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'''{{Nagahama}}'''
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=Increased production of fragrance for new food preservation method ''E.coli''=
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    <h1 id="firstHeading" class="firstHeading">
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        <span dir="auto">Team:Nagahama/Wiki Design</span>
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==ABSTRACT==
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To innovate the refrigerator without electricity, we invented a prototype of FRAVORATOR that is possible to preserve food by antibacterial volatiles synthesized by ''Escherichia coli''. For the high-efficiency synthetic process of preservation flavor, farnesol, we focused on improving its synthetic pathway. First, 1-deoxy-D-xylulose 5-phosphate（DXP）synthase, Dxs, is down-regulated when its downstream material has been produced to some extent. So, we tried to over-express, another DXP synthase, nDXP, that rarely has been used in normal conditions. Also, we created fusion gene for ispC-ribB protein for enzymatic function. Second, to avoid recombinant in the real usage, we tried to knock out synthase that produces unnecessary byproduct by genome editing.
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==TRACK==
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'''Food Nutrition'''
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==We certainly achieved GOLD Medal Criteria!==
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=== Bronze Medal ===
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<script src="//2016.igem.org/Team:Nagahama/Assets/Fudge_js?action=raw&amp;ctype=text/javascript"></script>
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{| class="wikitable"
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|-
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|1
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|Register for iGEM, have a great summer, and attend the Giant Jamboree.
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|Yes, we are looking forward to taking part in the Giant Jamboree.
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|-
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|2
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|Meet all deliverables on the Requirements page (section 3).
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|We meet all requirements.
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|-
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|3
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|Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.
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|Please check [https://2016.igem.org/Team:Nagahama/Attributions Here].
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|-
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|4
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|Document at least one new standard BioBrick Part or Device central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). You may also document a new application of a BioBrick part from a previous iGEM year, adding that documentation to the part's main page.
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|Please check [https://2016.igem.org/Team:Nagahama/Our_all_BioBricks Here].
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|-
  
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<!--<nav class="col-xs-3 bs-docs-sidebar" style="float:right;">
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|}
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        <ul id="sidebar" class="nav nav-stacked fixed">
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            <li>
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                <a href="#GroupA">Home</a>
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                <ul class="nav nav-stacked">
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                </ul>
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            </li>
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            <li>
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                <a href="#GroupB">Project</a>
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                <ul class="nav nav-stacked">
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                    <li><a href="#GroupBSub1">Description</a></li>
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                    <li><a href="#GroupBSub2">Make Your Own</a></li>
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                    <li><a href="#GroupBSub3">Gallery</a></li>
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                </ul>
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            </li>
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            <li>
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                <a href="#GroupC">Hardware</a>
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                <ul class="nav nav-stacked">
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                    <li><a href="#GroupCSub1">Design</a></li>
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                    <li><a href="#GroupCSub2">Specs</a></li>
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                    <li><a href="#GroupCSub3">3D Printing</a></li>
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                    <li><a href="#GroupCSub4">Modeling</a></li>
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                    <li><a href="#GroupCSub5">Stretch Goals</a></li>
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                <a href="#GroupD">Software</a>
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                    <li><a href="#GroupDSub1">Webshell</a></li>
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                    <li><a href="#GroupDSub2">MicroMaps</a></li>
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                    <li><a href="#GroupDSub3">Autofocus</a></li>
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                    <li><a href="#GroupDSub4">ImageJ</a></li>
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                    <li><a href="#GroupDSub5">Wiki Design</a></li>
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                </ul>
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            </li>
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                <a href="#GroupE">Community</a>
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                <ul class="nav nav-stacked">
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                    <li><a href="#GroupESub1">Outreach</a></li>
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                    <li><a href="#GroupESub2">Human Practises</a></li>
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                    <li><a href="#GroupESub3">Collaboration</a></li>
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                </ul>
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            </li>
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                        <li>
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                <a href="#GroupF">Our Lab</a>
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                <ul class="nav nav-stacked">
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                    <li><a href="#GroupFSub1">Notebook</a></li>
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                    <li><a href="#GroupFSub2">Safety</a></li>
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                    <li><a href="#GroupFSub3">Achievements</a></li>                 
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                </ul>
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            <a href="#GroupG">About Us</a>
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                    <li><a href="#GroupGSub1">Meet the Team</a></li>
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                    <li><a href="#GroupGSub2">Attributions</a></li>
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                    <li><a href="#GroupGSub3">Sponsors</a></li>
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    </nav>
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-->
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<div class="cam-container">
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===Silver Medal===
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    <div class="navbar navbar-inverse navbar-fixed-top navbar-pad">
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{| class="wikitable"
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        <div class="container">
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|-
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            <div class="navbar-header">
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|1
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                <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
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|Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected. Document the characterization of this part in the Main Page section of the Registry entry for that Part/Device. This working part must be different from the part you documented in Bronze medal criterion #4. Submit this part to the iGEM Parts Registry.
