From 571b49d5806058b40c83e394527f3826df72305d Mon Sep 17 00:00:00 2001
From: pankaj <pankaj@localhost>
Date: Thu, 20 Mar 2014 21:53:59 +0000
Subject: [PATCH] added addition Cycs and updated hyperlinks

svn path=/; revision=546
---
 pathways/html/metabolic.html | 73 ++++++++++++++++++++++++------------
 1 file changed, 48 insertions(+), 25 deletions(-)
diff --git a/pathways/html/metabolic.html b/pathways/html/metabolic.html
index 9243147..9f0b743 100644
--- a/pathways/html/metabolic.html
+++ b/pathways/html/metabolic.html
@@ -1,5 +1,9 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<HTML>
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html
+  PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html>
 <HEAD>
 <TITLE></TITLE>
 <META NAME="Generator" CONTENT="TextPad 4.6">
@@ -13,60 +17,60 @@
 
 <center><h1>Plant Metabolic Pathways</h1></center>
 <p></p>
- <table align="center" border="0" cellpadding="2" cellspacing="2" height="360" width="90%">
+ <table align="center" border="1" cellpadding="2" cellspacing="2" height="360" width="80%" bgcolor="#E1EDCF">
 
 <tr class="searchbody">
-<td valign="top" width="32%"><b>RiceCyc</b> ver 3.3&nbsp; <b><img alt="" src="http://archive.gramene.org/pathway/ricecyc.gif" align="right" height="40" width="84" /></b><i><br />
+<td valign="top" width="32%"><b>RiceCyc</b> ver 3.3&nbsp; <b><img alt="" src="http://pathways.cgrb.oregonstate.edu/img/ricecyc.gif" align="right" height="40" width="84" /></b><i><br />
 Oryza sativa japonica</i> <br />
 Strain: Nipponbare<br /><a href="http://palea.cgrb.oregonstate.edu:1555/RICE/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/RICE/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/ricecyc.shtml">More info</a><br />
 </td>
-<td valign="top" width="32%"><b>AraCyc*</b> ver 10.0&nbsp; <img alt="" src="http://archive.gramene.org/pathway/aracyc_logo.gif" align="right" height="38" width="65" /><br />
+<td valign="top" width="32%"><b>AraCyc*</b> ver 10.0&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/aracyc_logo.gif" align="right" height="38" width="65" /><br />
 <i>Arabidopsis thaliana</i> <br />
 Strain: Columbia<br /> <a href="http://palea.cgrb.oregonstate.edu:1555/ARA/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/ARA/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/aracyc.shtml">More info</a><br />
 </td>
-<td valign="top" width="35%"><b>EcoCyc*</b> ver 17.0&nbsp;&nbsp; <img alt="" src="http://archive.gramene.org/pathway/EcoCyc.gif" align="right" height="40" width="125" /><br />
+<td valign="top" width="35%"><b>EcoCyc*</b> ver 17.0&nbsp;&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/EcoCyc.gif" align="right" height="40" width="125" /><br />
 <i>Escherichia coli</i> <br />
 Strain: K-12 MG1655<br /><a
 href="http://palea.cgrb.oregonstate.edu:1555/ECOLI/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/ECOLI/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/ecocyc.shtml">More info</a><br /><br />
 </td>
 </tr>
 <tr class="searchbody">
-<td valign="top" width="32%"><b>SorghumCyc</b> ver 1.1&nbsp;&nbsp; <img alt="" src="http://archive.gramene.org/pathway/sorghumcyc.png" align="right" border="0" height="18" width="84" /> <br />
+<td valign="top" width="32%"><b>SorghumCyc</b> ver 1.1&nbsp;&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/sorghumcyc.png" align="right" border="0" height="18" width="84" /> <br />
 <i>Sorghum bicolor</i> <br />
 Strain: BTx623<br /><a href="http://palea.cgrb.oregonstate.edu:1555/SORGHUM/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/SORGHUM/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/sorghumcyc.shtml">More info</a><br /><br />
 </td>
-<td valign="top" width="32%"><b>MedicCyc*</b> ver 1.0.1&nbsp; <img alt="" src="http://archive.gramene.org/pathway/medicago.jpg" align="right" height="43" width="45" /><br />
+<td valign="top" width="32%"><b>MedicCyc*</b> ver 1.0.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/medicago.jpg" align="right" height="43" width="45" /><br />
 <i>Medicago truncatula</i>, Barrelclover<br />
 Unavailable<br /> <a href="http://palea.cgrb.oregonstate.edu:1555/MEDIC/class-tree?object=Pathways"-->Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/MEDIC/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/mediccyc.shtml">More info</a><br /><br />
 </td>
-<td valign="top" width="35%"><b>MetaCyc*</b> ver 17.0&nbsp; <img alt="" src="http://archive.gramene.org/pathway/MetaCyc.gif" align="right" height="30" width="125" /><br />
+<td valign="top" width="35%"><b>MetaCyc*</b> ver 17.0&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/MetaCyc.gif" align="right" height="30" width="125" /><br />
 Reference Pathway Database<br />
 Strain: not applicable<br /><a
 href="http://palea.cgrb.oregonstate.edu:1555/META/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/META/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/metacyc.shtml">More info</a><br /><br />
 </td>
 </tr>
 <tr class="searchbody">
-<td valign="top" width="32%"><b>MaizeCyc</b> ver 2.1&nbsp; <img alt="" src="http://archive.gramene.org/pathway/maizecyc.jpg" align="right" border="0" height="45" width="132" /> <br />
+<td valign="top" width="32%"><b>MaizeCyc</b> ver 2.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/maizecyc.jpg" align="right" border="0" height="45" width="132" /> <br />
 <i>Zea mays</i> <br />
 Strain: B73<br /><a href="http://palea.cgrb.oregonstate.edu:1555/MAIZE/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/MAIZE/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/maizecyc.shtml">More info</a><br /><br />
 </td>
-<td valign="top" width="35%"><b>PoplarCyc*</b> ver 5.0&nbsp; <img alt="" src="http://archive.gramene.org/pathway/poplarcyc_logo.gif" align="right" height="30" width="125" /><br />
+<td valign="top" width="35%"><b>PoplarCyc*</b> ver 5.0&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/poplarcyc_logo.gif" align="right" height="30" width="125" /><br />
 Populus trichocarpa (and other Populus species and hybrids)<br />
 Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/POPLAR/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/POPLAR/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/poplarcyc.shtml">More info</a><br /><br />
 </td>
 
