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if (typeof Application == "undefined" || !Application) {
	var Application = {};
}

Application.genocon = function() {
	this._init.apply(this, arguments);
};

Application.genocon.prototype = {
	
	_baseSequence : null,
	_methodList : null,
	
	_default : {
		baseSequenceContainerId : "baseSequenceContainer",
		hiddenBaseSequenceClass : "hdnBaseSequence",
		fixedSequenceClass : "fixedSequence",
		baseErrorMessageClass : "baseErrorMessage",
		errorMessageEnterSequence : "Please enter a sequence of minimum length {0}",
		useButtonClass : "useButton",
		nextButtonClass : "nextButton",
		nextButtonContainerClass : "nextButtonContainer",
		collapseButton : "collapseButton",
		expandButton : "expandButton",
		removeButton : "removeButton",
		appContainerClass : "applicationContainer",
		appDataContainerClass : "applicationDataContainer",
		actionButtonContainer : "actionButtonContainer",
		actionResultContainer : "actionResultContainer",
		baseSequenceBoxClass : "baseSequenceBox",
		baseSequenceClass : "baseSequence",
		selectDataBaseList : "databaseList",
		selectMethodList : "optionList",
		hiddenBaseSequence : "hdnBaseSequence",
		databaseFilteringProperty : "#motif%20sequence",
		methodUrlProperty : "#application%20URL",
		baseSequenceMinLength : 50
	},
	
	_tag : {
		databaseTag : "database",
		methodTag : "method"
	},
	
	_init : function() {
		this._methodList = [];
		this._initBaseInput();
		this._initLoadScript();
		this._initDefaultContainer();
		this._initUseButtonListener();
	},
	
	_initBaseInput : function() {
		var val = $("#" + this._default.baseSequenceContainerId + " ." + this._default.hiddenBaseSequenceClass).val();
		if (val && val.length < this._default.baseSequenceMinLength) {
			$errMsgEl = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseErrorMessageClass);
			$errMsgEl.html(self._default.errorMessageEnterSequence.replace("{0}", self._default.baseSequenceMinLength));
			$errMsgEl.show();
			return;
		}
		$baseInput = $("#" + this._default.baseSequenceContainerId + " ." + this._default.baseSequenceClass);
		var index = val.length - this._default.baseSequenceMinLength;
		$baseInput.attr("size", index);
		var inputVal = val.substring(0, index);
		var fixedVal = val.substring(index);
		$baseInput.val(inputVal);
		$("#" + this._default.baseSequenceContainerId + " ." + this._default.fixedSequenceClass).html(fixedVal);
		$baseInput.keyup(function() {
			var size = ($baseInput.val().length != 0) ? $baseInput.val().length : 1;
			$baseInput.attr("size", size);
		});
	},
	
	_initLoadScript : function() {
		var self = this;
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var getProperties = function(propertytList) {
						$.each(propertytList, function(propKey, propVal) {
							if (propVal.indexOf(self._default.methodUrlProperty) > -1) {
								self._loadPluginScriptList(workId, fileName, propVal);
								return false;
							}
						});
					}
					LinkData.getProperties(workId, fileName, getProperties);
					return false;
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.methodTag, getFilesByTag);
	},
	
	_initDefaultContainer : function() {
		this._initDatabase();
		this._initMethod();
		this._initActionButton();
		this._initDatabaseListener();
		this._initMethodListener();
	},
	
	_initDatabase : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectDataBaseList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Database --</option>");
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var dbKey = self._getDatabaseOptionKey(workId, fileName);
					$select.append("<option value='" + dbKey + "'>" + fileName + "</option>");
				});
			});
		}
		LinkData.getFilesByTag("", self._tag.databaseTag, getFilesByTag);
	},
	
	_initMethod : function() {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Option --</option>");
		var getFilesByTag = function(result) {
			$.each(result, function(workId, fileArray){
				$.each(fileArray, function(fileKey, fileName) {
					var getSubjects = function(subjectList) {
						$.each(subjectList, function(subKey, subVal) {
							var label = self._getLabel(subVal);
							$select.append("<option value='" + label + "'>" + label + "</option>");
							self._methodList.push(label);
						});
					}
					LinkData.getSubjects(workId, fileName, getSubjects);
				});
			});
		}
		LinkData.getFilesByTag(null, self._tag.methodTag, getFilesByTag);
	},
	
