.cvsignore 
Log Message:
usual



--- NEW FILE: .cvsignore ---
Makefile
pm_to_blib

[Genex-cvs-commit] genex-server/Genex/QuantitationTypeDimension .cvsignore,NONE,1.1

From: <jas...@us...> - 2002-10-15 19:22:30

Update of /cvsroot/genex/genex-server/Genex/QuantitationTypeDimension
In directory usw-pr-cvs1:/tmp/cvs-serv26016/Genex/QuantitationTypeDimension

Added Files:
	.cvsignore 
Log Message:
usual



--- NEW FILE: .cvsignore ---
Makefile

[Genex-cvs-commit] genex-server/DB/curated_data 1200-mangle-AD.txt,NONE,1.1 1200-mangle.txt,NONE,1.1 MAGE-ML.dtd,NONE,1.1

From: <jas...@us...> - 2002-10-15 19:21:46

Update of /cvsroot/genex/genex-server/DB/curated_data
In directory usw-pr-cvs1:/tmp/cvs-serv25496/DB/curated_data

Added Files:
	1200-mangle-AD.txt 1200-mangle.txt MAGE-ML.dtd 
Log Message:
new



--- NEW FILE: 1200-mangle-AD.txt ---
# id	a_row	a_col	row	col	name
1.1.1.1	1	1	1	1	reporter00000
1.1.1.2	1	1	1	2	reporter00001
1.1.1.3	1	1	1	3	reporter00002
1.1.1.4	1	1	1	4	reporter00003
1.1.1.5	1	1	1	5	reporter00004
1.1.1.6	1	1	1	6	reporter00005
1.1.1.7	1	1	1	7	reporter00006
1.1.1.8	1	1	1	8	reporter00007
1.1.1.9	1	1	1	9	reporter00008
1.1.1.10	1	1	1	10	reporter00009
1.1.1.11	1	1	1	11	reporter00010
1.1.1.12	1	1	1	12	reporter00011
1.1.2.1	1	1	2	1	reporter00012
1.1.2.2	1	1	2	2	reporter00013
1.1.2.3	1	1	2	3	reporter00014
1.1.2.4	1	1	2	4	reporter00015
1.1.2.5	1	1	2	5	reporter00016
1.1.2.6	1	1	2	6	reporter00017
[...5338 lines suppressed...]
14.4.7.5	14	4	7	5	reporter05277
14.4.7.6	14	4	7	6	reporter05278
14.4.7.7	14	4	7	7	reporter05279
14.4.7.8	14	4	7	8	reporter05280
14.4.7.9	14	4	7	9	reporter05281
14.4.7.10	14	4	7	10	reporter05282
14.4.7.11	14	4	7	11	reporter05283
14.4.7.12	14	4	7	12	reporter05284
14.4.8.1	14	4	8	1	reporter05285
14.4.8.2	14	4	8	2	reporter05286
14.4.8.3	14	4	8	3	reporter05287
14.4.8.4	14	4	8	4	reporter05288
14.4.8.5	14	4	8	5	reporter05289
14.4.8.6	14	4	8	6	reporter05290
14.4.8.7	14	4	8	7	reporter05291
14.4.8.8	14	4	8	8	reporter05292
14.4.8.9	14	4	8	9	reporter05293
14.4.8.10	14	4	8	10	reporter05294
14.4.8.11	14	4	8	11	reporter05295
14.4.8.12	14	4	8	12	reporter05296