-<td valign="top" width="35%"><b>PlantCyc*</b> ver 7.0&nbsp; <img alt="" src="http://archive.gramene.org/pathway/plantcyc_logo.gif" align="right" height="30" width="125" /><br />
+<td valign="top" width="35%"><b>PlantCyc*</b> ver 7.0&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/plantcyc_logo.gif" align="right" height="30" width="125" /><br />
 Plant Metabolic Pathway Database<br />
 Strain: not applicable<br /><a href="http://palea.cgrb.oregonstate.edu:1555/PLANT/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/PLANT/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/plantcyc.shtml">More info</a><br /><br />
 </td>
 </tr>
 <tr class="searchbody">
 <td valign="top" width="32%"><b>BrachyCyc</b> ver 2.0&nbsp; <img alt=""
-src="http://archive.gramene.org/pathway/brachycyc.jpg" align="right" border="0" height="45" width="132" /> <br /> <i>Brachypodium distachyon</i> <br />
+src="http://pathways.cgrb.oregonstate.edu/img/brachycyc.jpg" align="right" border="0" height="45" width="132" /> <br /> <i>Brachypodium distachyon</i> <br />
 Strain: Bd21<br /><a href="http://palea.cgrb.oregonstate.edu:1555/BRACHY/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/BRACHY/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/brachycyc.shtml">More info</a><br /><br />
 </td>
 