	_initActionButton : function() {
		var self = this;
		$("." + self._default.actionButtonContainer + " ." + self._default.collapseButton).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.appDataContainerClass).hide();
		});
		$("." + self._default.actionButtonContainer + " ." + self._default.expandButton).click(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.appDataContainerClass).show();
		});
		$("." + self._default.actionButtonContainer + " ." + self._default.removeButton).click(function() {
			$(this).closest("." + self._default.appContainerClass).remove();
		});
	},
	
	_initDatabaseListener : function() {
		var self = this;
		var $selectDb = $("." + self._default.appContainerClass + " ." + self._default.selectDataBaseList);
		$selectDb.change(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			$(parent).find("." + self._default.selectMethodList + " option").removeAttr("selected");
			$(parent).find("." + self._default.nextButtonContainerClass).hide();
			$container = $(parent).find("." + self._default.actionResultContainer);
			$container.html("");
			var dbKey = $("option:selected", $(this)).val();
			self._changeMethodList(dbKey);
		});
	},
	
	_initMethodListener : function() {
		var self = this;
		var $selectDb = $("." + self._default.appContainerClass + " ." + self._default.selectDataBaseList);
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$select.change(function() {
			var parent = $(this).closest("." + self._default.appContainerClass);
			var method = $("option:selected", $(this)).text();
			var database = $("option:selected", $(parent).find("." + self._default.selectDataBaseList)).val();
			if (database == -1) {
				return;
			}
			$container = $(parent).find("." + self._default.actionResultContainer);
			$container.html("Loading...");
			$(parent).find("." + self._default.nextButtonContainerClass).hide();
			var date = new Date();
			var id = "container_id_" + date.getTime();
			$container.attr("id", id);
			var func = function() {
				self._callback(self);
			}
			var arr = database.split("|");
			var obj = {
				workId : arr[0],
				fileName : arr[1],
				appName : method,
				baseSequence : self._baseSequence,
				callback : func
			};
			eval(method)(id, obj);
		});
	},
	
	_loadPluginScriptList : function(workId, fileName, property) {
		var getTripleList = function(tripleList) {
			$.each(tripleList, function(tKey, tVal) {
				LinkDataUtil.loadScript(tVal.object);
			});
		}
		LinkData.getTriplesByProperty(workId, fileName, property, getTripleList);
	},
	
	_changeMethodList : function(dbKey) {
		var self = this;
		var $select = $("." + self._default.appContainerClass + " ." + self._default.selectMethodList);
		$("option", $select).remove();
		$select.append("<option value='-1' selected='selected'>-- Select Option --</option>");
		if (dbKey == -1) {
			return;
		}
		var arr = dbKey.split("|");
		var workId = arr[0];
		var fileName = arr[1];
		$.each(self._methodList, function(key, method) {
			self._addValidMethod($select, workId, fileName, method);
		});
	},
	
	_addValidMethod : function($select, workId, fileName, method) {
		var getFilesByTag = function(fileList) {
			if (!fileList) {
				return;
			}
			$.each(fileList, function(fKey, fName) {
				if (fName === fileName) {
					$select.append("<option value='" + method + "'>" + method + "</option>");
					return false;
				}
			});
		}
		LinkData.getFilesByTag(workId, method, getFilesByTag);
	},
	
	_initUseButtonListener : function() {
		var self = this;
		$("#" + self._default.baseSequenceContainerId + " ." + self._default.useButtonClass).click(function() {
			$txtSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseSequenceClass);
			$fixedSeq = $("#" + self._default.baseSequenceContainerId + " ." + self._default.fixedSequenceClass);
			self._baseSequence = $txtSeq.val() + $fixedSeq.html();
			$errMsgEl = $("#" + self._default.baseSequenceContainerId + " ." + self._default.baseErrorMessageClass);
			$errMsgEl.hide();
			if (!self._baseSequence || self._baseSequence.length < self._default.baseSequenceMinLength) {
				$errMsgEl.html(self._default.errorMessageEnterSequence.replace("{0}", self._default.baseSequenceMinLength));
				$errMsgEl.show();
				//_showError($baseContainer, opts.msgEmptySequence);
			} else {
				$txtSeq.attr('readonly', true).addClass("noborder");
				$(this).hide();
				$("." + self._default.appContainerClass).show();
			}
		});
	},
	
