Difference between revisions of "Team:XJTU-China/Hardware"

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<html lang="en" dir="ltr">
  
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<div class="column full_size judges-will-not-evaluate">
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<head>
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<h3>★  ALERT! </h3>
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    <title>Team:XJTU-China/Contributions</title>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2021.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2021.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2021.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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    <meta name="keywords" content="iGEM,Xi'an Jiaotong University,XJTU-China,Tryptophan,
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        Trp,Biosynthesis,E.coli">
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        content="Welcome to 2021 XJTU-China. Please check our recent work on tryptophan biosynthesis via E.coli">
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<body>
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    <!--banner-->
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        <div class="container row fixedBackground">
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            <div class="fixedBackgroundImg"
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                style="background-image: url(https://static.igem.org/mediawiki/2021/4/40/T--XJTU-China--hardware-bg.jpg);">
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            </div>
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            <div class="pageHeadline"><span>Hardware</span></div>
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        </div>
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    </section>
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    <section class="main">
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        <div class="container mainBox" id="mainBox">
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            <div class="row" id="container">
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                <div class="side col-lg-3">
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                    <nav class="dr-menu">
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                        <h3>Hardware</h3>
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                        <ul>
 +
                            <li><a class="fa fa-plug" href="#overview">&nbsp;1. Overview</a></li>
 +
                            <li><a class="fa fa-plug" href="#design">&nbsp;2. Design</a>
 +
                                <ul>
 +
                                    <li><a class="fa fa-plug" href="#detecting-module">&nbsp;2.1 Detecting Module</a>
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                                    </li>
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                                    <li><a class="fa fa-plug" href="#controlling-module">&nbsp;2.2 Controlling
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                                            Module</a></li>
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                                    <li><a class="fa fa-plug" href="#cultivation-module">&nbsp;2.3 Cultivation
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                                            Module</a></li>
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                                </ul>
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                            </li>
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                            <li><a class="fa fa-plug" href="#program">&nbsp;3. Program</a></li>
 +
                            <li><a class="fa fa-plug" href="#showcase">&nbsp;4. Showcase</a></li>
  
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                        </ul>
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                    </nav>
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                <div class="col-lg-8 col-12 justify-content-center">
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                    <div class="page xjtuText">
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                            <div class="col-12">
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                                <!-- hardware -->
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                                <a class="anchor" id="hardware"></a>
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                                <h1>Hardware</h1>
 +
                                <a class="anchor" id="overview"></a>
 +
                                <h2 class="ml-5">1. Overview</h2>
 +
                                <p>In order to realize the coordination of hardware circuit and gene
 +
                                    circuit, we have made an automatic culture device. At the same time of
 +
                                    detecting the growth and production status of bacteria, the device can
 +
                                    feedback and adjust the conditions of culture, thus controlling the
 +
                                    toggle-switch circuit to allow cells to enter different states between
 +
                                    “proliferation” and “production”. Through the fitting of experimental
 +
                                    results and modeling prediction, we can calculate the best time to
 +
                                    change the cultivation conditions, and write it into the control program
 +
                                    to realize the automatic control of the production process. </p>
 +
                                <a class="anchor" id="design"></a>
 +
                                <h2 class="ml-5">2. Design</h2>
 +
                                <div class="imgWrapper centerize">
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                                    <img src="https://static.igem.org/mediawiki/2021/3/30/T--XJTU-China--POC-Fig1-3.jpeg"
 +
                                        alt="design of hardware" width="80%" class="hoverLarger">
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                                    <span class="description"><strong>Fig. 2.1 The design of
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                                            hardware</strong></span>
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                                </div>
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                                <a class="anchor" id="detecting-module"></a>
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                                <h3 class="ml-5">2.1 Detecting Module</h3>
 +
                                <p>We use a simple spectroscopic device to monitor the cell density and the
 +
                                    concentration of tryptophan in the medium. Our detecting module includes
 +
                                    two sets of tungsten light sources, filters of the corresponding
 +
                                    wavelength and CCDs. By measuring the absorbance of light filtered to
 +
                                    600nm wavelength, the cell density can be represented. While with the
 +
                                    presence of tryptophan detection circuit, the light passing through the
 +
                                    485nm optical filter can excite GFP and its emission light will be
 +
                                    detected by the CCD after a 510nm filter. After receiving by CCDs, all
 +
                                    optical signals of this module are converted into corresponding circuit
 +
                                    signals and transmitted to the control module for processing.</p>
 +
                                <a class="anchor" id="controlling-module"></a>
 +
                                <h3 class="ml-5">2.2 Controlling Module</h3>
 +
                                <p>This module contains a single chip microcomputer (SCM) with its
 +
                                    controlling program, controlling the parts in cultivation module by
 +
                                    receiving and analyzing the signals from detecting module. After
 +
                                    receiving the signal, according to the program written into the SCM, it
 +
                                    can calculate the state of the cell density and product concentration in
 +
                                    the culture medium. When certain conditions are met, corresponding
 +
                                    instructions are issued to control the temperature of culture medium and
 +
                                    the pumping of inducer, with the information fed back to users in real
 +
                                    time.</p>
 +
                                <a class="anchor" id="cultivation-module"></a>
 +
                                <h3 class="ml-5">2.3 Cultivation Module</h3>
 +
                                <p>All fermentation and culture conditions are provided by this module. The
 +
                                    electric heater and ventilator maintain the temperature of the incubator
 +
                                    and are controlled by the SCM to switch the temperature between 37 and
 +
                                    42 degrees Celsius. A ration pump can be used to add IPTG to the medium
 +
                                    upon receiving the SCM signal. The main part is a sterile tank made of
 +
                                    plexiglass, including a transparent and equal thickness area for
 +
                                    spectrophotometry and fluorescence detection. Plus, magnetic stirrer,
 +
                                    ventilation device and other devices for cultivation are also contained
 +
                                    in this module.</p>
 +
                                <a class="anchor" id="program"></a>
 +
                                <h2 class="ml-5">3. Program</h2>
 +
                                <p>The core function of this module is realized by STM32 single chip
 +
                                    microcomputer. The logic control program is designed as follows: the
 +
                                    digital temperature controller continuously monitors the temperature
 +
                                    changes in the container, and keeps communicating with the micro
 +
                                    controller. Micro controller controls the relay to turn on the light
 +
                                    source and photocell briefly every minute to detect the growth of
 +
                                    biological community in the container. If the electromagnetic wave of
 +
                                    600 nanometer wavelength reaches a certain threshold, the micro
 +
                                    controller opens the relay of the electric heating rod through the
 +
                                    digital temperature controller; If the wavelength of 485 nanometer to
 +
                                    510 nanometer, the micro controller through the digital temperature
 +
                                    controller to disconnect the relay of the electric heating rod, and
 +
                                    prompt to replace the solution.</p>
  