-<!--td valign="top" width="32%"><b>CapCyc*</b> ver 1.0.1.1&nbsp; <img alt="" src="http://archive.gramene.org/pathway/pepper.gif" align="right" height="26" width="45" /><br /-->
+<!--td valign="top" width="32%"><b>CapCyc*</b> ver 1.0.1.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/pepper.gif" align="right" height="26" width="45" /><br /-->
 <!--i>Capsicum anuum</i>, Pepper<br /-->
 <!--Strain: n/a<br /> <a href="/CAP/class-tree?object=Pathways">Browse</a> | <a href="/CAP/organism-summary?">Summary</a> |&nbsp; <a href="/gramene/capcyc.shtml">More info</a><br /><br /-->
 <!--/td-->
@@ -75,7 +79,7 @@ Strain: Bd21<br /><a href="http://palea.cgrb.oregonstate.edu:1555/BRACHY/class-t
 <!--tr class="searchbody"-->
 <!--td valign="top" width="32%"><br /-->
 <!--/td-->
-<td valign="top" width="32%"><b>PotatoCyc*</b> ver 1.0.1&nbsp; <img alt="" src="http://archive.gramene.org/pathway/potato.jpg" align="right" height="45" width="45" /><br />
+<td valign="top" width="32%"><b>PotatoCyc*</b> ver 1.0.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/potato.jpg" align="right" height="45" width="45" /><br />
 <i>Solanum tuberosum</i>, Potato<br />
 Strain: n/a <br /> <a href="http://palea.cgrb.oregonstate.edu:1555/POTATO/class-tree?object=Pathways"-->Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/POTATO/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/potatocyc.shtml">More info</a><br /><br />
 </td>
@@ -83,20 +87,23 @@ Strain: n/a <br /> <a href="http://palea.cgrb.oregonstate.edu:1555/POTATO/class-
 </td>
 </tr>
 <tr class="searchbody">
-<td valign="top" width="32%"><br />
+<td valign="top" width="32%"><b>VitisCyc*</b> ver 1.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/grape.jpg" align="right" height="46" width="45" /><br />
+<i>Vitis vinifera</i>, Grape<br />
+Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/VITIS/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/VITIS/organism-summary?"-->Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/vitiscyc.shtml">More info</a><br /><br />
 </td>
-<td valign="top" width="32%"><b>CoffeaCyc*</b> ver 1.1.1&nbsp; <img alt="" src="http://archive.gramene.org/pathway/coffee.jpg" align="right" height="46" width="45" /><br />
+<td valign="top" width="32%"><b>CoffeaCyc*</b> ver 1.1.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/coffee.jpg" align="right" height="46" width="45" /><br />
 <i>Coffea canephora</i>, Coffee<br />
 Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/COFFEA/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/COFFEA/organism-summary?"-->Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/coffeacyc.shtml">More info</a><br /><br />
 </td>
 <td valign="top" width="35%"><br />
 </td>
 </tr>
-
 <tr class="searchbody">
-<td valign="top" width="32%"><br />
+<td valign="top" width="32%"><b>EucalyptusCyc*</b> ver 1.7&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/eucalyptus.jpg" align="right" height="45" width="45" /><br />
+<i>Eucalyptus grandis</i>, Eucaplyptus<br />
+Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/EUCALYPTUS/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/EUCALYPTUS/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/eucalyptuscyc.shtml">More info</a><br /><br />
 </td>
-<td valign="top" width="32%"><b>LycoCyc*</b> ver 2.0.1&nbsp; <img alt="" src="http://archive.gramene.org/pathway/tomato.jpg" align="right" height="45" width="45" /><br />
+<td valign="top" width="32%"><b>LycoCyc*</b> ver 2.0.1&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/tomato.jpg" align="right" height="45" width="45" /><br />
 <i>Solanum lycopersicum</i>, Tomato<br />
 Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/LYCO/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/LYCO/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/lycocyc.shtml">More info</a><br /><br />
 </td>
@@ -105,13 +112,27 @@ Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/LYCO/class-tree
 </tr>
 
 <tr class="searchbody">
-<td colspan="3" rowspan="1" valign="top">
+<td valign="top" width="32%"><b>FragariaCyc*</b> ver 2.0&nbsp; <img alt="" src="http://pathways.cgrb.oregonstate.edu/img/strawberry.gif" align="right" height="45" width="45" /><br />
+<i>Fragaria vesca</i>, Strawberry<br />
+Strain: n/a<br /><a href="http://palea.cgrb.oregonstate.edu:1555/FRAGARIA/class-tree?object=Pathways">Browse</a> | <a href="http://palea.cgrb.oregonstate.edu:1555/FRAGARIA/organism-summary?">Summary</a> |&nbsp; <a href="http://palea.cgrb.oregonstate.edu:1555/jaiswallab/fragariacyc.shtml">More info</a><br /><br />
+</td>
+<td valign="top" width="32%">
+</td>
+<td valign="top" width="35%"><br />
 </td>
 </tr>
-
-</table>
-* Mirror database. Not curated by the Gramene database. Click on <b>more info</b> link for details.
+<tr class="searchbody">
+<td colspan="3" rowspan="1" valign="middle">
+*  Mirror database.
+<br>
+** Curated and developed by the Gramene database.
 <br>
+** Developed by the Naithani Lab.
+<br>
+</td>
+</tr>
+</table>
+<p>
 
