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expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo
(anatomy, morphogenesis). Currently, two organism models are described in Aniseed: Ciona intestinalis and halocynthia roretzi.">
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<?
/*
    ANISEED, NISEED System and Database
    Copyright (C) 2007 Olivier Tassy, Fabrice Daian, Patrick Lemaire

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

*/

include ("frames_header.php");
include ("logtrace.php");
?>




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		<!-- Picture of the month -->
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		<img border="0" style="border:0px solid black;padding:2px;" width="300" src="picWE/128vegetal_ciona_intestinalis.jpg"><!--</a>-->
		<br>
		<b><font color="#456898" size="2">Picture of the month:<br></font><font color="#656565" size="-1"> Vegetal view of a reconstructed 128-cell Ciona gastrula. Muscle and mesenchyme are in red, endoderm in blue, notochord in orange, TLC in green, and A-line neural cells in yellow. <br> Image communicated by F. Robin and P. Lemaire.
<br> </font></b></font><br>

		<!-- <font size="1"><i><div align="center">A digitalized ciona embryo at 16-cell stage - Olivier Tassy</div></i></font>  -->
		<font size="1" color="crimson">(Don't hesitate to <a href="mailto:aniseed@ibdm.univ-mrs.fr">send us</a> your own pictures with a short description !)</font>
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		<!-- ANISEED NEWS -->
			<div id="content">
			<table style="background:white;color:black;border:1px solid black;" border="0">
				<tr><td align="center" style="background:#c0d5e3;"><b><small>ANISEED news</small></b></td></tr>
				<tr>
					<td>
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								<td><font color="red"><small><b>18/12/2009</b></small></font>
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								<small>
								<br />
								<font color="red"><b> Due to system and database updates, the Aniseed website will be perturbed.<br> Thank you for your comprehension.</b></font>
								</small>
								<br />
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								<td><font color="red"><small><b>15/12/2009</b></small></font>
								<br />
								<img src="pictures/article_icon.gif"></td>
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								<small>
								<b><i>New articles</i></b>:
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								<small>
								<br />
								Articles recently added to the database
								
								<ul>
									<li>
										<a href="http://aniseed-ibdm.univ-mrs.fr/view-article.php?id=360">Imai and al. 2009-12-08</a> (Ciona neural GNR)

									</li>
									<li>
										<a href="http://aniseed-ibdm.univ-mrs.fr/view-article.php?id=350">Kawada 2008</a> (Ciona vasopressin)
									</li>
									<li>
										<a href="http://aniseed-ibdm.univ-mrs.fr/view-article.php?id=361">Keduka 2008</a> (MRas function)
									</li>
									<li>
										<a href="http://aniseed-ibdm.univ-mrs.fr/view-article.php?id=363">Auger 2009</a> (ROR-a cis-regulatory)
									</li>
									<li>
										<a href="http://aniseed-ibdm.univ-mrs.fr/view-article.php?id=358">Shi 2008</a> (FGF3 in ciona floor plate)
									</li>
									<li>
										<a href="http://aniseed-ibdm.univ-mrs.fr/view-article.php?id=357">Chiba 2008</a> (Brachyury function in juvenile )
									</li>
								</ul>
								If you are author of these articles, please check the annotation and don't hesitate <a  href="mailto:aniseed@ibdm.univ-mrs.fr">to contact us</a> if you have remarks.
								<br />
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								<td><font color="red"><small><b>15/12/2009</b></small></font>
								<br />
								<img src="pictures/hammer_icon.png"></td>
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								<small>
								<b><i>New pages</i></b>: </small>
								</td>
							</tr>
                                                        <tr>
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								<small>
								<ul>
									<li>
								<b>Upstream regulators page</b> (eg <a href = "http://aniseed-ibdm.univ-mrs.fr/gene-regulation-card.php?clusterid=cluster3592">otx regulation</a>)<br /><br />
								At the individual gene level, the "Upstream regulators tab" gives access to all genes regulating a gene of interest in the various territories across development.<br />
								For example, if the gene of interest is Otx,  you can access to evidences indicating that Ci-FGF9/16/20 upregulates Ci-otx in b6.5 cell pair (2 evidences) and a6.5 cell pair (2 evidences) at 32-cell stage.
									</li>
									<br />
									<br />
									<li>
								<b>Downstream targets page</b> (eg <a href = "http://aniseed-ibdm.univ-mrs.fr/gene-function-card.php?clusterid=cluster3592">otx function</a>)<br /><br />
									The "Downstream targets tab" lists targets of the gene of interest by territories and stages.<br />
									For example, if the gene of interest is Otx,  you can access to evidences indicating that Otx upregulates TWIST-like-b in   A8.12 cell pair (1 evidence)   A8.11 cell pair (1 evidence)   B8.5 cell pair (1 evidence)   B7.7 cell pair (1 evidence) at 112 cell stage.
									</li>
									<br />
									<br />
									<li>
								<b>Anatomy-regulation-card.php</b> (eg <a href = "http://aniseed-ibdm.univ-mrs.fr/anatomy-regulation-card.php?idanat=2770762">A8.11</a>)<br /><br />
										At the individual territory level, the "anatomical gene network card" indicates the regulatory interactions that take place in this territory. It shows a table in which genes in the columns are regulated by genes in the rows.
									</li>
								</ul>
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								<td><font color="red"><small><b>09/03/2009</b></small></font>
                                                                <br>
                                                                <img src="pictures/Gbrowse.jpg">
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								<td width="70%">
								<br>
								<small>
							        <i><b>New</b></i>: 
								</small>
							        </td>
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								<td colspan="2">
								<small>
							        Full ORF Gateway-compatible clones and KH transcript models are now accessible from the Aniseed website, in addition to their representation in the Aniseed Genome browser.
                                                                 <a href="http://aniseed-ibdm.univ-mrs.fr/help.php">How access these information?</a> </a> <br>
								</small>
								</td>
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								<td><font color="red"><small><b>05/05/2009</b></small></font></td>
								<td><img width="50" src="Icon-Travaux.gif"></td>
								<td>
								<small>
								<font color="red"><b> Due to major system and database updates, the Aniseed Genome Browser is out to work today.<br> Thank you for your comprehension.</b></font>
								</small>
								<br><br>
								</td>
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								<td><font color="red"><small>09/04/2009</small></font></td>
								<td><img src="pictures/Egg.jpg"></td>
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								<br>
								<small>
							        <i><b><font color="red" size="2">

