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GenoConPromoterCAD

This is the PromoterCAD program for the GenoCon2 Promoter Design Challenge A.


To make your own DNA CAD workspace, use the “Fork this app as your new one” button at the bottom. Then you will be able to record your work and submit it!
You can even modify and add new function modules as plugins to PromoterCAD.
For more information see: http://genocon.org/assignment-2012/assignment-a/manuals-a/


For guidelines on writing your report, see the "ReadMe" tab.



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  • Play
  • JavaScript
  • CSS
  • HTML
  • ReadMe
  • Snapshots

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。)


jquery-1.7.1.min.js
jquery-ui-1.8.18.min.js
http://code.highcharts.com/highcharts.js
http://code.highcharts.com/modules/exporting.js


Contributor Send Message
Run count 1098
Website
License
Fork count 2
Created date Oct 9, 2012
Last update date Dec 20, 2012

Forked (Child App)

A Promoter Design to Maintain the Fertility of Transgenic Plant by New Plugin MotifRanking Contributor: Masahiro Mochizuki Update: Dec 27, 2012 380 runs
forked:GenoConPromoterCAD Contributor: Koro_Nishikata Update: Nov 26, 2012 37 runs
  • LinkData work list used as input data in this application.
  • You can change input data and execute application if you change the checkbox.
  • [result_bottom]
    [result_top]
  • [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [heptamer]
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  • Circadian Genomic (DIURNAL + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    916 Downloads
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
  • Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    935 Downloads
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,MotifMaxCircadian2,HighChart2]
  • Speedup Lists of Circadian Genomic (DIURNAL + PPDB promoter motif) Gene Contributor: GenoCon Update: Jan 15, 2013
    566 Downloads
    [result_top]
    [result_top]
    [result_top]
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  • GenoCon2 Challenge A - Sequence Function Plugins Contributor: GenoCon Update: Nov 26, 2012
    47 Downloads
    [method]
  • [result_bottom]
    [result_top]
  • Developmental Genomic (AtGenExpress + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 22, 2013
    409 Downloads
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [database,MotifMaxExpress2,MotifMinExpress2,HighChart2]
    [octamer]
  • Add New Data

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