 +
                                <a class="anchor" id="showcase"></a>
 +
                                <h2 class="ml-5">4. Showcase</h2>
 +
                                <p>Worked by our skillful teammates in hardware group, the prototype of our hardware is
 +
                                    built and tested. We record and document a clip of video of this machine, upload it
 +
                                    to
 +
                                    iGEM repository, and append it below.</p>
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                                <div class="row">
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                                    <div class="col-12 d-flex justify-content-center">
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                                        <video src="https://static.igem.org/mediawiki/2021/e/ef/T--XJTU-China--Hardware.mp4"
 +
                                            width="70%" controls preload="metadata"></video>
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                                    </div>
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                                </div>
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                            </div>
  
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                    </div>
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<h1>Hardware</h1>
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                </div>
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<p>For Hardware Track teams, while you are not eligible for the Hardware Special Prize, you can use this page to document your work.</p>
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                <div class="col-lg-1"></div>
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</div>
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            </div>
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        </div>
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<div class="column two_thirds_size">
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    </section>
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<h3>Best Hardware Special Prize</h3>
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    <!--JS-->
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<p>In addition to encouraging teams to work with DNA parts and build biological devices in the lab, iGEM also encourages other types of technical solutions for synthetic biology. This can include physical devices (hardware) related to robotic assembly, microfluidics, low-cost measurement devices, to name a few examples. There are many exciting opportunities for hardware innovation in synthetic biology.
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    <script type="text/javascript"
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</p>
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        src="https://2021.igem.org/wiki/index.php?title=Template:XJTU-China/jquery&action=raw&ctype=text/javascript"></script>
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    <script type="text/javascript"
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<p>This is a prize for the team that has developed a piece of hardware for synthetic biology. Hardware in iGEM should make synthetic biology based on standard parts easier, faster, better or more accessible to our community. Did your team make a sensor to help teams characterize parts? Did you make a robot that can help teams perform experiments or do cloning more easily? Tell us what your team did for this award!</p>
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        src="https://2021.igem.org/wiki/index.php?title=Template:XJTU-China/bootstrapJS&action=raw&ctype=text/javascript"></script>
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<p>
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    <script type="text/javascript"
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To compete for the <a href="https://2021.igem.org/Judging/Awards">Best Hardware prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2021.igem.org/Judging/Judging_Form">judging form</a>.
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        src="https://2021.igem.org/wiki/index.php?title=Template:XJTU-China/lottie&action=raw&ctype=text/javascript"></script>
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                var scroll = $(window).scrollTop();
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                var pageHeight = $(window).height();
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<h3>Inspiration</h3>
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                var pageWidth = $(window).width();
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<p>You can look at what other teams did to get some inspiration! <br />
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                var drMenu = $(".dr-menu");
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Here are a few examples:</p>
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                var containerHeight = $("#container").height();
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<ul>
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                var drMenuHeight = drMenu.height();
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<li><a href="https://2018.igem.org/Team:Valencia_UPV/Hardware">2018 Valencia UPV</a></li>
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<li><a href="https://2018.igem.org/Team:Unesp_Brazil/Hardware">2018 Unesp Brazil</a></li>
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<li><a href="https://2019.igem.org/Team:BIT/Hardware">2019 BIT</a></li>
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<li><a href="https://2019.igem.org/Team:Bielefeld-CeBiTec/Hardware">2019 Bielefeld CeBiTec</a></li>
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<li><a href="https://2019.igem.org/Team:Nanjing-China/Hardware">2019 Nanjing China</a></li>
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<li><a href="https://2020.igem.org/Team:Vilnius-Lithuania/Hardware">2020 Vilnius Lithuania</a></li>
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<li><a href="https://2020.igem.org/Team:Aachen/Hardware">2020 Aachen</a></li>
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<li><a href="https://2020.igem.org/Team:ZJUT_China_B/Hardware">2020 ZJUT China B</a></li>
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</ul>
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                    drMenu.show();
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                            "top": (headerHeight + 100).toString() + "px"
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                        drMenu.css({
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                            "position": "relative",
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{{XJTU-China/header}}
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{{XJTU-China/footer}}