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                    <span class="icon-bar"></span>
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|We created 3 new BioBrick devices for silver medal criterion. Please look at [http://parts.igem.org/wiki/index.php?title=Part:BBa_K1950010 BBa_K1950010] , [http://parts.igem.org/wiki/index.php?title=Part:BBa_K1950008 BBa_K1950008], and [http://parts.igem.org/wiki/index.php?title=Part:BBa_K1950007 BBa_K1950007].
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                    <span class="icon-bar"></span>
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|-
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                    <span class="icon-bar"></span>
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|2
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                </button>
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|Convince the judges you have helped any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synthetic biology problem.
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                <a class="navbar-brand" href="//2016.igem.org/Team:Nagahama">CAMBRIDGE-JIC</a>
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|Please check [https://2016.igem.org/Team:Nagahama/Collaborations here].
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            </div>
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|-
 +
|3
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|iGEM projects involve important questions beyond the lab bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. Demonstrate how your team has identified, investigated, and addressed one or more of these issues in the context of your project. Your activity could center around education, public engagement, public policy issues, public perception, or other activities (see the human practices hub for more information and examples of previous teams' exemplary work).
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|Please check [https://2016.igem.org/Team:Nagahama/Human_Practice here].
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|}
  
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===Gold Medal===
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            <div class="navbar-collapse collapse">
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{| class="wikitable"
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                <ul class="nav navbar-nav navbar-right">
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|-
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                    <li><a href="//2016.igem.org/Team:Nagahama">HOME</a></li>
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|1
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                    <li><a href="//2016.igem.org/Team:Nagahama/Project">PROJECT</a>
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|Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the design and/or execution of your project.
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                        <div class="navsub">
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|Please check [https://2016.igem.org/Team:Nagahama/Intgrated_Human_Practice here].
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                            <ul>
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|-
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                                <li><a href="//2016.igem.org/Team:Nagahama/Description">DESCRIPTION</a></li>
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|2
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                                <li><a href="//2016.igem.org/Team:Nagahama/Design">APPLIED DESIGN</a></li>
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|Improve the function OR characterization of an existing BioBrick Part or Device and enter this information in the Registry. Please see the Registry help page on how to document a contribution to an existing part. This part must NOT be from your 2016 part number range.  
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                                <li><a href="//2016.igem.org/Team:Nagahama/Make_Your_Own">MAKE YOUR OWN</a></li>
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|Please check [http://parts.igem.org/Part:BBa_K1230000 here].
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                                <li><a href="//2016.igem.org/Team:Nagahama/Downloads">DOWNLOADS</a></li>
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|-
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                                <li><a href="//2016.igem.org/Team:Nagahama/Gallery">GALLERY</a></li>
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|3
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                            </ul>
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|Demonstrate a functional proof of concept of your project. Your proof of concept must consist of a BioBrick device; a single BioBrick part cannot constitute a proof of concept. (Remember, biological materials may not be taken outside the lab.)
