Difference between revisions of "Team:Peking/Model"

 
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         <meta name="author" content="Li Jiamian & Wang Yuqing"/>
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                                     <li><a href="https://2018.igem.org/Team:Peking/Design" class="barfont1">Design</a></li>
 
                                     <li><a href="https://2018.igem.org/Team:Peking/Design" class="barfont1">Design</a></li>
 
                                     <li><a href="https://2018.igem.org/Team:Peking/Demonstrate" class="barfont1">Demonstration</a></li>
 
                                     <li><a href="https://2018.igem.org/Team:Peking/Demonstrate" class="barfont1">Demonstration</a></li>
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                                     <li><a href="https://2018.igem.org/Team:Peking/Prospective" class="barfont1">Prospective</a></li>
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                                     <li><a href="https://2018.igem.org/Team:Peking/Perspective" class="barfont1">Perspective</a></li>
 
                                 </ul>
 
                                 </ul>
 
                             </li>
 
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                             <li class="dropdown menu-3"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Modeling</a>
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                             <li class="menu-3"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Model">Modeling</a>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Model">Overview</a></li>
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                                    <li><a href="https://2018.igem.org/Team:Peking/SPOT_Formation" class="barfont1">SPOT Formation</a></li>
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                                    <li><a href="https://2018.igem.org/Team:Peking/Application" class="barfont1">Application</a></li>
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                             </li>
 
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                             <li class="menu-4"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Software">Software</a>
 
                             <li class="menu-4"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Software">Software</a>
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                                <li class="dropdown menu-6"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Human Practices</a>
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                            <li class="menu-6"><a class="colapse-menu1" href="https://2018.igem.org/Team:Peking/Human_Practices">Human Practices</a>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Human_Practices" class="barfont1">Overview</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Modeling_Spot Formation" class="barfont1">Spot Formation</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Public_Engagement" class="barfont1">Public Engagement</a></li>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Other" class="barfont1">Other</a></li>
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                                 <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Achievement</a>
 
                                 <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Achievement</a>
 
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                                         <li><a href="https://2018.igem.org/Team:Peking/Collaborations" class="barfont1">Collaborations</a></li>
 
                                         <li><a href="https://2018.igem.org/Team:Peking/Collaborations" class="barfont1">Collaborations</a></li>
 
                                         <li><a href="https://2018.igem.org/Team:Peking/Safety" class="barfont1">Safety</a></li>
 
                                         <li><a href="https://2018.igem.org/Team:Peking/Safety" class="barfont1">Safety</a></li>
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                                                                            <li><a href="https://2018.igem.org/Team:Peking/Acknowledgement" class="barfont1">Acknowledgement</a></li></ul>
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                                        <li><a href="https://2018.igem.org/Team:Peking/Acknowledgement" class="barfont1">Acknowledgement</a></li>
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                     <h1>Human Practices</h1>
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                     <h1>Modeling</h1>
 
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                                     <h4><a href="javascript:void(0);" onclick="naver('A')">Overview</a></h4>
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                                     <h4><a href="javascript:void(0);" onclick="naver('A')">&bull;Overview</a></h4>
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                                     <h4><a href="https://static.igem.org/mediawiki/2018/3/30/T--Peking--Modelling_Revise.pdf">&bull;PDF&#160;Version&#160;Download</a></h4>                                
 
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                             <div class="texttitle">Overview
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<a id="A"></a></div>  
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                             <div class="texttitle"><a id="A"></a>Overview
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                                     <p>Our team seeks to synthesize membrane-less organelles and turn it into a multi-functional toolbox for synthetic biology based on basic phase separation principles, which is a rather fundamental field in condensed matter physics. Therefore, it’s not really a reality application so far. Nonetheless, it’s definitely not the reason that we are confined in the laboratory coping with experiments and mathematical models without making a difference to the society directly. Meanwhile, we need to get to know about the demand of engineers and consumers. Thus we did an integrated human practice in several different ways.</p>
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                                     <div align="center"><img src="https://static.igem.org/mediawiki/2018/2/20/T--Peking--mod_fig1.png"></div>
 