Latest revision as of 17:07, 21 October 2021

Team:XJTU-China/Contributions

Hardware

Hardware

1. Overview

In order to realize the coordination of hardware circuit and gene circuit, we have made an automatic culture device. At the same time of detecting the growth and production status of bacteria, the device can feedback and adjust the conditions of culture, thus controlling the toggle-switch circuit to allow cells to enter different states between “proliferation” and “production”. Through the fitting of experimental results and modeling prediction, we can calculate the best time to change the cultivation conditions, and write it into the control program to realize the automatic control of the production process.

2. Design

design of hardware Fig. 2.1 The design of hardware

2.1 Detecting Module

We use a simple spectroscopic device to monitor the cell density and the concentration of tryptophan in the medium. Our detecting module includes two sets of tungsten light sources, filters of the corresponding wavelength and CCDs. By measuring the absorbance of light filtered to 600nm wavelength, the cell density can be represented. While with the presence of tryptophan detection circuit, the light passing through the 485nm optical filter can excite GFP and its emission light will be detected by the CCD after a 510nm filter. After receiving by CCDs, all optical signals of this module are converted into corresponding circuit signals and transmitted to the control module for processing.

2.2 Controlling Module

This module contains a single chip microcomputer (SCM) with its controlling program, controlling the parts in cultivation module by receiving and analyzing the signals from detecting module. After receiving the signal, according to the program written into the SCM, it can calculate the state of the cell density and product concentration in the culture medium. When certain conditions are met, corresponding instructions are issued to control the temperature of culture medium and the pumping of inducer, with the information fed back to users in real time.

2.3 Cultivation Module

All fermentation and culture conditions are provided by this module. The electric heater and ventilator maintain the temperature of the incubator and are controlled by the SCM to switch the temperature between 37 and 42 degrees Celsius. A ration pump can be used to add IPTG to the medium upon receiving the SCM signal. The main part is a sterile tank made of plexiglass, including a transparent and equal thickness area for spectrophotometry and fluorescence detection. Plus, magnetic stirrer, ventilation device and other devices for cultivation are also contained in this module.

3. Program

The core function of this module is realized by STM32 single chip microcomputer. The logic control program is designed as follows: the digital temperature controller continuously monitors the temperature changes in the container, and keeps communicating with the micro controller. Micro controller controls the relay to turn on the light source and photocell briefly every minute to detect the growth of biological community in the container. If the electromagnetic wave of 600 nanometer wavelength reaches a certain threshold, the micro controller opens the relay of the electric heating rod through the digital temperature controller; If the wavelength of 485 nanometer to 510 nanometer, the micro controller through the digital temperature controller to disconnect the relay of the electric heating rod, and prompt to replace the solution.

4. Showcase

Worked by our skillful teammates in hardware group, the prototype of our hardware is built and tested. We record and document a clip of video of this machine, upload it to iGEM repository, and append it below.

contact us

Xi'an Jiaotong University
28 Xianning West Road
Xi'an, Shaanxi, China, 710049
xjtu_igem@xjtu.edu.cn
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XJTU-iGEMers