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                        </div>
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|Please check [https://2016.igem.org/Team:Nagahama/Proof_of_concept here].
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                    </li>
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|-
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                    <li><a href="//2016.igem.org/Team:Nagahama/Hardware">HARDWARE</a>
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|4
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                        <div class="navsub">
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|Show your project working under real-world conditions. To achieve this criterion, you should demonstrate your whole system, or a functional proof of concept working under simulated conditions in the lab (Remember, biological materials may not be taken outside the lab.)  
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                            <ul>
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|Please check [https://2016.igem.org/Team:Nagahama/Demonstrate_your_work here].
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                                <li><a href="//2016.igem.org/Team:Nagahama/Tech_Specs">TECHNICAL SPECIFICATIONS</a></li>
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|-
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                                <li><a href="//2016.igem.org/Team:Nagahama/Modeling">MODELING</a></li>
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|}
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                                <li><a href="//2016.igem.org/Team:Nagahama/3D_Printing">3D PRINTING</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Stretch_Goals">STRETCH GOALS</a></li>
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                    <li><a href="//2016.igem.org/Team:Nagahama/Software">SOFTWARE</a>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Webshell">WEBSHELL</a></li>
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                                <!--<li><a href="//2015.igem.org/Team:Nagahama/ScopeScratch">SCOPESCRATCH</a></li>-->
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                                <li><a href="//2016.igem.org/Team:Nagahama/MicroMaps">MICROMAPS</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Autofocus">AUTOFOCUS</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/ImageJ">IMAGEJ</a></li>
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                            </ul>
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                        </div>
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                    </li>
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                    <li><a href="//2015.igem.org/Team:Cambridge-JIC/Practices">COMMUNITY</a>
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                        <div class="navsub">
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                            <ul>
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                                <li><a href="//2015.igem.org/Team:Cambridge-JIC/Outreach">OUTREACH</a></li>
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                                <li><a href="//2015.igem.org/Team:Cambridge-JIC/OpenHardwareRevolution">OPEN HARDWARE LICENSING</a></li>
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                                <li><a href="//2015.igem.org/Team:Cambridge-JIC/Collaborations">COLLABORATION</a></li>
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                                <li><a href="//2015.igem.org/Team:Cambridge-JIC/Wiki_Design">WIKI DESIGN</a></li>
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                            </ul>
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                    </li>
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                    <li><a href="//2016.igem.org/Team:Nagahama/Lab">OUR LAB</a>
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                            <ul>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Notebook">NOTEBOOK</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Safety">SAFETY</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Achievements">ACHIEVEMENTS</a></li>
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                            <2/ul>
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                    <li><a href="//2016.igem.org/Team:Nagahama/People">ABOUT US</a>
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                            <ul>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Team">MEET THE TEAM</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Attributions">ATTRIBUTION</a></li>
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                                <li><a href="//2016.igem.org/Team:Nagahama/Sponsors">SPONSORS</a></li>
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<h1 style="line-height:1.295em"> Wiki Design Guide </h1>
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<p> Make your wiki more beautiful than our team. </p>
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<p> This guide briefly dives into incorporating CSS, Java Script and JQuery into your wiki, a few graphic design tips, and ways to improve the user experience.
