Team:ZJU-China/Tools

From 2014.igem.org

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{{ZJU-China/Tools}}
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<div class="zju_frame">
<div class="zju_frame">
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    <h2 id="border" style="text-align:center;color:white;background-color:#6bf886;font-size:50px;"><br><br>GS-Box<br><br>An useful bioinformatics tool for Gene-Socket<br><br><br><br></h2>
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    <p style="background-color:#99dbe3;font-size:24px;padding-left:50px;padding-right:50px;LINE-HEIGHT:50px;">
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        <br>
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        <br>
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        <BIG><em>E</em></BIG>very excellent technique should be simple and efficient to use! As an excellent technique, gene-socket also does well in this respect------ it has its' own optimization tool: GS-BOX. GS-BOX is a bioinformatics tool which is designed for customs to build their own gen-sockets easily and efficiently. What need the customs do with the tool? Just input the gene circuit sequences and then GS-BOX will design the experimental process automatically and every detail that customs will need to use!
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        <br>
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        <br>
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        <br>
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        <br>
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    </p>
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    <ul class="test3">
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        <li>
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            <div class="handle3">
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                <img src='images/com_01.gif'>
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            </div>
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            <h3>Service</h3>
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            <p style="background-color:#e5ed82;font-size:18px;">
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                Mauris sed mauris. Praesent imperdiet, nunc ut sollicitudin hendrerit, nisi tellus mollis leo, blandit pharetra nulla orci id eros. Nullam ut nunc. Praesent lacus lacus, tempor a, dignissim eu, tristique ac, tortor. Sed faucibus. Integer eleifend lacus ac neque. Fusce tempus. In hac habitasse platea dictumst. Nulla arcu neque, gravida at, rhoncus id, pharetra vitae, tortor. Aenean vestibulum consequat augue.</p>
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        </li>
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        <li>
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            <div class="handle3">
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                <img src='images/com_02.gif'>
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            </div>
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            <h3>Design Principle</h3>
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            <p style="background-color:#e5ed82;font-size:18px;">Homeodomains:
 +
                <br>1.Don't have similar sequences with E.coli (to avoid off-target effects)
 +
                <br>2.Don't have similar sequences with custom's parts (to avoid off-target effects)
 +
                <br>3.Fit the subsequent steps' requiring
 +
                <br>
 +
                <br>Primer:
 +
                <br>1.GC content & TM value
 +
                <br>2.Duplex formation and hairpin
 +
                <br>3.proper length</p>
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        </li>
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        <li>
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            <div class="handle3">
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                <img src='images/com_03.gif'>
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            </div>
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            <h3>Design Method</h3>
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            <p style="background-color:#e5ed82;font-size:18px;">Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Vivamus vestibulum metus sed massa. Pellentesque pharetra felis a enim. Aliquam sapien nisl, iaculis ac, hendrerit placerat, iaculis congue, augue. Quisque eget mi quis purus vestibulum eleifend. Maecenas condimentum eros vel eros. Ut facilisis leo id mi. Suspendisse nisl magna, consequat quis, pretium eget, laoreet vel, orci.
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                <br>
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                <br>Mauris sed mauris. Praesent imperdiet, nunc ut sollicitudin hendrerit, nisi tellus mollis leo, blandit pharetra nulla orci id eros. Nullam ut nunc. Praesent lacus lacus, tempor a, dignissim eu, tristique ac, tortor. Sed faucibus. Integer eleifend lacus ac neque. Fusce tempus. In hac habitasse platea dictumst. Nulla arcu neque, gravida at, rhoncus id, pharetra vitae, tortor. Aenean vestibulum consequat augue.</p>
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        </li>
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        <li>
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            <div class="handle3">
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                <img src='images/com_04.gif'>
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            </div>
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            <h3>How to use</h3>
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            <p style="background-color:#e5ed82;font-size:18px;">If you just want to build a normal gene circuit, input your mount of parts and sequences; If your circuit contains some particular parts(for example, an terminator primer or want to make your parts seamless connection),please choose the "special mode" according to your situation.</p>
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        </li>
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        <li>
 +
            <div class="handle3">
 +
                <img src='images/com_05.gif'>
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            </div>
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            <h3>Contact</h3>
 +
            <p style="background-color:#e5ed82;font-size:18px;">If you have any questions when using GS-Box, please contact us.</p>
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        </li>
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    </ul>
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    <div style="clear:both;"></div>
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    <br />
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    <br />
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    <br />
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    <br />
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    <div id="page-wrap">
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        <h1><span>DIY  <em>YOUR OWN GENE-SOCKET</em></span></h1>
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        <br>
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        <br>
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        <br>
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        <form name="input">
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            <fieldset id="step_1">