	_callback : function(self) {
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonContainerClass).show();
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).unbind('click');
		$("." + self._default.appContainerClass + " ." + self._default.nextButtonClass).click(function() {
			$parent = $(this).closest("." + self._default.appContainerClass);
			var clone = $parent.clone(true);
			var text = $(clone).find(".replaceSequence").text();
			if (text && text.trim().length != 0) {
				self._baseSequence = text;
			}
			$(clone).find("." + self._default.actionResultContainer).html("");
			$(clone).find("." + self._default.nextButtonContainerClass).hide();
			$parent.parent().append(clone);
		});
	},
	
	_getDatabaseOptionKey : function(workId, fileName) {
		return workId + "|" + fileName;
	},
	
	_getLabel : function(value) {
		var propLabel = value;
		var arr = value.split("#");
		if (arr.length > 1) {
			propLabel = decodeURIComponent(arr[1]);
		}
		return propLabel;
	}
	
};

$(document).ready(function() {
	new Application.genocon();
});

body {
    font-family: sans-serif;
    font-size: 14px;
}

a {
    color: #3B5998;
    font-weight: bold;
    text-decoration: none;
}

#gcAppContainer {
	width: 900px;
}

.hidden {
	display:none;
}

.left {
    float: left;
}

.label {
	color: #E87B10;
    font: 1.1em "Trebuchet MS","Helvetica","Arial","Verdana","sans-serif";
    height: 24px;
    min-width: 125px;
}

input.baseSequence {
	/*width: 100%;*/
}

.highlight-sequence {
	font-weight: bold;
}

.resultArea {
    font-family: "Courier New","Lucida Console";
    margin: 10px 0;
    min-width: 410px;
    overflow: auto;
    width: 100%;
	background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
	/*word-wrap: break-word;*/
}

.resultArea .userSequence {
	white-space: nowrap;
}

.replaceSequence {
    background-color: #FFFFFF;
    border: 1px solid #DDDDDD;
    margin: 10px 0 0;
	font-family: "Courier New","Lucida Console";
	overflow: auto;
	/*word-wrap: break-word;*/
}

.replace {
    color: #E80010;
}

.baseErrorMessage,
.errorMessage {
	color: #FF0000;
	text-align: center;
}

.applicationContainer {
    background-color: #F6F6F6;
    border: 1px solid #CCCCCC;
    margin: 5px 0 0;
    padding: 5px;
}

.actionButtonContainer {
    text-align: right;
}

.actionBtn {
    border: 1px solid #DDDDDD;
    cursor: pointer;
    display: inline-block;
    font-weight: bold;
    padding: 5px 2px;
    text-align: center;
    width: 25px;
}

.row {
    padding: 5px 0;
}
.row:after {
    clear: left;
    content: "";
    display: block;
}
.row input[type="text"] {
    width: 200px;
}

.noborder {
    border: medium none;
}

#baseSequenceContainer .baseSequenceBox {
	width: 100%;
	overflow: auto;
	white-space: nowrap;
}
#baseSequenceContainer .baseSequenceBox span,
#baseSequenceContainer .baseSequenceBox .baseSequence {
	font-family: Courier;
}

#baseSequenceContainer .baseSequenceBox .fixedSequence {
	position: relative;
	left: -6px;
	color: #AAAAAA;
	font-weight: bold;
}

.applicationContainer .nextButtonContainer {
	margin-top: 10px;
}

.databaseInfo .motif {
	width: 70%;
}

/**
 * button css
 */

a.useButton {
	width: 80px;
}

.actionBtn {
	border: 1px solid #DDDDDD;
    cursor: pointer;
    display: inline-block;
    font-weight: bold;
    padding: 5px 2px;
    text-align: center;
    width: 25px;
}

