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Application Information

forked: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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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.

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.


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
MotifMaxExpress2
MotifMaxCircadian2
HighChart2
MotifMinExpress2


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Forked from (Parent App) GenoCon 's GenoConPromoterCAD
Run count 74
Website
License
Fork count 0
Created date Nov 26, 2012
Last update date Nov 26, 2012

Forked from (Parent App)

GenoConPromoterCAD Contributor: GenoCon Update: Dec 20, 2012 1198 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]
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  • [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [heptamer]
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  • Circadian Genomic (DIURNAL + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    1226 Downloads
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
  • Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    1250 Downloads
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,MotifMaxCircadian,HighChart]
  • Speedup Lists of Circadian Genomic (DIURNAL + PPDB promoter motif) Gene Contributor: GenoCon Update: Jan 15, 2013
    722 Downloads
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  • GenoCon2 Challenge A - Sequence Function Plugins Contributor: GenoCon Update: Nov 26, 2012
    52 Downloads
    [method]
  • [result_bottom]
    [result_top]
  • Developmental Genomic (AtGenExpress + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 22, 2013
    553 Downloads
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [database,MotifMaxExpress,MotifMinExpress,HighChart]
    [octamer]
  • Add New Data

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