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                <legend>Step 1</legend>
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                <label for="num_attendees">
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                    How many parts do you want to insert?
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                </label>
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                <p>(each no less than 20 bp)</p>
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                <select id="num_attendees">
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                    <option id="opt_0" value="0">Please Choose</option>
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                    <option id="opt_1" value="1">1</option>
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                    <option id="opt_2" value="2">2</option>
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                    <option id="opt_3" value="3">3</option>
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                    <option id="opt_4" value="4">4</option>
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                    <option id="opt_5" value="5">5</option>
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                </select>
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 +
                <br />
 +
 +
                <div id="attendee_1_wrap" class="name_wrap push">
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                    <h3>Please provide each part's sequences:</h3>
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                    <label for="name_attendee_1">
 +
                        Part 1:
 +
                    </label>
 +
                    <input type="text" id="name_attendee_1" class="name_input" name="sequence1" value="">
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                </div>
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 +
                <div id="attendee_2_wrap" class="name_wrap">
 +
                    <label for="name_attendee_2">
 +
                        Part 2:
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                    </label>
 +
                    <input type="text" id="name_attendee_2" class="name_input" name="sequence2" value="">
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                </div>
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                <div id="attendee_3_wrap" class="name_wrap">
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                    <label for="name_attendee_3">
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                        Part 3:
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                    </label>
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                    <input type="text" id="name_attendee_3" class="name_input" name="sequence3" value="">
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                </div>
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 +
                <div id="attendee_4_wrap" class="name_wrap">
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                    <label for="name_attendee_4">
 +
                        Part 4:
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                    </label>
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                    <input type="text" id="name_attendee_4" class="name_input" name="sequence4" value="">
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                </div>
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                <div id="attendee_5_wrap" class="name_wrap">
 +
                    <label for="name_attendee_5">
 +
                        Part 5:
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                    </label>
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                    <input type="text" id="name_attendee_5" class="name_input" name="sequence5" value="">
 +
                </div>
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 +
            </fieldset>
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 +
            <fieldset id="step_2">
 +
 +
                <legend>Step 2</legend>
 +
 +
                <p>
 +
                    Please select the mode
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                </p>
 +
                <select id="modevalue" name="mode">
 +
                    <option value="1" selected="selected">don't contain primer & terminator</option>
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                    <option value="2">contain primer</option>
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                    <option value="3">contain terminator</option>
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                    <option value="4">contain both primer and terminator</option>
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                </select>
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 +
                <p style="font-size:15px">
 +
                    <br>If you don't know what these modes mean, please read "How to use" carfully. Are you sure you have selected the right mode?
 +
                    <br>
 +
                </p>
 +
 +
                <input type="radio" id="company_name_toggle_on" name="company_name_toggle_group"></input>
 +
                <!--<label for="company_name_toggle_on">No</label>-->
 +
                <!--&emsp;-->
 +
                <!--<input type="radio" id="company_name_toggle_off" name="company_name_toggle_group"></input>-->
 +
                <label for="company_name_toggle_off">Yes</label>
 +
 +
                <!--<div id="company_name_wrap">
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<label for="company_name">
 +
Company Name:
 +
</label>
 +
<input type="text" id="company_name"></input>
 +
</div>-->
 +
 +
                <div class="push">
 +
                    <p style="font-size:15px">
 +
                        You shuld learn that your mode is for all of your parts. If you just want to change only one of them, Please see the "Help". Are you sure this mode suits for most of your parts?
 +
                    </p>
 +
 +
                    <!--<input type="radio" id="special_accommodations_toggle_on" name="special_accommodations_toggle"></input>
 +
<label for="special_accommodations_toggle_on">Yes</label>
 +
&emsp;-->
 +
                    <input type="radio" id="special_accommodations_toggle_off" name="special_accommodations_toggle"></input>
 +
                    <label for="special_accommodations_toggle_off">Yes</label>
 +
                </div>
 +
                <!--<div id="special_accommodations_wrap">
 +
<label for="special_accomodations_text">
 +
Please explain below:
 +
</label>
 +
<textarea rows="10" cols="10" id="special_accomodations_text"></textarea>
 +
</div>-->
 +
 +
            </fieldset>
 +
 +
            <fieldset id="step_3">
 +
                <legend>Step 3</legend>
 +
 +
                <label for="rock">
 +
                    Are you ready to generate your GENE-SOCKET?
 +
                </label>
 +
                <input type="checkbox" id="rock"></input>
 +
 +
                <input type="button" id="submit_button" class="push" value="Complete Design" onclick="sendpost()"></input>
 +
            </fieldset>
 +
 +
        </form>
 +
 +
    </div>
 +
 +
    <!-- <iframe id="print" src="/10.15/js/index.php" width="100%" height="1000" frameborder="0" scrolling="no"></iframe> -->
 +
<p class="cutline">&nbsp;</p>
<p class="cutline">&nbsp;</p>
<div class="zju_sec" style="padding:0;height:650px">
<div class="zju_sec" style="padding:0;height:650px">