                                                                ANISEED BIG GAME!!!!!!

                                                                </font></b></i><br>
							         Heard of Easter egg hunts<br><br>
                                                                 Results: nobody found the 15 eggs.
                                                                 The three first will receive a big chocolate egg in Okinawa Tunicate meeting:  <br>
                                                                                                                                                <br>
                                                                 - 12 eggs: Florian Razy                                                        <br>
                                                                 - 10 eggs: Shota Chiba                                                         <br>
                                                                 - 9 eggs: Stacie Whitaker and Sebastien Darras


                                                                </a> </a> <br>
								<br>
								</small>
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								</td>
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                                                        <tr>
								<td colspan="2"><font color="red"><small>09/03/2009</small></font>
                                                                <br>
                                                                <img src="pictures/Gbrowse.jpg">
                                                                </td>

								<td>
								<br>
								<small>
							        <i><b>New</b></i>: Full ORF Gateway-compatible clones and KH transcript models are now accessible from the Aniseed website, in addition to their representation in the Aniseed Genome browser.
                                                                 <a href="http://aniseed-ibdm.univ-mrs.fr/help.php">How access these information?</a> </a> <br>
								<br>
								</small>
								<br>
								</td>
							</tr>

                                                        <tr>
								<td><font color="red"><small>16/07/2008</small></font></td>
								<td><img src="pictures/article_icon.gif"></td>
								<td>
								<small>
								<i>New</i>: You can visualize all wild type insitu expression pictures for a given gene by clicking on the "Expression at a glance" tab in the gene cards.<a href="gene-picture.php?clusterid=cluster3592">Example</a> </a> <br>
								<br>
								</small>
								<br>
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							<tr>
								<td><font color="red"><small>08/02/2008</small></font></td>
								<td><img src="pictures/article_icon.gif"></td>
								<td>
								<small>
								<i>New</i>: New Article Card search interfaces are available. You can search by <a href="bib-search-mol.php">Gene analyzed</a> or by <a href="bib-search-anatomy.php">Territories affected</a> <br>
								<br>
								</small>
								<br>
								</td>
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							<tr>
								<td><font color="red"><small>10/01/2008</small></font></td>
								<td><img width="50" src="comment.png"></td>
								<td>
								<small>
								<b><i>Update</i></b>: User friendly In Situ search interfaces are now online on Aniseed. (Bugs fixed 14/01/08) <br>
								<br>
								</small>
								</td>
							</tr> 


