Team:UQ-Australia/Modeling

From 2011.igem.org

(Difference between revisions)
(→Synchronisation)
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<!-- ------------------------------------------------From 2011 Macquarie--------------------------------------------- -->
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{{:Team:UQ-Australia/Template:Header}}
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|At the completion of the experimental work, we should expect a working clock BioBrick, which should exhibit oscillatory behaviour. We wish to characterise how our clock BioBrick oscillates.
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<html>
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<body>
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<body style="background-color:#772288">
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</body>
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<head>
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<style type="text/css">
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body {background-color:#A11F37;}
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color:transparent;
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background-color:transparent;
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line-height:1em;
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top:10px;
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margin-top:-12px;
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top:15px;
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z-index:25;
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}
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img[src*="/wiki/skins/common/images/wiki.png"]{
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    width:0;
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    height:60px;
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    padding-right:975px;
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    background:#transparent;
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}
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ul#list-nav {
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list-style:none;
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margin:7px 75px 7px;
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padding:0;
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width:1000px
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}
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display:inline
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padding:5px 0;
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width:100px;
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background:#A11F37;
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color:#eee;
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float:left;
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text-align:center;
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border-left:1px solid #fff;
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}
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ul#list-nav li a:hover {
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background:#a2b3a1;
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color:#000
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}
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<!-- End of Wiki Hacks -->
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</body>
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</html>
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<!-- -------------------------------------------------From 2009 UQ--------------------------------------------------- -->
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__NOTOC__
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<html>
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<body style="background-color:#772288">
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<style>
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h1.firstHeading { display: none; }
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p {text-align: justify;}
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a:link { color: #603371; text-decoration: none}
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a:visited { color:#603371; 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_members { text-align: justify; border: 0; }
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table#team_members h2, table#team_members 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: 50px;
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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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  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;
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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: 90px;
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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: 40px; /* Keep height + padding-top + padding-bottom sync with the menu bar height. */
+
-
  color: #ffffff;
+
-
  padding-top: 4px;
+
-
  padding-bottom: 4px;
+
-
  padding-left: 1em; /* Sets the left space between top-level items. */
+
-
  padding-right: 1em; /* Sets the right space between top-level items. */
+
-
  text-decoration: none;
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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. */
+
-
  height: 1em;
+
-
  padding: 1px; /* Sets the drop-down menu "effective border" width. */
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-
  position: absolute;
+
-
  top: 23px; /* Places the drop-down menu under the menu bar.
+
-
                Keep it sync with the menu bar height. */
+
-
  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.
+
-
                            Use MenuTailor.css to customize. */
+
-
  height: 1em;
+
-
  padding-left: 0;
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-
  padding-right: 0;
+
-
  background-color: black; /* Selected item. */
+
-
  color: #FFFFFF;
+
-
}
+
-
ul.DropDownMenu li a span {
+
-
  display: block;
+
-
  padding-left: 0.75em; /* Sets the left space of each drop-down menu item. */
+
-
  padding-right: 0.25em; /* Sets the right space of each drop-down menu item. */
+
-
  text-align: right; /* Aligns the >> symbol to the right. */
+
-
}
+
-
ul.DropDownMenu li a span span {
+
-
  float: left; /* Aligns the text (back) to the left. */
+
-
  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
+
-
  height: 20px;
+
-
  color: #FFFFFF;
+
-
}
+
-
/*----------------------------------------------------------------------------------- Side Menus */
+
-
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 {
+
-
  display: block;
+
-
  width: 11em; /* Side menu width.
+
-
                  Use MenuTailor.css to customize. */
+
-
  padding: 1px; /* Sets the side menu "effective border" width. */
+
-
  position: absolute;
+
-
  top: -1px; /* Aligns the side menu to its drop-down menu item.
+
-
                Keep it sync with the side menu "effective border" width. */
+
-
  left: 13em; /* Places the side menu to the right of the drop-down menu.
+
-
                            Keep it sync with the drop-down menu width.
+
-
                            Use MenuTailor.css to customize. */
+
-
}
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
+
-
  width: 11em; /* Keep it sync with the side menu width.
+
-
                            Use MenuTailor.css to customize. */
+
-
  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
+
-
  left: 13em; /* Places the side menu to the right of the drop-down menu.
+
-
                            Keep it sync with the drop-down menu width.
+
-
                            Use MenuTailor.css to customize. */
+
-
}
+
-
div.MenuBar ul li ul.DropDownMenu li ul.SideMenu li a span {
+
-
  padding-left: 1.5em; /* Sets the left space of each side menu item. */
+
-
  padding-right: 0.5em; /* Sets the right space of each side menu item. */
+
-
  text-align: left;
+
-
  font: 12px arial, helvetica, sans-serif; /* Required for IE55. */
+
-
  left: 13em; /* Places the side menu to the right of the drop-down menu.
+
-
                            Keep it sync with the drop-down menu width.
+
-
                            Use MenuTailor.css to customize. */
+
-
}
+
-
/*----------------------------------------------------------------------------- Browser Specific */
+
-
* html div.MenuBar ul li a {
+
-
  float: left; /* Required for IE55 and IE6.
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-
                            Breaks O9.
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-
                            Hidden (* html) from non-IE browsers. */
+
-
}
+
-
* html ul.DropDownMenu li a:hover {
+
-
  cursor: hand; /* Required for IE55.
+
-
                  Hidden (* html) from non-IE browsers. */
+
-
}
+
-
ul.DropDownMenu li a:hover {
+
-
  cursor: pointer; /* Required for IE6 and IE7.
+
-
                      Hidding it (* html) from non-IE browsers breaks IE7!
+
-
}
+
-
* html div.MenuBar a:hover {
+
-
  text-decoration: none; /* Required for IE55 and IE6.
+
-
                            Hidden (* html) from non-IE browsers. */
+
-
}
+
-
* html div.MenuBar ul li table,
+
-
* html div.MenuBar ul li table td {
+
-
  border: 0; /* Required for IE55 and IE6.
+
-
                Hidden (* html) from non-IE browsers. */
+
-
}
+
-
/*------------------------------------------------------------------------------- Default Colors */
+
-
div.MenuBar {
+
-
  background-color: Menu;
+
-
  border-bottom: 1px solid ButtonShadow;
+
-
}
+
-
div.MenuBar a {
+
-
  background-color: Menu; /* Top-level unselected items. */
+
-
  color: MenuText;
+
-
}
+
-
div.MenuBar ul li:hover a,
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-
div.MenuBar ul li a:hover {
+
-
  color: #ea7f16;
+
-
  background-color: Highlight; /* Top-level selected item. */
+
-
  color: HighlightText;
+
-
}
+
-
/*...............................................................................................*/
+
-
div.MenuBar ul li:hover ul.DropDownMenu,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu {
+
-
  background-color: ButtonShadow; /* Sets the drop-down menu "effective border" color. */
+
-
}
+
-
div.MenuBar ul li:hover ul.DropDownMenu li a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a {
+
-
  background-color: Menu;  Drop-down menu unselected items.
+
-
                            Sets the drop-down menu "effective background" color. */
+
-
  color: MenuText;
+
-
}
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover {
+
-
  background-color: Highlight; /* Drop-down menu selected item. */
+
-
  color: HighlightText;
+
-
}
+
-
/*...............................................................................................*/
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
+
-
  background-color: ButtonShadow; /* Sets the side menu "effective border" color. */
+
-
}
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
+
-
  background-color: Menu; /* Side menu unselected items.
+
-
                            Sets the side menu "effective background" color. */
+
-
  color: MenuText;
+
-
}
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a:hover,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a:hover {
+
-
  background-color: Highlight; /* Side menu selected item. */
+
-
  color: HighlightText;
+
-
}
+
-
/*-----------------------------------------------------------------------------------------------*/
+
-
/*Script-Free 3-Level Menu 1.2 Tailor
+
-
  www.CesarDaniel.info
+
-
/*-------------------------------------------------------------------------------------- General */
+
-
body {
+
-
  background: white;
+
-
  color: black;
+
-
  margin: 0;
+
-
  border: 0;
+
-
  padding: 0;
+
-
}
+
-
 