--- NEW FILE: 1200-mangle.txt ---
Begin Protocol Info	
Units	Microns
Array Rows	14
Array Columns	4
Rows	8
Columns	12
Array Row Spacing	4000
Array Columns Spacing	4500
Spot Rows Spacing	400		
Spot Columns Spacing	350		
Spot Diameter	250		
Interstitial	0	"0 is off, 1 is first one missing, 2 is second one missing"	
Spots Per Array	96		
Total Spots	5376		
Data is not crosstalk corrected.			
Data is not background subtracted.			
Quantification Method	Adaptive		
Quality Confidence Calculation	Minimum		
End Protocol Info			
[...5374 lines suppressed...]
5357	14	4	7	5	reporter05277	271.193542	87.069145	193.489059	133.097336	2.037558	11736.38184	242.36702	9844.553711	225.320969	52.087393
5358	14	4	7	6	reporter05278	248.89357	64.63298	221.981308	116.133789	2.143162	1117.037109	295.882965	524.095398	251.581345	4.440063
5359	14	4	7	7	reporter05279	455.931183	75.38298	371.614319	132.375549	3.444225	6706.828613	267.148926	5243.911621	243.655319	27.525886
5360	14	4	7	8	reporter05280	395.098145	76.5	314.195129	114.603317	3.447528	4873.20459	281.739349	3172.605225	257.580536	18.919149
5361	14	4	7	9	reporter05281	323.783661	109.340424	220.764313	159.638062	2.028236	1392.178223	366.191498	557.284119	308.216278	4.516887
5362	14	4	7	10	reporter05282	860.363647	93.047874	653.306519	129.055771	6.666603	1940.236328	283.973419	1040.633667	280.621674	6.914064
5363	14	4	7	11	reporter05283	446.971008	89.521278	361.904846	142.394821	3.138956	5533.947266	307.335114	3142.605957	277.997742	19.906447
5364	14	4	7	12	reporter05284	636.818542	122.553192	535.882629	203.275848	3.13278	7532.585938	377.579773	4881.692383	337.563568	22.31457
5365	14	4	8	1	reporter05285	1749.861694	74.643616	1376.627319	118.612053	14.752815	3125.299316	293.026581	1756.28125	219.318695	14.250036
5366	14	4	8	2	reporter05286	312.947449	64.457443	304.875305	124.737946	2.508839	1464.710815	244.372345	861.868164	227.027283	6.451695
5367	14	4	8	3	reporter05287	367.127655	88.05851	383.722961	152.763611	2.40324	1343.520386	275.101074	706.62207	260.85144	5.150519
5368	14	4	8	4	reporter05288	962.354675	65.69149	905.243347	102.990425	9.344118	7439.330566	230.813828	5742.22168	250.317535	29.719574
5369	14	4	8	5	reporter05289	1124.123779	85.478722	963.005676	130.811554	8.593459	1166.902466	250.829788	647.818665	328.546204	3.551715
5370	14	4	8	6	reporter05290	241.440231	93.994682	171.06572	142.485367	1.694491	743.024048	221.271271	345.772583	205.077728	3.623134
5371	14	4	8	7	reporter05291	1158.184448	69.957443	918.66449	119.851234	9.663517	1628.745483	273.946808	823.055664	248.461334	6.555328
5372	14	4	8	8	reporter05292	443.557037	80.61702	397.396179	129.158157	3.434216	1442.10791	278.49469	735.886658	251.635117	5.730949
5373	14	4	8	9	reporter05293	783.551575	93.228722	667.687195	159.412582	4.915243	4368.387695	317.771271	2099.566162	262.669312	16.63075
5374	14	4	8	10	reporter05294	525.073181	82.38298	469.331024	120.91935	4.342342	2580.049805	295.085114	1622.092651	257.034729	10.037748
5375	14	4	8	11	reporter05295	403.451752	117.776596	271.68515	166.662659	2.420769	2283.482666	344.287231	1049.236328	335.958527	6.796918
5376	14	4	8	12	reporter05296	780.031128	130.627655	482.258331	190.472534	4.095242	1952.742432	278.664886	996.180115	264.244812	7.389899

--- NEW FILE: MAGE-ML.dtd ---
<!--
	MAGE-ML.dtd

	(c) Copyright 2001 by
	EMBL-EBI (European Bioinformatics Institute)
	Rosetta Inpharmatics

	The organizations listed above hereby grant a royalty-free license to the 
	Object Management Group, Inc. (OMG) for world-wide distribution of this document 
	or any derivative works thereof, so long as the OMG reproduces the copyright 
	notices and the below paragraphs on all distributed copies.

	The material in this document is submitted to the OMG for evaluation.  
	Submission of this document does not represent a commitment to implement any portion 
	of this specification in the products of the submitters.
	WHILE THE INFORMATION IN THIS PUBLICATION IS BELIEVED TO BE ACCURATE, THE COMPANIES 
	LISTED ABOVE MAKE NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL INCLUDING 
	BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A 
	PARTICULAR PURPOSE.  The companies listed above shall not be liable for errors 
[...4898 lines suppressed...]
    CompositeSequence's BioMaterial.
    
    Associations
        Inherites associations from base class SequencePosition.
    
        reporter: A reporter that comprises part of a CompositeSequence.
    
        mismatchInformation: Differences in how the reporter matches its 
    compositeSequence's sequence.
    
    Attributes
        Inherites attributes from base class SequencePosition.
-->
<!ELEMENT ReporterPositionSources_assnlist (ReporterPosition+) >

<!ELEMENT ReporterPosition ((%SequencePosition_content;),
		Reporter_assnref,
		MismatchInformation_assnlist?) >
<!ATTLIST ReporterPosition %SequencePosition_attrs; >

[Genex-cvs-commit] genex-server/Genex/QuantitationDimension Makefile.PL,1.1,NONE QuantitationDimension.pm,1.3,NONE

From: <jas...@us...> - 2002-10-15 19:20:45

Update of /cvsroot/genex/genex-server/Genex/QuantitationDimension
In directory usw-pr-cvs1:/tmp/cvs-serv25034/Genex/QuantitationDimension

Removed Files:
	Makefile.PL QuantitationDimension.pm 
Log Message:
renamed



--- Makefile.PL DELETED ---

--- QuantitationDimension.pm DELETED ---

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