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Team:USTC-Software/clotho.html
From 2012.igem.org
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<p class="h1">Clotho</p> | <p class="h1">Clotho</p> | ||
| - | <img src="" alt=""> | + | <img src="https://static.igem.org/mediawiki/2012/b/b5/USTC-Software-images-logo.png" alt="Clotho Logo"> |
<p class="main">Regulon lib is a clotho application written on Java platform. Based on the database, this app includes following functions:</p> | <p class="main">Regulon lib is a clotho application written on Java platform. Based on the database, this app includes following functions:</p> | ||
<p class="list">Searching for proper regulators and regulatees to complete users' GRN</p> | <p class="list">Searching for proper regulators and regulatees to complete users' GRN</p> | ||
| + | <img src="https://static.igem.org/mediawiki/2012/6/6f/USTC-Software-images-mainpage.png" alt=""> | ||
<p class="list">Searching for regulatory relation in database.</p> | <p class="list">Searching for regulatory relation in database.</p> | ||
| + | <img src="https://static.igem.org/mediawiki/2012/1/11/USTC-Software-images-searchPage.png" alt=""> | ||
<p class="main">In this app, only the regulatory information is used, namely the operon-operon regulatory matrix and the gene-promoter regulatory matrix. </p> | <p class="main">In this app, only the regulatory information is used, namely the operon-operon regulatory matrix and the gene-promoter regulatory matrix. </p> | ||
<p class="h2">1. Searching for GRN candidates.</p> | <p class="h2">1. Searching for GRN candidates.</p> | ||
<p class="main">Main page has the function for users to search for proper Genetic Regulatory Network(GRN) candidates. Users can input there matrix size in the text field click "commit". Then users are required to input their regulatory matrix. In the GUI, two modes are provided to users on their choice. Mode one utilizes operon-operon matrix and mode two the gene-promoter matrix. Users can click right or chose "File" menu to save the results.</p> | <p class="main">Main page has the function for users to search for proper Genetic Regulatory Network(GRN) candidates. Users can input there matrix size in the text field click "commit". Then users are required to input their regulatory matrix. In the GUI, two modes are provided to users on their choice. Mode one utilizes operon-operon matrix and mode two the gene-promoter matrix. Users can click right or chose "File" menu to save the results.</p> | ||
| + | <img src="https://static.igem.org/mediawiki/2012/6/6c/USTC-Software-images-inputMatrix.png" alt=""> | ||
<p class="h2">2. Searching for regulons</p> | <p class="h2">2. Searching for regulons</p> | ||
<p class="main">Regulatees and regulators are all called regulons. In search page of our clotho app, all operon names, gene names, promoter names are presented in tables. And users can easily chose one regulator in the regulator table and regulate in regulatee table. By clicking "iGEM" logo, the regulations will appear between the regulator and the regulatee.</p> | <p class="main">Regulatees and regulators are all called regulons. In search page of our clotho app, all operon names, gene names, promoter names are presented in tables. And users can easily chose one regulator in the regulator table and regulate in regulatee table. By clicking "iGEM" logo, the regulations will appear between the regulator and the regulatee.</p> | ||
| + | <img src="https://static.igem.org/mediawiki/2012/9/9b/USTC-Software-images-findRegulation.png" alt=""> | ||
<p class="main">Some tips about the clotho app are listed here:</p> | <p class="main">Some tips about the clotho app are listed here:</p> | ||
Revision as of 04:00, 27 October 2012
Clotho
Regulon lib is a clotho application written on Java platform. Based on the database, this app includes following functions:
Searching for proper regulators and regulatees to complete users' GRN
Searching for regulatory relation in database.
In this app, only the regulatory information is used, namely the operon-operon regulatory matrix and the gene-promoter regulatory matrix.
1. Searching for GRN candidates.
Main page has the function for users to search for proper Genetic Regulatory Network(GRN) candidates. Users can input there matrix size in the text field click "commit". Then users are required to input their regulatory matrix. In the GUI, two modes are provided to users on their choice. Mode one utilizes operon-operon matrix and mode two the gene-promoter matrix. Users can click right or chose "File" menu to save the results.
2. Searching for regulons
Regulatees and regulators are all called regulons. In search page of our clotho app, all operon names, gene names, promoter names are presented in tables. And users can easily chose one regulator in the regulator table and regulate in regulatee table. By clicking "iGEM" logo, the regulations will appear between the regulator and the regulatee.
Some tips about the clotho app are listed here:
1. The app contains regulatory information of 117 genes, 772 operons and 941 prmoters.
2. Since the recursive algorithm is used, for searching in operon-promoter matrix, the complexity makes the searching process much more time consuming. Therefore, mode one is recommended over mode two.
For more details about the usage of the aiding application, here is a user manual for you to look up at.
User Manual