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    <div class="texttitle"><a id="B"></a>SIMULATION FOR PHASE SEPARATION
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                                    <p>Inside the iGEM community, we made statistics of the education background and numbers of igemers each year in order to investigate how iGEM has been broadcasted internationally and how the field of synthetic biology has changed over the last 14 years. We noticed that most iGEM teams are becoming more and more diverse, which promotes the development of iGEM community but make it more challenging for team members to communicate. This can also be read as more people from different disciplines especially mathematics and physics have been devoted to systems and synthetic biology, which are interdisciplinary sciences needing various knowledge while on the same time, they can feed back to enrich the individual scientific disciplines and biology-based solutions for societal problems can be worked out.</p>
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                                    <p>We also tried to play an active part in public engagement. We communicated with people from various backgrounds in universities, high schools, kindergartens and on the internet. We realized that there has always been a gap between the achievements in scientific research and reality application. People from academic world and industrial world barely know each others’ requirements most of the time. Thus we discussed this topic in detail using fluorescence microscope as an example.</p>
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                                    <p>Our human practice reinforced our team construction creating more chance for the team members to communicate and collaborate with each other. We tried to make synthetic biology accessible for as many people as possible and we do expect our efforts may make a difference. Meanwhile, we’d be more than glad if our work may give the synthetic biology community some inspiration. To gain a deeper understanding of biology in the 21st century, we need to integrate knowledge from various disciplines while biology-based solutions to societal problems can influence the world more profoundly. </p>
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                                    <p>In the following sections, you will go through our human practice in details.</p>
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                                <div class="texttitle"><a id="B"></a>Investigation on the education background of iGEMers
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<div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2018/d/d6/T--Peking--HP1.jpeg">
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<br/>Figure 1<br/></div>
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                                    <p>Figure 1 shows the geographical distribution of the number of teams. (2007-2018)
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/3/31/T--Peking--mod_fig2.png"></div>                                 
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/0/08/T--Peking--mod_fig4.png"></div>
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<img src="https://static.igem.org/mediawiki/2018/7/7e/T--Peking--HP2.png">
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/9/94/T--Peking--mod_fig5.png"></div>
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Figure 2.A
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<img src="https://static.igem.org/mediawiki/2018/3/3c/T--Peking--HP3.png">
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Figure 2.B
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/2/25/T--Peking--mod_fig10.png"></div>  
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                                    <p>Figure 2.A, B show teams attending iGEM from different regions. Figure 2.A shows the number while Figure 2.B shows the proportion of teams in each year (2007-2018) . Different colors of columns represent different regions. </p>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/1/1e/T--Peking--mod_fig11.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/4/48/T--Peking--mod_fig12.png"></div>
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                                    <p>In 2007, only 61 teams from around the world participated in iGEM, but iGEM has now attracted more than 300 teams from around the world for three consecutive years(305 teams in 2016, 338 teams in 2017, 370 teams in 2018). Especially since 2015, IGEM has teams from Africa every year.</p>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/b/b1/T--Peking--mod_fig16.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/a/a7/T--Peking--mod_fig17.gif"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/5/5e/T--Peking--mod_fig18.png"></div>
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<br/></div>
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                                    <p>Overall, it could be found that the number of teams increases with the year. Though teams mainly come from Asia, North America and Europe, we still find more and more African and Latin American teams participating in this important event in the field of synthetic biology. We have reasons to believe that the influence of iGEM in developing countries is gradually increasing.</p>
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                                    <p>In addition, we find that iGEM's influence in Asia, especially in the Western Pacific, is gradually increasing. Asia has become an important pillar in iGEM that cannot be ignored.</p>
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                            </div>
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<img src="https://static.igem.org/mediawiki/2018/4/40/T--Peking--HP4.png">
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−
Figure 3.A
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<img src="https://static.igem.org/mediawiki/2018/8/88/T--Peking--HP5.png">
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Figure 3.B
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                                <div class="content">
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                                    <p>Figure 3.A.B show the proportion of track selections in 10 years. Figure3.A shows the proportion in 2009-2013 and Figure3.B in 2014-2018. Different colors of columns represent different tracks.</p>
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                                    <p>In the 2009-2013 track selection, ‘Foundational Research’ entered the Top 3 tracks that were most popular in the past five times, followed by ‘Enviroment’ 4 times, ‘Health’ 3 times, and ‘New application’ 3 times.</p>
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                                    <p>In 2014, iGEM officially made major adjustments to the track. Added the resources of ‘Community labs’, ‘Hardware’, ‘Measurement’, ‘Microfluids’, ‘Arts & Design’, and split the original ‘Food & Energy’ into ‘Energy’, ‘Food & Nutrition’ (2014)；and split ‘Health’ into ‘Diagnostics' and ‘Therapeutics’ in 2016. After the adjustment, if we do not count ‘High school’ as a scientific research track, then the Top 3 list is as shown in the table below.</p>
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                                    <p><div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2018/d/d6/T--Peking--HP6.png" width="70%">
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−
<br/>Table 1<br/></div>Table 1 shows the top three tracks that are most popular among the participating teams in 10 years.</p>
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                            </div>
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                                    <p>We find that in 2009-2018, iGEM's participating teams are more concerned with the four aspects of Environment, Foundational Research, Health & Medicine, and New application. This implies that environmental pollution and health care are still the most popular issues in the world.</p>
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                            </div>
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                                    <p>It is worth noting that compared with 2009, the choice of track in 2018 is more diversified, and the track of ‘Art & Design’ and other humanities and social sciences has received enough attention.</p>
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<img src="https://static.igem.org/mediawiki/2018/7/7f/T--Peking--HP7.png">
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−
Figure 4.A
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<img src="https://static.igem.org/mediawiki/2018/5/57/T--Peking--HP8.png">
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Figure 4.B
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<div class="coll">
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                                <div class="content">
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                                    <p>Figure4.A, B show the academic background of the participants. Different colors of columns represent different subjects.</p>
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                                </div>
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                            </div>
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                                    <p>We obtained information about the participants’ academic background by counting the Wiki of each team. It should be noted that since many teams do not introduce the academic background of the team members, we have not been able to record all the subject information of each individual.</p>
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                                    <p>Judging from the information we recorded, the number of players participating each year has gradually increased. Among them, members from Biology & Health Science accounts for the majority, followed by Multidisciplinary and Computer & Engineering. In particular, compared to 2007, the academic background of the contestants in 2016 is more diverse. Other than this, every year, in addition to members of other natural sciences from mathematics, physics, chemistry, environment, etc., there are also members from the social sciences and humanities. We believe that iGEM is playing an increasingly important role in promoting multidisciplinary communication and promoting engineering in the field of synthetic biology.</p>
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                            </div>
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                            <div class="texttitle">Public engagement
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<a id="C"></a></div>
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                                    <p>Talking with high school students</p>
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                                    <p>One of our team members Guo Fuyu went to Hutian Middle School in Huaihua, Hunan Province. He introduced systems and synthetic biology to the students while helped them with biology in high school as well. To our point of view, it’s of foundamental significance to provide as much middle school students in second-tier cities in China as possible with access to frontier science, for quality education is definitely as important as examination-oriented education.
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<div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2018/7/7f/T--Peking--hp11.jpeg">
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<br/>XXXXXXX. 1</div>
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</p>
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                                    <p>According to a survey in Peking University, freshmen who have had a sense of high education and sought for their interest in high school get accustomed to college life and study remarkably faster than those who haven’t. We genuinely hope university students and professors across China can communicate more with high school students and help every single one find his or her own interest worth pursuing their whole life as soon as possible. We especially hope the students in second-tier cities and rural areas get the same chance of quality education as those in supercities.</p>
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 +
<div class="texttitle"><a id="C"></a>Simulation for metabolic regulation with phase separation
  