.actionBtn:hover {
	border: 1px solid #000000;
}

.btn {
  display: inline-block;
  *display: inline;
  /* IE7 inline-block hack */

*zoom: 1;
  padding: 4px 10px 4px;
  margin-bottom: 0;
  font-size: 13px;
  line-height: 18px;
  color: #333333;
  text-align: center;
  text-shadow: 0 1px 1px rgba(255, 255, 255, 0.75);
  vertical-align: middle;
  background-color: #f5f5f5;
  background-image: -moz-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -ms-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));
  background-image: -webkit-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: -o-linear-gradient(top, #ffffff, #e6e6e6);
  background-image: linear-gradient(top, #ffffff, #e6e6e6);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);
  border-color: #e6e6e6 #e6e6e6 #bfbfbf;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
  border: 1px solid #cccccc;
  border-bottom-color: #b3b3b3;
  -webkit-border-radius: 4px;
  -moz-border-radius: 4px;
  border-radius: 4px;
  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.2), 0 1px 2px rgba(0, 0, 0, 0.05);
  cursor: pointer;
  *margin-left: .3em;
}

.btn:hover,
.btn:active,
.btn.active,
.btn.disabled,
.btn[disabled] {
  background-color: #e6e6e6;
}

.btn:hover {
  color: #333333;
  text-decoration: none;
  background-color: #e6e6e6;
  background-position: 0 -15px;
  -webkit-transition: background-position 0.1s linear;
  -moz-transition: background-position 0.1s linear;
  -ms-transition: background-position 0.1s linear;
  -o-transition: background-position 0.1s linear;
  transition: background-position 0.1s linear;
}

.btn-blue,
.btn-blue:hover,
.btn-yellow,
.btn-yellow:hover,
.btn-red,
.btn-red:hover,
.btn-green,
.btn-green:hover,
.btn-lightblue,
.btn-lightblue:hover,
.btn-black,
.btn-black:hover {
  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
  color: #ffffff;
}

.btn-blue {
  background-color: #0074cc;
  background-image: -moz-linear-gradient(top, #0088cc, #0055cc);
  background-image: -ms-linear-gradient(top, #0088cc, #0055cc);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#0088cc), to(#0055cc));
  background-image: -webkit-linear-gradient(top, #0088cc, #0055cc);
  background-image: -o-linear-gradient(top, #0088cc, #0055cc);
  background-image: linear-gradient(top, #0088cc, #0055cc);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#0088cc', endColorstr='#0055cc', GradientType=0);
  border-color: #0055cc #0055cc #003580;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}

.btn-blue:hover,
.btn-blue:active,
.btn-blue.active,
.btn-blue.disabled,
.btn-blue[disabled] {
  background-color: #0055cc;
}

.btn-green {
  background-color: #5bb75b;
  background-image: -moz-linear-gradient(top, #62c462, #51a351);
  background-image: -ms-linear-gradient(top, #62c462, #51a351);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#51a351));
  background-image: -webkit-linear-gradient(top, #62c462, #51a351);
  background-image: -o-linear-gradient(top, #62c462, #51a351);
  background-image: linear-gradient(top, #62c462, #51a351);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#51a351', GradientType=0);
  border-color: #51a351 #51a351 #387038;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}
.btn-green:hover,
.btn-green:active,
.btn-green.active,
.btn-green.disabled,
.btn-green[disabled] {
  background-color: #51a351;
}
.btn-green:active,
.btn-green.active {
  background-color: #408140 ¥9;
}
.btn-lightblue {
  background-color: #49afcd;
  background-image: -moz-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -ms-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#2f96b4));
  background-image: -webkit-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: -o-linear-gradient(top, #5bc0de, #2f96b4);
  background-image: linear-gradient(top, #5bc0de, #2f96b4);
  background-repeat: repeat-x;
  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#2f96b4', GradientType=0);
  border-color: #2f96b4 #2f96b4 #1f6377;
  border-color: rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);
  filter: progid:dximagetransform.microsoft.gradient(enabled=false);
}
.btn-lightblue:hover,
.btn-lightblue:active,
.btn-lightblue.active,
.btn-lightblue.disabled,
.btn-lightblue[disabled] {
  background-color: #2f96b4;
}