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<h3> Creating new pages </h3>
+
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<p>To create a new page, simply type in the name of the page in your address bar, e.g. https://2016.igem.org/Team:YourTeam/OurNewPage, and edit it. MediaWiki (iGEM's website engine) will automatically create the page for you</p>
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<h3> Using HTML </h3>
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<p> To use html, simply wrap everything in html tags: <code>&lt;html&gt;...&lt;/html&gt;</code>. It's useful to note that these html tags will <em>not</em> actually appear in your page source&#8212;they just tell MediaWiki to output the html within directly, without modification (almost; lone ampersands will be replaced with <code>&amp;amp;</code>, which won't be a problem unless they're in some javascript code. If this is a problem, try externalising your JS code, see below for instructions.) </p>
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<h3> Using Templates </h3>
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<p>Using templates helps to avoid typing in the same html again and again, and also allows you to make changes in one place that apply to all your pages. We have two templates we use, <code>Team:Cambridge/Templates/Menu</code> and <code>Team:Cambridge/Templates/Footer</code>. These templates are created as normal new pages, and are then directly <em>included</em> in your page using MediaWiki syntax:</p>
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<pre>{{:Team:YourTeam/Templates/OurHeader}}
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&lt;html&gt;Our page&lt;/html&gt;
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{{:Team:YourTeam/Templates/OurFooter}}</pre>
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<p>Note carefully the above notice regarding the function of the html tags - this means that your template can end without closing all its tags and it won't mess up your page! For example, you can wrap your site in a container div by opening the tag in your header template, and then closing it in your footer template.</p>
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<h3> Using CSS and JS </h3>
+
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<p>As iGEM teams are unable to upload and refer to CSS and Javascript files, styling your webpages takes a different method to the standard way. Instead, we have created new pages within our wiki which we then ask MediaWiki to treat as <em>raw</em> files when we link to them in the html of our other pages. We tend to use page names that end in _CSS and _JS.</p>
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<code> &lt;script src="//2015.igem.org/Team:YourTeam/file_js?action=raw&amp;ctype=text/javascript">&lt;/script&gt;</code>
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<p>
+
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for javascript and:</p>
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<code>&lt;link href="//2015.igem.org/Team:YourTeam/file_css?action=raw&amp;ctype=text/css" rel="stylesheet"&gt;</code>
+
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<p>for css. This takes the raw code that was entered as if it was an uploaded file.</p>
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<p>Note how we've removed the http: from the beginning of the URLs above. This allows the browser to choose http: or https: depending on how you're connecting to iGEM and improves security! We apply it to all our URLs.</p>
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+
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<h3> JQuery </h3>
+
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<p> Visit JQuery's website <a href="//jquery.com"> <u>here</u></a>. JQuery is a javascript library that allows for easy implementation of various javascript functions. Our website's gallery, notebook and quizzes all use JQuery. Even our OpenScope Webshell was developed with JQuery. Try it out and save some time!</p>
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<h2> Graphic Design </h2>
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<h3> Colours </h3>
+
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<p>Before creating too many images and colouring in your wiki, deciding on a colour scheme can ensure your wiki looks professional. </p>
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+
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<p>Colours in HTML are given as RGB values. These can be difficult to visualise and match. Instead pick your colours first with HSL (hue, saturation and lightness) values. As a guide, three to four different hues is easy to work with.</p>
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<img src="//2015.igem.org/wiki/images/2/2f/CamJIC-Colours.png" style="height: 300px; margin-right: 70px">
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<li class="list">We used four different hues that were all delicate temperatures</li><br>
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<li class="list">Each hue was split into two or three shades, made by changing the lightness and saturation.</li><br>
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<li class="list">For backgrounds, avoid using highly saturated colours. None of the colours we chose were very saturated, this is to reduce the strain on viewers' eyes. This is why pastel palettes can be so visually pleasing.</li><br>
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<li class="list"> It's useful to have both dark (around 80/255 lightness) and light (around 220/250 lightness) colours when considering text on backgrounds. High contrast is needed to easily make out the features of words. Note also that fine details in bright blue can be hard to resolve with the human eye due to the lower abundance of S-cone receptor cells in the eye.</li><br>
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<li class="list"> Once you have picked a few colours then find their RGB values, ready to use for your website!</li><br>