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                                    <p>pre school scientific education</p>
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 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/e/e5/T--Peking--mod_fig19.png"></div>                                 
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/8/8d/T--Peking--mod_fig20.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/7/7d/T--Peking--mod_fig21.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/9/91/T--Peking--mod_fig22.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/4/46/T--Peking--mod_fig23.png"></div> 
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/c/c2/T--Peking--mod_fig24.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/3/37/T--Peking--mod_fig25.png"></div> 
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/4/4e/T--Peking--mod_fig26.png"></div>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/f/fa/T--Peking--mod_fig27.png"></div> 
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/9/94/T--Peking--mod_fig28.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/b/bb/T--Peking--mod_fig29.png"></div>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/1/12/T--Peking--mod_fig30.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/7/7d/T--Peking--mod_fig31.gif"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/7/74/T--Peking--mod_fig32.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/9/95/T--Peking--mod_fig33.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/f/f1/T--Peking--mod_fig34.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/e/e5/T--Peking--mod_fig35.png"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/a/a0/T--Peking--mod_fig36.gif"></div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/6/63/T--Peking--mod_fig37.png"></div>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/5/57/T--Peking--mod_fig38.png"></div>
 +
<div align="center"><img src="https://static.igem.org/mediawiki/2018/c/c8/T--Peking--mod_fig39.png"></div>
 +
<br/></div>
 