+
-
 
+
-
div.MenuBar {
+
-
  font: 13px arial, helvetica, sans-serif;
+
-
}
+
-
div.MenuBar ul {
+
-
  font: 13px arial, helvetica, sans-serif; /* Required for IE55. */
+
-
}
+
-
/*--------------------------------------------------------------------------------------- Colors */
+
-
div.MenuBar {
+
-
  background-color: black; /* Selected item. */
+
-
  color: #FFFFFF;
+
-
  border-bottom: 1px solid ButtonShadow;
+
-
}
+
-
div.MenuBar a,
+
-
div.MenuBar ul li:hover ul.DropDownMenu li a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a,
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a {
+
-
  background-color: black; /* Selected item. */
+
-
  color: #FFFFFF;
+
-
}
+
-
div.MenuBar ul li:hover a,
+
-
div.MenuBar ul li a:hover,
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover a,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover,
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu li a:hover,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu li a:hover {
+
-
  background-color: #603371; /* Selected item. */
+
-
  color: #FFFFFF;
+
-
}
+
-
div.MenuBar ul li:hover ul.DropDownMenu,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu,
+
-
div.MenuBar ul li:hover ul.DropDownMenu li:hover ul.SideMenu,
+
-
div.MenuBar ul li a:hover ul.DropDownMenu li a:hover ul.SideMenu {
+
-
  background-color: ButtonShadow; /* Sets the drop-down and side menus "effective border" color. */
+
-
}
+
-
/*--------------------------------------------------------------------------------------- Widths */
+
-
/*
+
-
 
+
-
/*
+
-
Menu Bar 1
+
-
Drop-Down Menu #2
+
-
*/
+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM4,
+
-
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM4,
+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM4 li a,
+
-
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM4 li a {
+
-
  width: 11em; /* Drop-down menu width. */
+
-
}
+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM5,
+
-
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM5,
+
-
div.MenuBar#navi ul li:hover ul.DropDownMenu#MB1-DDM5 li a,
+
-
div.MenuBar#navi ul li a:hover ul.DropDownMenu#MB1-DDM5 li a {
+
-
  width: 12em; /* Drop-down menu width. */
+
-
}
+
-
 