 
 <h2>Other Tools</h2>
@@ -187,11 +208,13 @@ reactions, pathways, compounds, proteins, transporters and/or transcription unit
          </tr>
 </table>
 
+<!--
 <a name = "download"></a><h2>Download</h2>
 	<ul>
 		<li><a href="ftp://ftp.gramene.org/pub/gramene/pathways/">Downloads</a> from our ftp archive.
 		<li>For other species, please follow the links from the <a href="#acknowledgements">Acknowledgements</a></li>
 	</ul>
+-->
 
  <h2>Useful external links</h2>
 <table width="80%" cellpadding="6" cellspacing="4" align="center">
@@ -227,7 +250,7 @@ reactions, pathways, compounds, proteins, transporters and/or transcription unit
 <a name="acknowledgements"></a><h2>Acknowledgements</h2>
 <ul>
 <p>
-	RiceCyc, SorghumCyc, MaizeCyc and BrachyCyc pathway databases were created using the <a href="http://bioinformatics.ai.sri.com/ptools/">Pathway Tools</a> software developed by Peter D. Karp</a> and coworkers in the <a href="http://bioinformatics.ai.sri.com/">Bioinformatics Research Group</a> at SRI International.
+	Pathway databases were created using the <a href="http://bioinformatics.ai.sri.com/ptools/">Pathway Tools</a> software developed by Peter D. Karp</a> and coworkers in the <a href="http://bioinformatics.ai.sri.com/">Bioinformatics Research Group</a> at SRI International.
 </p>
 
 <p>
-- 
2.34.1


RiceCyc ver 3.3 +	RiceCyc ver 3.3 Oryza sativa japonica Strain: Nipponbare Browse \| Summary \| More info	AraCyc* ver 10.0 +	AraCyc* ver 10.0 Arabidopsis thaliana Strain: Columbia Browse \| Summary \| More info	EcoCyc* ver 17.0 +	EcoCyc* ver 17.0 Escherichia coli Strain: K-12 MG1655 Browse \| Summary \| More info
SorghumCyc ver 1.1 +	SorghumCyc ver 1.1 Sorghum bicolor Strain: BTx623 Browse \| Summary \| More info	MedicCyc* ver 1.0.1 +	MedicCyc* ver 1.0.1 Medicago truncatula, Barrelclover Unavailable Browse \| Summary \| More info	MetaCyc* ver 17.0 +	MetaCyc* ver 17.0 Reference Pathway Database Strain: not applicable Browse \| Summary \| More info
MaizeCyc ver 2.1 +	MaizeCyc ver 2.1 Zea mays Strain: B73 Browse \| Summary \| More info	PoplarCyc* ver 5.0 +	PoplarCyc* ver 5.0 Populus trichocarpa (and other Populus species and hybrids) Strain: n/a Browse \| Summary \| More info	PlantCyc* ver 7.0 +	PlantCyc* ver 7.0 Plant Metabolic Pathway Database Strain: not applicable Browse \| Summary \| More info
BrachyCyc ver 2.0 Brachypodium distachyon +src="http://pathways.cgrb.oregonstate.edu/img/brachycyc.jpg" align="right" border="0" height="45" width="132" /> Brachypodium distachyon Strain: Bd21 Browse \| Summary \| More info	PotatoCyc* ver 1.0.1 +	PotatoCyc* ver 1.0.1 Solanum tuberosum, Potato Strain: n/a Browse \| Summary \| More info	+	VitisCyc* ver 1.1 +Vitis vinifera, Grape +Strain: n/a Browse \| Summary \| More info	CoffeaCyc* ver 1.1.1 +	CoffeaCyc* ver 1.1.1 Coffea canephora, Coffee Strain: n/a Browse \| Summary \| More info
+	EucalyptusCyc* ver 1.7 +Eucalyptus grandis, Eucaplyptus +Strain: n/a Browse \| Summary \| More info	LycoCyc* ver 2.0.1 +	LycoCyc* ver 2.0.1 Solanum lycopersicum, Tomato Strain: n/a Browse \| Summary \| More info	+			FragariaCyc* ver 2.0 +Fragaria vesca, Strawberry +Strain: n/a Browse \| Summary \| More info +	+