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                                    <p>May it be a crazy idea to introduce the most cutting-edge science to the kids in kindergarten, the kids and us can still spend a nice day with science. Two of our team members did this in the kindergarten attached to Peking University. We designed a series of games with the background of science: demonstrating the three phases of water, observing phase separation, constructing a “phase separation” system with magnet ball and water drawing. The kids liked these games very much which inspired us a lot.</p>
 
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                                    <p>It’s a big challenge for us to tell the children about basic science, but we’re happy to see them enjoying the games which is also interesting and relaxing for us. We enjoyed the fascination of science which is believed to cross the boundary of age and life experience.</p>
 
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                                     <p>This activity made us confident about the perspective of scientific communication, and we realized we can communicate in a both “meaningful” and “interesting” way, where all the talkers are equal and relaxed and the conversation is much more efficient.</p>
+
                                     <p> You can see the pdf version of our modelling <a href="https://static.igem.org/mediawiki/2018/9/9e/T--Peking--Modeling.pdf"> here</a></p>
 
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                                    <p>Documentation of Peking iGEM as enlightenment for beginners</p>
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<div class="left" text-align="center">
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<object  class="center" data="https://static.igem.org/mediawiki/2018/9/9e/T--Peking--Modeling.pdf" style="height: 626px; width: 602px; margin-top: 48px; margin-right: 0px;margin-left: 0px; float: left" max-width="600px" max-height="100px"><p>no pdf, download here<a href="https://static.igem.org/mediawiki/2018/9/9e/T--Peking--Modeling.pdf">click here to
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  download the PDF file.</a></p>    </object>
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                                    <p>We have built up a WeChat public platform which is a worldwide platform with billions of users for documentation, communication and popularization. To give the future iGEMers a taste of iGEM projects and help them learn the basic rudiments of synthetic biology we have reviewed the projects of Peking iGEM in the past 14 years. All these articles are rather approachable and most of them received positive feedbacks. We demonstrate here the articles and hope it may help more people who want to get to know about synthetic biology.</p>
 
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    <th><a href="https://mp.weixin.qq.com/s/AMd0rNq9AQDu02cUu7HvWw"><img src="https://static.igem.org/mediawiki/2018/c/c3/T--Peking--2007.png"></a></th>
 
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    <th><a href="https://mp.weixin.qq.com/s/uhbTZHsgPL8b3YPLm_K9kQ"><img src="https://static.igem.org/mediawiki/2018/c/cb/T--Peking--2008.png"></a></th>
 
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    <td>2007</td>
 
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    <td>2008</td>
 
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    <th><a href="https://mp.weixin.qq.com/s/dQj9qOFF_kKO_d7QDMsanQ"><img src="https://static.igem.org/mediawiki/2018/1/1b/T--Peking--2009.png"></a></th>
 
−
    <th><a href="https://mp.weixin.qq.com/s/5qaRHr0pBmB0SphxrpDanQ"><img src="https://static.igem.org/mediawiki/2018/7/7f/T--Peking--2010.png"></a></th>
 
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  </tr>
 
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  <tr>
 
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    <td>2009</td>
 
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    <td>2010</td>
 
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    <th><a href="https://mp.weixin.qq.com/s/O8sPYmyyIwO_evpzao0DhQ"><img src="https://static.igem.org/mediawiki/2018/1/14/T--Peking--2011.png"></a></th>
 
−
    <th><a href="https://mp.weixin.qq.com/s/Xt5fROM6MSL6DHWSaDWaew"><img src="https://static.igem.org/mediawiki/2018/3/3d/T--Peking--2012.png"></a></th>
 
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  </tr>
 
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  <tr>
 
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    <td>2011</th>
 
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    <td>2012</th>
 
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  </tr>
 
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    <th><a href="https://mp.weixin.qq.com/s/m-Ttirv-yjhokSnFQa0qMA"><img src="https://static.igem.org/mediawiki/2018/0/08/T--Peking--2013.png"></a></td>
 