							<tr>
								<td><font color="red"><small>23/10/2007</small></font></td>
								<td><img src="pictures/hammer_icon.png"></td>
								<td>
								<small>
								<b><i>New</i></b>: A new Molecular Tool interface is now available on the website accessible from the Gene Card page or from Article Card page. You can also search for any molecular tool by using <a href="moltool-search.php">this page</a><br>
								<br>
								</small>
								</td>
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							<tr>
								<td><font color="red"><small>23/10/2007</small></font></td>
								<td><img src="pictures/article_icon.gif"></td>
								<td>
								<small>
								<b><i>New</i></b>: A new Article Card interface is now available on the website which pools all Aniseed Data related to a given article.<br>
								<a href="show-article.php">Show all articles present in the database</a>
								<br>
								</small>
								<br>
								</td>
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								<td><font color="red"><small>05/09/2007</small></font></td>
								<td><img  width="50" src="picWE/embryo16.jpg"></td>
								<td style="padding:5px; border:1px solid red;">
								<small><b><i><font color="red">PATCH</font></i></b>: Following a server migration, the 3D Virtual Embryo has to be patched to connect to the database. Explanations and Download are <a href="virtual_embryo.php">here</a>
								<br>
								</small>
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						<!--	<tr>
								<td><font color="red"><small>28/06/2007</small></font></td>
								<td><img  width="50" src="picWE/embryo16.jpg"></td>
								<td>
								<small><b><i>New</i></b>: Individual transcript models (JGI, ENSEMBL, Kyotograil) have been grouped into Gene models and a new search interface created: <br>
								Find a Gene : <a href="gene-search.php">Find a Gene into Aniseed</a><br>
								An example of a Gene Card: <a href="gene-card.php?clusterid=cluster3592">Otx Gene Card</a><br>
								</small>
								</td>
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								<td><font color="red"><small>11/06/2007</small></font></td>
								<td><img  width="50" src="mappro.jpg"></td>
								<td><small><b><i>Update</i></b>: Gene expression profile card for JGI gene model + Expression Curves (<a href="molecule-gene.php?name=ci0100133709">see an example</a>)</small>
								</td>
							</tr>-->
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		<!-- FIN ANISEED NEWS -->
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				<table style="background:white;color:black;border:1px solid black;" border="0">
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						<td align="center" style="background:#c0d5e3;"><b><font color="black"><small>Community news</small></b></font></td>
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									<font color="red"><small>17/04/2007</small></font>
									</td>
									<td  valign="top" style="background:white;">
									<small>
									<a target="_blank" style="text-decoration:none;" href="http://biodev.obs-vlfr.fr/tunicatemeeting/">
									4th International Tunicate Meeting.Saturday June 23rd to Wednesday June 27th.<br>
									Villefranche-sur-Mer, Observatoire Oceanologique Saint-Jean Cap Ferrat, Residence Delcloy<br>
									<a href="http://biodev.obs-vlfr.fr/tunicatemeeting/">http://biodev.obs-vlfr.fr/tunicatemeeting/</a>
									</a>
									</small>
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		<TR>
		<TD valign="middle">
		<font color="#D64242" size="3"><b>ANISEED version 3:<br> <i>A model organism database for Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata</i></b></font>
		</TD>
		<TD>
		<div align="right"><a href="http://www.tunicate-portal.org"><img style="border:1px dashed black;padding:2px;background-color:white;" width="150" src="pictures/Logo5.jpg"></a></div>
		</TD>
		</TR>
		</TABLE>
		<p align="justify"><font color="#656565" size="-1">
			Welcome to ANISEED version 3<br />
			Aniseed is a database designed to offer a representation of ascidian embryonic development at the level
			of the genome (cis-regulatory sequences, spatial gene expression, protein annotation),
			of the cell (cell shapes, fate, lineage) or of the whole embryo (anatomy, morphogenesis).
			Currently, the anatomy of four organism models are represented in Aniseed: Ciona intestinalis,
			Ciona savignyi, Halocynthia roretzi and Phallusia mammillata.
			Extensive molecular data can be found for Halocynthia roretzi and Ciona intestinalis.
			In particular, this version supports four sets of Ciona intestinalis transcript models: JGI v1.0,
			KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models.
			You can explore gene expression profiles during normal or experimentally manipulated development,
			access validated cis-regulatory regions, get the molecular tools used to assay gene function,
			or all articles related to the function, or regulation of a given gene.
			Known transcriptional regulators and targets are listed for each gene,
			as are the gene regulatory networks acting in individual anatomical territories.
			The archived ANISEED v2.0 can still be accessed from the "about" tab of the menu.<br />
			Have fun and as usual, please send us feedback on this version at <a href="mailto:aniseed@ibdm.univ-mrs.fr">aniseed@ibdm.univ-mrs.fr</a>.<br />
			The aniseed team 
		</font></p>
			<!-- EO INTRO TEXT -->
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		<!--<td valign="top" style="background-color:white;">-->
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		<!--ANISEARCH -->
		<br>
		<img width="250" src="anisearch.jpg" >&nbsp;<br>
		<p align="justify"><font color="#656565" size="-1">If you don't know where to start ... Use anisearch to perform a keyword search on the whole database except cDNA clones, which can be accessed via the "genes/clones" menu at the top of the page. <br>
		eg. "otx" retrieves all data associated to otx. You can also combine words for example "otx 32 cell a6.5" will retrieve all in situs for otx at the 32 cell stage showing staining in the a6.5 blastomere.</font></p>
			<div align="center">
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						<td>&nbsp;</td>
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							<div id="cadre">
							<br>
							<form name="global" method="POST" action="anisearch2.php" target="_blank">
							<input type="text" name="search" value="" size="50" onclick="this.value='';"/>
							&nbsp;&nbsp;<input type="submit" value="&nbsp;&nbsp;&nbsp;Search&nbsp;&nbsp;&nbsp;" />&nbsp;&nbsp;
							<br>
							<font color="black">
							<input type="radio" name="OP" value="OR" > <small>OR </small>
							&nbsp;&nbsp;&nbsp;
							<input type="radio" name="OP" value="AND" checked> <small>AND </small>
							&nbsp;&nbsp;&nbsp;
							<input type="radio" name="OP" value="whole"> <small>Complete sentence </small>
							<!--RAJOUT POUR LE BLAST -->
							<input type="hidden" name="blast" value="blast">
							<!--RAJOUT POUR LES ORTHOLOGS -->
							<input type="hidden" name="ortho" value="ortho">
							</font>
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						<td>&nbsp;</td>
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		<!-- EO ANISEARCH -->
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<!--
			<font color="#456898" size="2"><b><a target="_blank" href="http://www.tunicate-portal.org"><font color="#456898">Tunicate Web Portal</font></a></b></font><br>
			<TABLE>
			<TR>
			<TD>
			<font color="#656565" size="-1">Tunicate Web Portal is an access point to Websites and Databases dealing with Tunicates. <a target="_blank" href="http://www.tunicate-portal.org">Here</a></font>
			</TD>
			<TD>
			<a border="0" target="_blank" href="http://www.tunicate-portal.org"><img border="0" width="150" src="pictures/Logo5.jpg"></a>
			</TD>
			<TD width="40%">&nbsp;</TD>
			</TR>
			</TABLE>
			<br>
-->