+
-
/*...............................................................................................*/
+
-
/*
+
-
Menu Bar 1
+
-
Drop-Down Menu #2
+
-
Side Menu #1
+
-
*/
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At the completion of the experimental work, we should expect a working clock BioBrick, which should exhibit oscillatory behaviour. We wish to characterise how our clock BioBrick oscillates.
+
Of interest is the frequency and regularity at which it oscillates and whether multiple cells containing our BioBrick oscillate in time with each other.
Of interest is the frequency and regularity at which it oscillates and whether multiple cells containing our BioBrick oscillate in time with each other.
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|[[File:IGEM basic Logo stylized.png|125x125px|link=https://2011.igem.org]]
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The modelling will involve the mathematical characterisation of the kinetics and synchronisation of the oscillation of our bacteria.
+
|-
 +
|The modelling will involve the mathematical characterisation of the kinetics and synchronisation of the oscillation of our bacteria.
The kinetics involve modelling how fast our bacteria cells will oscillate and the shape of their oscillation pattern.
The kinetics involve modelling how fast our bacteria cells will oscillate and the shape of their oscillation pattern.
The synchronisation is to characterise how quickly nearby cells would couple any synchronise their oscillation.
The synchronisation is to characterise how quickly nearby cells would couple any synchronise their oscillation.
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|[[File:UQ-Australia_logo_2011.png|125x125px|link=https://2011.igem.org/Team:UQ-Australia]]
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To give a rough idea of how our cells should be oscillating, mathematical models were described from literature. These would ideally be compared with experimental characterisation of the oscillation.
+
|-
 +
|To give a rough idea of how our cells should be oscillating, mathematical models were described from literature. These would ideally be compared with experimental characterisation of the oscillation.
 +
|}
== <span style="color:#558822">Kinetics</span> ==
== <span style="color:#558822">Kinetics</span> ==
Line 665: Line 23:
Many expressions in language rely on the idea of time. Here, we shall take a journey through time, from the idea of clock synchronisation, first shown about 400 years ago by Christiaan Huygens, to the recent observations of this synchronisation phenomenon in nature. Currently, an understanding of this process is currently being carried out at the genetic level. A union of physical modelling with mathematical theory and biological experimentation is leading to a deeper understanding of synchronisation in all disciplines, but particularly in the biological sciences.
Many expressions in language rely on the idea of time. Here, we shall take a journey through time, from the idea of clock synchronisation, first shown about 400 years ago by Christiaan Huygens, to the recent observations of this synchronisation phenomenon in nature. Currently, an understanding of this process is currently being carried out at the genetic level. A union of physical modelling with mathematical theory and biological experimentation is leading to a deeper understanding of synchronisation in all disciplines, but particularly in the biological sciences.
-
[[wiki/images/d/d6/PHYS3900-LitReview-Ann-PrettiedUp.pdf]]
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[https://static.igem.org/mediawiki/2011/d/d6/PHYS3900-LitReview-Ann-PrettiedUp.pdf '''Read the full synchronisation discussion here!''']

Revision as of 04:29, 17 September 2011




At the completion of the experimental work, we should expect a working clock BioBrick, which should exhibit oscillatory behaviour. We wish to characterise how our clock BioBrick oscillates.

Of interest is the frequency and regularity at which it oscillates and whether multiple cells containing our BioBrick oscillate in time with each other.

IGEM basic Logo stylized.png
The modelling will involve the mathematical characterisation of the kinetics and synchronisation of the oscillation of our bacteria.

The kinetics involve modelling how fast our bacteria cells will oscillate and the shape of their oscillation pattern. The synchronisation is to characterise how quickly nearby cells would couple any synchronise their oscillation.

UQ-Australia logo 2011.png
To give a rough idea of how our cells should be oscillating, mathematical models were described from literature. These would ideally be compared with experimental characterisation of the oscillation.

Kinetics

The BioBrick circuit has been represented as a network in a figure yet to be uploaded. For every reaction indicated in imaginary figure, we have assumed a first order reaction rate. The reaction constants have been taken from literature. From this, we would then have a system of first order linear ordinary differential equations. This should be solvable and thus give us a prediction as to the nature of the oscillatory behaviour of a cell. To test the appropriateness of this model, we would then experimentally measure the expression of arbitrary protein and see how close it fits.

Synchronisation

Many expressions in language rely on the idea of time. Here, we shall take a journey through time, from the idea of clock synchronisation, first shown about 400 years ago by Christiaan Huygens, to the recent observations of this synchronisation phenomenon in nature. Currently, an understanding of this process is currently being carried out at the genetic level. A union of physical modelling with mathematical theory and biological experimentation is leading to a deeper understanding of synchronisation in all disciplines, but particularly in the biological sciences.

Read the full synchronisation discussion here!

Retrieved from "http://2011.igem.org/Team:UQ-Australia/Modeling"