−
    <th><a href="https://mp.weixin.qq.com/s/mVa2p41Yc8yHtqFg4Akwcg"><img src="https://static.igem.org/mediawiki/2018/5/5a/T--Peking--2015.png"></a></td>
 
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  </tr>
 
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  <tr>
 
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    <td>2013</th>
 
−
    <td>2015</th>
 
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  </tr>
 
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−
    <th><a href="https://mp.weixin.qq.com/s/o2e5y0g0luZuYS957KLMJQ"><img src="https://static.igem.org/mediawiki/2018/8/8a/T--Peking--2016.png"></a></td>
 
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    <th><a href="https://mp.weixin.qq.com/s/VwFxEy7ab46vAF9Q3A9vcg"><img src="https://static.igem.org/mediawiki/2018/f/fe/T--Peking--2017.png"></a></td>
 
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  <tr>
 
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    <td>2016</th>
 
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    <td>2017</th>
 
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                                    <p>Popular video of phase separation</p>
 
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                                    <p>We made a popular video of phase separation in biology to introduce it to more people studying biology. We posted it on several websites in China and many undergraduates and graduates have got to known phase separation through our video. We also found it necessary to communicate more about basic knowledge of different disciplines in the area of systems biology. Only in this way can people know better about the system they work on and cooperate better with each other.
 
−
(张蔚phase视频，网盘上有)
 
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</p>
 
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                                <div class="texttitle"><a id="D"></a>Making low-cost experimental instrument</div>
 
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                                    <p>We find it an essential problem in synthetic biology to fill the gap between foundational research and practical application. We hope our human practice can propose some possible solutions to this problem. Taking our time and energy into consideration, we chose a minor project, the design and usage of low-cost equipment, as the main subject.</p>
 
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                                    <p>Most of the results of iGEM research have been achieved in the laboratory, but there’s a big difference between the environment of laboratory and reality use. For example, it’s more than common to use microscope in laboratory, but people rarely get access to microscope in production for the sake of expense and precision. Can differences like this be an impediment of the transformation from laboratory achievements to industrial production? What can we do about these problems?</p>
 
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                                    <p>We talked with Professor Xu Luping from Tsinghua University, who designed a low-cost microscope from 3D-printer. We got to know from the interview that most of the parts are easy to get, while it’s also not difficult to assemble. We talked about the possible application of this kind of microscopes and the probability to expand it into fluorescence microscopes.
 
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<div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2018/5/5b/T--Peking--hp12.png">
 
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<br/>XXXXXXX. 1</div>
 
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</p>
 
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                                    <p>So far, this kind low-cost microscope is still conceptual productions which is mainly used for popular science or education, but it’s still helpful to the future work. To Professor Xu’s point of view, realizing a possibility in engineering is of great significance in itself. This has enlighten us to summarize some abstract and modularized ‘potential properties’ in our project apart from seeking for practical application of our bioparts.</p>
 
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                                    <p>It also came to us that the main difficulty of our subject to build a low-cost fluorescence microscope lies in the cost of equipping fluorescence light source. Fluorescence technology plays a significant part in synthetic biology scientific research, but it’s much too expensive in industry. We talked about the possibility to lower the cost of fluorescence technology and think it probably necessary to try to develop low precision and low cost fluorescence technology, especially when it’s quite usual to combine fluorescence technology with biotechnology now.</p>
 
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                                    <p>So we communicated with Dr Zong Yeqing, who showed us his self-made fluorescence stereomicroscope. Fluorescence stereomicroscope is needed in a project but there isn’t one in the institute he works in and it’s not worthwhile to spend millions of RMB yuan to buy one for one single project. So he built one himself. The total cost of his self-made fluorescence stereomicroscope is 1000 RMB yuan. It can be used for observation, incubation and heating. The communication with Dr. Zong Yeqing not only gave us the hope of building low-cost fluorescence instrument for production and medication, but also reminded us of the significance of building low-cost instrument for scientific research itself.
 
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Latest revision as of 03:04, 18 October 2018

Modeling

Overview
SIMULATION FOR PHASE SEPARATION

Simulation for metabolic regulation with phase separation

You can see the pdf version of our modelling here