Team:Caltech/Notebook

From 2012.igem.org

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__NOTOC__
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{{Template:Caltech_Header}}
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<html>
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<style type="text/css">
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body {background: #EBA243}
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.firstHeading {
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display:none !important;
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}  
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#p-logo { height:1px; overflow:hidden; display: none;}
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#top-section {
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background-image:url('https://static.igem.org/mediawiki/2012/2/28/IDcard.jpg');;
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height:300px  ! important;;
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}
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p {text-align: justify;}
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a:link { color: #00b0e6; text-decoration: none}
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a:visited { color:#00b0e6; text-decoration: none}
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a:hover { color:#f29400; text-decoration: none}
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a:active { color:#f29400; text-decoration: none}
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#bodyContent { padding: 10px auto; width: 910px; margin: auto; clear: none; }
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table#Team { text-align: justify; border: 0; }
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table#Team h2, table#Team h3 { clear: both; }
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/*-----------------------------------------------------------------------------------------------*/
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div.MenuBar ul li ul.DropDownMenu {
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  display: none; /* Hides all drop-down menus. */
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}
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/*
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li:hover works in IE7 and FF2.
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a:hover works in IE6 and FF2.
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a:hover breaks li:hover in FF2.
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*/
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div.MenuBar ul li:hover ul.DropDownMenu li ul.SideMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu li a ul.SideMenu {
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  display: none; /* Hides all side menus. */
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}
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/*------------------------------------------------------------------------------------- Menu Bar */
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div.MenuBar {
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  font: arial, helvetica, sans-serif;
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  height: 30px;
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  width: 910px;
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  /*width: 100%*/
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  margin: 0;
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  border-top: 0;
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  border-right: 0;
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  border-left: 0;
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  padding: 0;
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  background: black;
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}
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div.MenuBar ul {
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  font: arial, helvetica, sans-serif;
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  text-align: center;
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  list-style-type: none;
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  margin: 0.5em auto;
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  border: 0;
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  padding: 0;
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  background: black;
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}
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div.MenuBar ul li {
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  font: arial, helvetica, sans-serif;
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  display: block;
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  padding: 0;
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  margin: 0;
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  font-size: 1.3em;
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  float: left;
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  background: black;
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  text-align: center;
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  width: 107px;
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  position: relative; /* Sets the positioning context for each drop-down menu. */
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}
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div.MenuBar ul li a {
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  font: arial, helvetica, sans-serif;
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  display: block;
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  background: black;
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  height: 22px; /* Keep height + padding-top + padding-bottom sync with the menu bar height. */
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  color: #ffffff;
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  padding-top: 4px;
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  padding-bottom: 4px;
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  padding-left: 1em; /* Sets the left space between top-level items. */
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  padding-right: 1em; /* Sets the right space between top-level items. */
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  text-decoration: none;
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}
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/*------------------------------------------------------------------------------ Drop-Down Menus */
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div.MenuBar ul li:hover ul.DropDownMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu {
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  display: block;
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  width: 10em; /* Drop-down menu width.
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                  Use MenuTailor.css to customize. */
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  height: 1em;
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  padding: 1px; /* Sets the drop-down menu "effective border" width. */
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  position: absolute;
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  top: 23px; /* Places the drop-down menu under the menu bar.
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                Keep it sync with the menu bar height. */
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  left: 0; /* Aligns the drop-down menu to its top-level item. */
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  background-color: black; /* Selected item. */
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  color: #FFFFFF;
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}
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div.MenuBar ul li:hover ul.DropDownMenu li a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a {
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  width: 10em; /* Keep it sync with the drop-down menu width.
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                            Use MenuTailor.css to customize. */
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  height: 1em;
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  padding-left: 0;
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  padding-right: 0;
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  background-color: black; /* Selected item. */
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  color: #FFFFFF;
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}
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ul.DropDownMenu li a span {
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  display: block;
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  padding-left: 0.75em; /* Sets the left space of each drop-down menu item. */
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  padding-right: 0.25em; /* Sets the right space of each drop-down menu item. */
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  text-align: right; /* Aligns the >> symbol to the right. */
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}
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ul.DropDownMenu li a span span {
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  float: left; /* Aligns the text (back) to the left. */
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  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
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  height: 20px;
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  color: #FFFFFF;
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}
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/*----------------------------------------------------------------------------------- Side Menus */
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
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  display: block;
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  width: 11em; /* Side menu width.
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                  Use MenuTailor.css to customize. */
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  padding: 1px; /* Sets the side menu "effective border" width. */
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  position: absolute;
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  top: -1px; /* Aligns the side menu to its drop-down menu item.
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                Keep it sync with the side menu "effective border" width. */
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  left: 13em; /* Places the side menu to the right of the drop-down menu.
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                            Keep it sync with the drop-down menu width.
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                            Use MenuTailor.css to customize. */
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}
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
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  width: 11em; /* Keep it sync with the side menu width.
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                            Use MenuTailor.css to customize. */
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  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
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  left: 13em; /* Places the side menu to the right of the drop-down menu.