			<font color="#456898" size="2"><b><a href="http://crfb.univ-mrs.fr/aniseed/ARCHIVE_2.0/"><font color="#456898">Aniseed V2.0 - Archive</font></a></b></font><br>
			<font color="#656565" size="-1">Aniseed in its previous version is still available by clicking <a href="http://crfb.univ-mrs.fr/aniseed/ARCHIVE_2.0/">Aniseed V2.0</a></font>
			<br>
			<br>
			<font color="#456898" size="2"><b><a href="virtual_embryo.php"><font color="#456898">Virtual embryo</font></a></b></font><br>
			<font color="#656565" size="-1">The 3D Virtual embryo is available to download in the download section of the website. <br>
			It's well supported on the majority of platform (MacOS, Windows, Linux).</font>
			<br>
			<br>
			<font color="#456898" size="2"><b><a href="Download_data.php"><font color="#456898">Download</font></a></b></font><br>
			<font color="#656565" size="-1">All the data present in our website are now freely downloadable (Insitu data, clones, anatomical ontologies, ...) Visit our download page for more informations.</font>
			<br>
			<br>
			<font color="#456898" size="2"><b><a href="help.php"><font color="#456898">Tutorials</font></a></b></font><br>
			<font color="#656565" size="-1">Many tutorials (text and movies) are online and may be useful ...</font>
			<br>

			<br>


			<br>
			<font color="#456898" size="2"><b><a href="exchange_format.php"><font color="#456898">MISFISHIE Exchange Format</font></a></b></font><br>
			<font color="#656565" size="-1">In Situs Exchange Format used by ANISEED.</font>
		</td>
	</tr>
</table>
<!-- FIN COTE DROIT -->
</td>

</tr>
</table>

<br>

<center>
<font color="#656565" size="2"><b>Part of information found in aniseed could be also found in</b></font><br><br>
<a href="http://ghost.zool.kyoto-u.ac.jp/"><img border="0" src="mini-ghost.jpg"></a>&nbsp;&nbsp;<a href="http://www.genome.jp/magest/"><img border="0" src="MAGESTlogo.jpg"></a>&nbsp;&nbsp;<a href="http://www.ncbi.nlm.nih.gov/"><img border="0" src="ncbi2.gif"></a>&nbsp;&nbsp;<a href="http://genome.jgi-psf.org/ciona4/ciona4.home.html"><img width="70" border="0" src="pictures/jgi_logo.jpg"></a>&nbsp;&nbsp;<a href="http://www.ensembl.org/"><img border="0" src="ensembl.gif"></a></font>
</center>








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