tab2mage-svn Mailing List for ArrayExpress Tab2MAGE

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Revision: 2399
          http://tab2mage.svn.sourceforge.net/tab2mage/?rev=2399&view=rev
Author:   farne
Date:     2012-01-03 14:41:14 +0000 (Tue, 03 Jan 2012)
Log Message:
-----------
tab2mage submissions no longer supported by ArrayExpress. submission pages updated.

Modified Paths:
--------------
    branches/ae-dev/Tab2MAGE/automation/tab2mage.cgi
    branches/ae-dev/Tab2MAGE/lib/ArrayExpress/AutoSubmission/templates/intro.html

Modified: branches/ae-dev/Tab2MAGE/automation/tab2mage.cgi
===================================================================

--- branches/ae-dev/Tab2MAGE/automation/tab2mage.cgi	2011-12-15 17:12:15 UTC (rev 2398)
+++ branches/ae-dev/Tab2MAGE/automation/tab2mage.cgi	2012-01-03 14:41:14 UTC (rev 2399)
@@ -26,22 +26,34 @@
 		alt         => 'ArrayExpress',
 	    },
 	    {
-		image       => '/microarray/T2M_logo_small.png',
-		destination => 'http://tab2mage.sourceforge.net/',
-		alt         => 'Tab2MAGE',
+		image       => '/microarray/MAGETAB_logo_small.png',
+		destination => 'http://tab2mage.sourceforge.net/docs/magetab_subs.html',
+		alt         => 'MAGE-TAB',
 		width       => 100,
 	    },
 	],
 	sidebar_links   => [
 	    {
-		text        => 'Introduction',
-		destination => 'http://www.ebi.ac.uk/miamexpress/help/tab2mage_help.html',
+		text        => 'Submitting MAGE-TAB to ArrayExpress',
+		destination => 'http://tab2mage.sourceforge.net/docs/magetab_subs.html',
 	    },
 	    {
-		text        => 'Creating a spreadsheet',
-		destination => 'http://tab2mage.sourceforge.net/docs/spreadsheet.html',
+		text        => 'MAGE-TAB overview',
+		destination => 'http://tab2mage.sourceforge.net/docs/magetab_docs.html',
 	    },
 	    {
+		text        => 'IDF detailed notes',
+		destination => 'http://tab2mage.sourceforge.net/docs/idf.html',
+	    },
+	    {
+		text        => 'SDRF detailed notes',
+		destination => 'http://tab2mage.sourceforge.net/docs/sdrf.html',
+	    },
+	    {
+		text        => 'MAGE-TAB specification',
+		destination => 'http://www.mged.org/mage-tab/',
+	    },
+	    {
 		text        => 'Microarray data submissions',
 		destination => 'http://www.ebi.ac.uk/microarray/submissions.html',
 	    },

Modified: branches/ae-dev/Tab2MAGE/lib/ArrayExpress/AutoSubmission/templates/intro.html
===================================================================
--- branches/ae-dev/Tab2MAGE/lib/ArrayExpress/AutoSubmission/templates/intro.html	2011-12-15 17:12:15 UTC (rev 2398)
+++ branches/ae-dev/Tab2MAGE/lib/ArrayExpress/AutoSubmission/templates/intro.html	2012-01-03 14:41:14 UTC (rev 2399)
@@ -2,70 +2,32 @@
     <h1><!-- TMPL_VAR NAME=TITLE --></h1>
 
 <table class="contenttable_lmenu">
- <tr>
-  <td>
-<b>The Tab2MAGE format will be phased out for submissions by the end of 2011.<br> The MAGE-TAB format should be used instead.<b> 
-  </td>
- </tr>
+<tr>
+<th>Tab2MAGE submissions no longer supported</th>
+</tr>
+<tr>
+<td class="leftsubheading"><br/>As of January 2012 ArrayExpress no longer accepts submissions in Tab2MAGE format. <br/><br/>
+
+Please submit your experiment description in MAGE-TAB format using the MAGE-TAB submission page: <br/> <a href="http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi">ArrayExpress MAGE-TAB submission page</a>
+<br/><br/>
+Existing Tab2MAGE submitters: Your Tab2MAGE submission page login details will work on the MAGE-TAB submission page. Contact us for advice at <a href="mailto:mia...@eb...">mia...@eb...</a> if you already have a Tab2MAGE spreadsheet and need help converting it to MAGE-TAB format, 
+or if you need to modify an experiment previously submitted using Tab2MAGE.
+<br/><br/>
+Please see <a href="http://tab2mage.sourceforge.net/docs/magetab_vs_tab2mage.html">this comparison page</a> for more information about why we are now using MAGE-TAB instead of Tab2MAGE.
+</td>
+</tr>
+<tr></tr>
 </table>
 
-    <p class="text">Welcome to the <!-- TMPL_VAR NAME=EXPT_TYPE -->
-    submissions system. This web page will allow you to submit your
-    data files with experimental annotation entered in a
-    spreadsheet. If you wish, you may have a template spreadsheet
-    automatically generated for you. Alternatively, if you are an
-    experienced user of Tab2MAGE, you may create your own spreadsheet
-    using the <a
-    href="http://tab2mage.sourceforge.net/docs/index.html">Tab2MAGE
-    documentation</a>.</p>
 
-    <p class="text">Note that if you wish to submit your data using
-    the more flexible <a
-    href="http://tab2mage.sourceforge.net/docs/magetab_docs.html">MAGE-TAB
-    format</a>, you should use our <a
-    href="http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi">MAGE-TAB
-    submissions web page</a>. MAGE-TAB is particularly recommended
-    in the following circumstances:</p>
 
-    <ul>
-
-      <li>Submission of high-throughput sequencing data (e.g., Solexa,
-      454).</li>
-
-      <li>Submission of other non array-based data (e.g.,
-      metabolomics, proteomics).</li>
-
-      <li>Cases in which you wish to precisely specify annotation
-      terms and their source <br/> (e.g., disease state terms, and their
-      accession numbers, from a disease ontology).</li>
-
-    </ul>
-
-    <p class="text">Please see <a
-    href="http://tab2mage.sourceforge.net/docs/magetab_vs_tab2mage.html">this
-    comparison page</a> for more detail. ArrayExpress will continue to
-    support both Tab2MAGE and MAGE-TAB submissions; if, however, you
-    wish to convert your Tab2MAGE spreadsheet into a MAGE-TAB
-    document, a <a
-    href="http://tab2mage.sourceforge.net/index.html#tabconverter">Tab2MAGE
-    to MAGE-TAB converter tool</a> has been created and made <a
-    href="http://sourceforge.net/project/showfiles.php?group_id=120325&package_id=226041">available
-    for download here</a>.</p>
-
-    <p class="text">Login to start a submission and generate a
-    template. Please use the "New submitter" link on this page if you
-    need to create a new account.</p>
-
-    <p class="text">Full help documentation is available using the links to
-    the side of this page.</p>
-
     <form method="post" action="<!-- TMPL_VAR NAME=CGI_BASE -->" enctype="multipart/form-data">
 
       <div class="navbar">
-      <input type="submit"
+      <input type="hidden"
 	     name="<!-- TMPL_VAR NAME=RM -->"
              value="<!-- TMPL_VAR NAME=LOGIN -->"/>
-      <input type="submit"
+      <input type="hidden"
 	     name="<!-- TMPL_VAR NAME=RM -->"
              value="<!-- TMPL_VAR NAME=SIGNUP -->"/>
       </div>

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