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                            Keep it sync with the drop-down menu width.
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                            Use MenuTailor.css to customize. */
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}
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div.MenuBar ul li ul.DropDownMenu li ul.SideMenu li a span {
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  padding-left: 1.5em; /* Sets the left space of each side menu item. */
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  padding-right: 0.5em; /* Sets the right space of each side menu item. */
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  text-align: left;
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  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
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  left: 13em; /* Places the side menu to the right of the drop-down menu.
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                            Keep it sync with the drop-down menu width.
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                            Use MenuTailor.css to customize. */
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}
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/*----------------------------------------------------------------------------- Browser Specific */
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* html div.MenuBar ul li a {
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  float: left; /* Required for IE55 and IE6.
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                            Breaks O9.
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                            Hidden (* html) from non-IE browsers. */
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}
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* html ul.DropDownMenu li a:hover {
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  cursor: hand; /* Required for IE55.
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                  Hidden (* html) from non-IE browsers. */
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}
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ul.DropDownMenu li a:hover {
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  cursor: pointer; /* Required for IE6 and IE7.
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                      Hidding it (* html) from non-IE browsers breaks IE7!
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}
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* html div.MenuBar a:hover {
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  text-decoration: none; /* Required for IE55 and IE6.
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                            Hidden (* html) from non-IE browsers. */
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}
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* html div.MenuBar ul li table,
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* html div.MenuBar ul li table td {
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  border: 0; /* Required for IE55 and IE6.
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                Hidden (* html) from non-IE browsers. */
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}
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/*------------------------------------------------------------------------------- Default Colors */
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div.MenuBar {
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  background-color: Menu;
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  border-bottom: 1px solid ButtonShadow;
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}
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div.MenuBar a {
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  background-color: Menu; /* Top-level unselected items. */
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  color: MenuText;
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}
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div.MenuBar ul li:hover a,
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div.MenuBar ul li a:hover {
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  color: #ea7f16;
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  background-color: Highlight; /* Top-level selected item. */
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  color: HighlightText;
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}
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/*...............................................................................................*/
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div.MenuBar ul li:hover ul.DropDownMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu {
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  background-color: ButtonShadow; /* Sets the drop-down menu "effective border" color. */
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}
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div.MenuBar ul li:hover ul.DropDownMenu li a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a {
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  background-color: Menu;  Drop-down menu unselected items.
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                            Sets the drop-down menu "effective background" color. */
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  color: MenuText;
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}
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div.MenuBar ul li:hover ul.DropDownMenu li:hover a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover {
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  background-color: Highlight; /* Drop-down menu selected item. */
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  color: HighlightText;
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}
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/*...............................................................................................*/
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
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  background-color: ButtonShadow; /* Sets the side menu "effective border" color. */
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}
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
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  background-color: Menu; /* Side menu unselected items.
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                            Sets the side menu "effective background" color. */
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  color: MenuText;
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}
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a:hover,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a:hover {
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  background-color: Highlight; /* Side menu selected item. */
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  color: HighlightText;
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}
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/*-----------------------------------------------------------------------------------------------*/
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/*Script-Free 3-Level Menu 1.2 Tailor
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  www.CesarDaniel.info
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/*-------------------------------------------------------------------------------------- General */
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body {
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  background:  style="color:#BB4400";
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  color: black;
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  margin: 0;
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  border: 0;
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  padding: 0;
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}
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div.MenuBar {
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  font: 13px arial, helvetica, sans-serif;
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}
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div.MenuBar ul {
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  font: 13px arial, helvetica, sans-serif; /* Required for IE55. */
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}
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/*--------------------------------------------------------------------------------------- Colors */
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div.MenuBar {
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  background-color: black; /* Selected item. */
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  color: #FFFFFF;
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  border-bottom: 1px solid ButtonShadow;
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}
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div.MenuBar a,
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div.MenuBar ul li:hover ul.DropDownMenu li a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a,
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
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  background-color: black; /* Selected item. */
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  color: #FFFFFF;
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}
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div.MenuBar ul li:hover a,
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div.MenuBar ul li a:hover,
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div.MenuBar ul li:hover ul.DropDownMenu li:hover a,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover,
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div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a:hover,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a:hover {
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  background-color: #00b0e6; /* Selected item. */
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  color: #FFFFFF;
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}
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div.MenuBar ul li:hover ul.DropDownMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu,
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-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
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div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
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  background-color: ButtonShadow; /* Sets the drop-down and side menus "effective border" color. */
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}
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/*--------------------------------------------------------------------------------------- Widths */
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/*
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/*
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Menu Bar 1
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Drop-Down Menu #2
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*/
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div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM4,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM4,
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div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM4 li a,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM4 li a {