/* Dialog css */

.motifViewDialog .explanation {
	color: #AAAAAA;
	font-size: 12px;
}

.motifViewDialog .moreInfo {
	color: #3B5998;
	cursor: pointer;
}

.motifViewDialog .position {
	width: 70px;
}

.motifViewDialog .dialogErrorMessage {
	font-size: 12px;
}

.ui-corner-all, .ui-corner-top, .ui-corner-left, .ui-corner-tl {
    border-top-left-radius: 1px;
}
.ui-corner-all, .ui-corner-top, .ui-corner-right, .ui-corner-tr {
    border-top-right-radius: 1px;
}
.ui-corner-all, .ui-corner-bottom, .ui-corner-left, .ui-corner-bl {
    border-bottom-left-radius: 1px;
}
.ui-corner-all, .ui-corner-bottom, .ui-corner-right, .ui-corner-br {
    border-bottom-right-radius: 1px;
}

.loadingImageContainer .loadingMessage {
	color: #FF0000;
}

<div id="baseSequenceContainer">
	<div class="label">Base Sequence</div>
	<div class="baseSequenceBox">
		<input type="hidden" class="hdnBaseSequence" value="CGATAAAGGAAAGGCCATCGTTGAAGATGCCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGACGTTCCAACCACGTCTTCAAAGCAAGTGGATTGATGTGATAACATGGTGGAGCACGACACACTTGTCTACTCCAAAAATATCAAAGATACAGTCTCAGAAGACCAAAGGGCAATTGAGACTTTTCAACAAAGGGTAATATCCGGAAACCTCCTCGGATTCCATTGCCCAGCTATCTGTCACTTTATTGTGAAGATAGTGGAAAAGGAAGGTGGCTCCTACAAATGCCATCATTGCGATAAAGGAAAGGCCATCGTTGAAGATGCCTCTGCCGACAGTGGTCCCAAAGATGGACCCCCACCCACGAGGAGCATCGTGGAAAAAGAAGACGTTCCAACCACGTCTTCAAAGCAAGTGGATTGATGTGATATCTCCACTGACGTAAGGGATGACGCACAATCCCACTATCGATCCCAAGACCCTTCCTCTATATAAGGAAGTTCATTTCATTTGGAGAGG"/>
		<span>
			<input type="text" class="baseSequence" value=""/></span>
		<span class="fixedSequence"></span>
	</div>
	<div style="margin-top:5px;"><a class="useButton btn btn-green">Use</a></div>
	<div class="baseErrorMessage hidden"></div>
</div>
<div class="applicationContainer hidden">
	<div class="actionButtonContainer">
		<span class="appSummery"></span>
		<span class="collapseButton actionBtn" title="collapse">_</span>
		<span class="expandButton actionBtn" title="expand">+</span>
		<span class="removeButton actionBtn" title="remove">x</span>
		<br clear="all"/>
	</div>
	<div class="applicationDataContainer">
		<div class="row">
			<div class="label left">Select Database</div>
			<div class="left"><select class="databaseList"></select></div>
		</div>
		<div class="row">
			<div class="label left">Sequence App</div>
			<div class="left"><select class="optionList"></select></div>
		</div>
		<div class="actionResultContainer"></div>
		<div class="nextButtonContainer hidden"><a class="btn nextButton">Next</a></div>
	</div>
</div>
</div>

Below is a description of the GenoCon CAD Application. For the GenoCon2 Promoter Design Challenge, you should replace this with a report of your promoter design.

以下にはGenoCon2課題A PromoterCADシステムについての説明が書かれています。GenoCon2のプロモータデザインチャレンジでは、以下にあなたのプロモータデザインのレポートを書いてください。

Title: Plant Promoter Design for Tissue/Time Specific Expression of Firefly Luciferase in Arabidopsis Plant Body

Name: RIKEN GenoCon

Affiliation: RIKEN The Institute of Physical and Chemical Research

Date: 2012-10-17

Abstract

GenoConPromoterCAD is a DNA computer aided design (CAD) program which uses plant gene sequence and expression data to create synthetic promoters for tissue and time specific expression. The experimental test of such synthetic promoters will be to measure firefly Luciferase in Arabidopsis plant body. The program provides a graphical user interface (GUI), so anyone can design promoters using options in a series of select menus and push buttons. The program is written in JavaScript, on an open platform that allows for easy user customization.