Revision as of 20:19, 15 October 2014

Team SponsorContact us

Zhejiang University ZJU International Education Fundation College of Life Sciences ZJU School of Medicine Zhejiang University

College of Agriculture & Biotechnology ZJU Faculty of Science Zhejiang University Undergraduate School of ZJU Department of Polymer Sciencce and Engneering Zhejiang University

International Relations Zhejiang University Vazyme Nanking ™ Co.

 Team Forum(BBS): ZJU-China 2014 Team Forum on www.zjubiolab.zju.edu.cn
Post Address: Biolab Center Room 413, ZJU Zijin'gang Campus,
Yuhang Tang Road No.866, Hangzhou, Zhejiang
Powered by . Zhejiang University. Email Address: zjuchina2014 @ 163.com
GS-Box



GS-Box

An useful bioinformatics tool for Gene-Socket





Every excellent technique should be simple and efficient to use! As an excellent technique, gene-socket also does well in this respect------ it has its' own optimization tool: GS-BOX. GS-BOX is a bioinformatics tool which is designed for customs to build their own gen-sockets easily and efficiently. What need the customs do with the tool? Just input the gene circuit sequences and then GS-BOX will design the experimental process automatically and every detail that customs will need to use!



  • Service

    Mauris sed mauris. Praesent imperdiet, nunc ut sollicitudin hendrerit, nisi tellus mollis leo, blandit pharetra nulla orci id eros. Nullam ut nunc. Praesent lacus lacus, tempor a, dignissim eu, tristique ac, tortor. Sed faucibus. Integer eleifend lacus ac neque. Fusce tempus. In hac habitasse platea dictumst. Nulla arcu neque, gravida at, rhoncus id, pharetra vitae, tortor. Aenean vestibulum consequat augue.

  • Design Principle

    Homeodomains:
    1.Don't have similar sequences with E.coli (to avoid off-target effects)
    2.Don't have similar sequences with custom's parts (to avoid off-target effects)
    3.Fit the subsequent steps' requiring

    Primer:
    1.GC content & TM value
    2.Duplex formation and hairpin
    3.proper length

  • Design Method

    Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Vivamus vestibulum metus sed massa. Pellentesque pharetra felis a enim. Aliquam sapien nisl, iaculis ac, hendrerit placerat, iaculis congue, augue. Quisque eget mi quis purus vestibulum eleifend. Maecenas condimentum eros vel eros. Ut facilisis leo id mi. Suspendisse nisl magna, consequat quis, pretium eget, laoreet vel, orci.

    Mauris sed mauris. Praesent imperdiet, nunc ut sollicitudin hendrerit, nisi tellus mollis leo, blandit pharetra nulla orci id eros. Nullam ut nunc. Praesent lacus lacus, tempor a, dignissim eu, tristique ac, tortor. Sed faucibus. Integer eleifend lacus ac neque. Fusce tempus. In hac habitasse platea dictumst. Nulla arcu neque, gravida at, rhoncus id, pharetra vitae, tortor. Aenean vestibulum consequat augue.

  • How to use

    If you just want to build a normal gene circuit, input your mount of parts and sequences; If your circuit contains some particular parts(for example, an terminator primer or want to make your parts seamless connection),please choose the "special mode" according to your situation.

  • Contact

    If you have any questions when using GS-Box, please contact us.





DIY YOUR OWN GENE-SOCKET




Step 1

(each no less than 20 bp)


Please provide each part's sequences:

Step 2

Please select the mode


If you don't know what these modes mean, please read "How to use" carfully. Are you sure you have selected the right mode?

You shuld learn that your mode is for all of your parts. If you just want to change only one of them, Please see the "Help". Are you sure this mode suits for most of your parts?

Step 3

 

 

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