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  width: 11em; /* Drop-down menu width. */
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}
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div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM5,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM5,
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div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM5 li a,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM5 li a {
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  width: 12em; /* Drop-down menu width. */
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}
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/*...............................................................................................*/
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/*
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Menu Bar 1
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Drop-Down Menu #2
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Side Menu #1
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*/
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM1,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM1 {
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  left: 15.5em !important; /* Places the side menu to the right of the drop-down menu.
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                            Keep it sync with the drop-down menu width. */
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}
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM1,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM1,
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM1 li a,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM1 li a {
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  width: 10em; /* Side menu width. */
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}
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/*...............................................................................................*/
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/*
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Menu Bar 1
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Drop-Down Menu #2
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Side Menu #2
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*/
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2 {
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  left: 15.5em  !important; /* Places the side menu to the right of the drop-down menu.
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-
                            Keep it sync with the drop-down menu width. */
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-
}
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2,
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-
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM2 li a,
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-
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM2 li a {
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  width: 10em; /* Side menu width. */
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-
}
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/*...............................................................................................*/
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/*
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Menu Bar 1
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Drop-Down Menu #2
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Side Menu #3
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*/
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div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3,
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div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3 {
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-
  left: 15.5em  !important; /* Places the side menu to the right of the drop-down menu.
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-
                            Keep it sync with the drop-down menu width. */
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-
}
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-
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3,
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-
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3,
+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu li:hover ul.SideMenu#MB1-DDM2-SM3 li a,
+
-
div.MenuBar#navi ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu#MB1-DDM2-SM3 li a {
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  width: 10em; /* Side menu width. */
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-
}
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/*...............................................................................................*/
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</style>
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<body>
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<div id="header">
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<center><div style="font-size:24pt;"><font face="georgia" style="color:#BB4400">
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<img src="https://2012.igem.org/File:TurtlePond.jpg" alt="Caltech iGEM 2012"\> </div>
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-
<div class='MenuBar' id="navi">
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<ul>
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<li>
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<a href="https://2012.igem.org/Team:Caltech" style="color:#BB4400">Home
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<!--[if gt IE 6]><!--></a><!--<![endif]-->
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-
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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<!--[if lte IE 6]></td></tr></table></a><![endif]-->
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-
</li>
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<li>
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<a href="https://2012.igem.org/Team:Caltech/Team" style="color:#BB4400">Team<!--[if gt IE 6]><!--></a><!--<![endif]-->
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-
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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<ul class="DropDownMenu" id="MB1-DDM1">
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<li><a href="https://2012.igem.org/Team:Caltech/Team#Mentors"><span><span>Mentors</span></span></a>
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<li><a href="https://2012.igem.org/Team:Caltech/Team#Undergraduates"><span><span>Undergraduates</span></span></a></li>
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</ul>
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<!--[if lte IE 6]></td></tr></table></a><![endif]-->
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</li>
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<li>
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<a href="https://2012.igem.org/Team:Caltech/Project" style="color:#BB4400">Project<!--[if gt IE 6]><!--></a><!--<![endif]-->
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<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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<ul class="DropDownMenu" id="MB1-DDM1">
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<li><a href="https://2012.igem.org/Team:Caltech/Project"><span><span>Overall Project</span></span></a></li>
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<li><a href="https://2012.igem.org/Team:Caltech/Notebook/material"><span><span>Materials & Methods</span></span></a>
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<li><a href="https://2012.igem.org/Team:Caltech/Project/Degradation"><span><span>Degradation</span></span></a></li>
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<li><a href="https://2012.igem.org/Team:Caltech/Project/Proteorhodopsin"><span><span>Proteorhodopsin</span></span></a></li>
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-
<li><a href="https://2012.igem.org/Team:Caltech/Project/Biodiesel"><span><span>Biodiesel </span></span></a></li>
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</ul>
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-
<!--[if lte IE 6]></td></tr></table></a><![endif]-->
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</li>
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{|
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='''Overall Project'''=
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You should make use of the calendar feature on the wiki and start a lab notebook.  This may be looked at by the judges to see how your work progressed throughout the summer.  It is a very useful organizational tool as well.
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Our overall project is do degrade things like lignin and alginate and generate biofuel.  Our notebook is organized by project.  Below we summarize each project.
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==='''Degradation'''===
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Degradation summary: we degrade things.
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Degradation summary
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[[https://2012.igem.org/Team:Caltech/Notebook/Degradation Degradation Notebook]]
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[[https://2012.igem.org/Team:Caltech/Notebook/Degradatio/Notebook Degradation Notebook]]
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The production pathways we plan to introduce in ''E. coli'' require NADH for the reactions; however, ''E. coli'' require NADH to donate protons and generate the proton-motive force that drives its ATP synthase to produce ATP. ''E. coli'' uses NADH dehydrogenase to convert NADH to NAD+ and expel the proton outside of the cell membrane. We plan to make the production pathways by reducing the bacteria's inherent need for NADH in two ways: 1. Lambda Red removal of Nuo, an NADH dehydrogenase found in ''E. coli''; 2. introduction of proteorhodopsin, a light-powered proton pump, into ''E. coli'' to replace the electron transport chain.
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==='''Proteorhodopsin'''===
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When testing the effects of proteorhodopsin in ''E. coli'' with the proteorhodopsin gene added and nothing removed, we realize that ''E. coli'' will not make use of proteorhodopsin under normal conditions, since the electron transport chain is more optimal for ATP production. Thus, we must grow ''E. coli'' under stressful conditions to induce it to [].
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Summary of proteorhodopsin project
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[[https://2012.igem.org/Team:Caltech/Notebook/Proteorhodopsin Proteorhodopsin Notebook]]
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==='''Biofuel'''===
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Summary of biofuel project.
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[[https://2012.igem.org/Team:Caltech/Notebook/Biofuel Biofuel Notebook]]
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Summary of biofuel project.
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[[https://2012.igem.org/Team:Caltech/Notebook top of page]]
[[https://2012.igem.org/Team:Caltech/Notebook top of page]]
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Latest revision as of 19:17, 3 July 2012