The program provides several plugin functions for promoter designs MotifMaxExpress function, MotifMinExpress function, and MotifMaxCircadian function, as well as HighChart function for graph visualization of expression data. MotifMaxExpress function picks up the sequence motifs from the gene with maximum expression in a specific developmental condition. MotifMinExpress function picks up the motifs with minimum expression in a specific developmental condition. MotifMaxCircadian function picks up the motifs with maximum circadian amplitude. HighChart function provides graph visualization of expression data under experimental conditions (AtGenExpress) and time evolution of expression under circadian conditions (DIURNAL). Programmer participants can fork and add to these functions for the GenoCon2 Special Programming Challenge A.

タイトル:植物のシロイヌナズナでホタルルシフェラーゼを組織/時期特異的に発現するためのプロモータの設計

名前: 理研ゲノコン

所属: 独立行政法人理化学研究所

日付: 2012-10-17

日本語要旨

GenoConPromoterCADは、コンピュータ支援でDNA設計を行うプログラムです。このプログラムは植物の遺伝子と発現データを用いて、組織/時期特異的に遺伝子発現を調節する人工プロモータを創ります。デザインした人工プロモータの実験検証は、シロイヌナズナの植物体内でホタルルシフェラーゼを用いて行います。このプログラムではグラフィカルなインターフェース(GUI)を提供していますので、一連のメニュー選択とボタン操作を行うことで、どなたでもプロモータをデザインできます。プログラムはJavaScriptで書かれていますので、簡単にカスタマイズできます。

このプログラムでは、プロモータデザインのためのプラグイン関数 MotifMaxExpress, MotifMaxExpress, MotifMaxCircadian と、発現データをグラフ表示する HighChart 関数を提供しています。 MotifMaxExpress 関数は、特定の成長条件で発現量を最大にする遺伝子に関連したモチーフ配列を見つけ出します。 MotifMaxExpress 関数は、特定の成長条件で発現量を最小にするモチーフを見つけ出します。 MotifMaxCircadian 関数は、概日振動の振幅を最大にするモチーフを見つけ出します。 HighChart 関数は、AtGenExpressの様々な成長条件における発現データをグラフ表示します。また、DIURNALの概日条件における発現値の時間変化をグラフ表示します。プログラムが得意な方は、これらのプラグイン関数をコピー(fork)して、新たな関数を作り出すことができます。 (詳細は、課題A スペシャルプログラミングチャレンジを参照してください。)

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GenoCon2課題A PromoterCADシステム

タイトル:
植物のシロイヌナズナでホタルルシフェラーゼを組織/時期特異的に発現するためのプロモータの設計

要旨:

アプリケーション

Title: Plant Promoter Design for Tissue/Time Specific Expression of Firefly Luciferase in Arabidopsis Plant Body

Abstract

タイトル:植物のシロイヌナズナでホタルルシフェラーゼを組織/時期特異的に発現するためのプロモータの設計

日本語要旨

Forkして作られたアプリ

ニュースフィード

オープンデータを使ってアプリを作ろう

アプリケーションの作成と公開をサポートするサイト

アプリ作品の情報

GenoCon2課題A PromoterCADシステム

タイトル: 植物のシロイヌナズナでホタルルシフェラーゼを組織/時期特異的に発現するためのプロモータの設計

要旨:

アプリケーション

Title: Plant Promoter Design for Tissue/Time Specific Expression of Firefly Luciferase in Arabidopsis Plant Body

Abstract

タイトル:植物のシロイヌナズナでホタルルシフェラーゼを組織/時期特異的に発現するためのプロモータの設計

日本語要旨

Forkして作られたアプリ

ニュースフィード

タイトル:
植物のシロイヌナズナでホタルルシフェラーゼを組織/時期特異的に発現するためのプロモータの設計