Overall Project

Our overall project is do degrade things like lignin and alginate and generate biofuel. Our notebook is organized by project. Below we summarize each project.


Degradation Project and Strategy

Degradation summary: we degrade things.

[Degradation Notebook]


Proteorhodopsin Project and Strategy

The production pathways we plan to introduce in E. coli require NADH for the reactions; however, E. coli require NADH to donate protons and generate the proton-motive force that drives its ATP synthase to produce ATP. E. coli uses NADH dehydrogenase to convert NADH to NAD+ and expel the proton outside of the cell membrane. We plan to make the production pathways by reducing the bacteria's inherent need for NADH in two ways: 1. Lambda Red removal of Nuo, an NADH dehydrogenase found in E. coli; 2. introduction of proteorhodopsin, a light-powered proton pump, into E. coli to replace the electron transport chain.

When testing the effects of proteorhodopsin in E. coli with the proteorhodopsin gene added and nothing removed, we realize that E. coli will not make use of proteorhodopsin under normal conditions, since the electron transport chain is more optimal for ATP production. Thus, we must grow E. coli under stressful conditions to induce it to [].

[Proteorhodopsin Notebook]


Biofuel Project and Strategy

Summary of biofuel project.

[Biofuel Notebook]


Coliroid Project and Strategy

Summary of biofuel project.

[Coliroid Notebook]

[top of page]

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