+
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</ul></p>
+
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<h3> Fonts </h3>
+
−
<p>Unify your fonts across your webpage. Ideally, decide on one or two serif fonts and one or two sans-serif fonts. Serifs are the ticks on text that can make it easier to read, as letters are identified more easily. Our wiki uses three fonts: Sabon - a serif font, Open Sans, and Hiragino Sans GB.</p>
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<hr>
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<img src="//2015.igem.org/wiki/images/5/5b/CamJIC-Font.png" style="width: 600px; margin-right: 70px">
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<hr>
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<p>When including fonts in style tags in your wiki, assign a family of fonts using <code>font-family: font1, font2,...</code> where font1, font2,... is the preferential order of similar fonts to be displayed in case a certain font isn't supported by the user's browser.</p><br>
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<h3> Making Images with Inkscape </h3>
+
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<p>Almost all of our images have been made on the program Inkscape. Inkscape is a free multi platform graphic designing software which is extremely easy to pick up and make graphics with. Three of our team learned the basics over night and created all of the back-panels of this website subsequently with it.</p>
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+
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<p> Check out Inkscape <a style="color:#123a68;" href="//inkscape.org"><u>here</u></a>.</p>
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<section style="background-color:#123a68">
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<h2>User Experience </h2>
+
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<h3>Responsive Design</h3>
+
−
<p>Most iGEM Wiki pages aren't made with a responsive design. This means that when viewing the pages on a phone or tablet, or by simply shrinking the browser window, the wiki loses its formatting. Our website has used various JQuery functions, CSS and Bootstrap, so that the same design will work and scale for any screen size - giving support for mobiles, tablets and desktops/laptops alike.
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<h3>Navigation</h3>
+
−
<p>Navigation is really important in an iGEM wiki. Users need to be guided through the website, with out losing the freedom to navigate quickly to any other location. Whereever you are in a team's wiki, having an impression of how much information is on the page, and on the other pages keeps the user from feeling lost.</p>
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+
−
<p>Our approach to the navigation of our website involves two depth levels of information. The top menu bar contains the six different aspects of our project and going one by one through these allows for a brief overview of everything that we've done. Links to each of these pages are available from our home page. Each page has links to the deeper level of information, clicking on one of these from our home page gives you the details and specifics, including downloads and reports.</p>
+
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+
−
<p> And the best part, at any point you can swap between the brief overviews and detailed information. Just click "learn more" for details.</p>
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<br>
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<center>
+
−
<img src="//2016.igem.org/wiki/images/e/ea/CamJIC-SiteMap.png" style="width:90%">
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</center>
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<br>
+
−
<p> By structuring the website as a 2 layer deep hierarchy, users can travel through our wiki to get an overall idea and go indepth on anything that catches their eye. Of course, they are also free to teleport to any page with the menu bar above. Finally, our downloads page contain all the possible downloads found throughout the website for ease of access.</p>
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<center>
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−
<p>Happy Navigating!</p>
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<style>img.sponsor{max-width:90%; filter: grayscale(100%);-webkit-filter: grayscale(100%); opacity:0.7; max-height:30px; margin:10px} img.sponsor:hover {filter:grayscale(0%); -webkit-filter: grayscale(0%);opacity:1; max-height:30px; margin:10px}</style>
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            <div class="row  pad-bottom">
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                <div class="col-md-3">
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                    <h4> <strong>ABOUT US</strong> </h4>
+
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                    <p>
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                    We are a team of Cambridge undergraduates, competing in the Hardware track in iGEM 2016.
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                    </p>
+
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                    <a href="//2016.igem.org/Team:Nagahama/Team">read more</a>
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                </div>
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                <div class="col-md-3">
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                    <h4> <strong>FOLLOW US ON</strong> </h4>
+
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                    <p>
+
−
                    <a href="https://www.facebook.com/CambridgeJIC2015" target="_blank"><i class="fa fa-facebook-square fa-3x"></i></a> 
+
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                    <a href="https://twitter.com/iGEMCambridge" target="_blank"><i class="fa fa-twitter-square fa-3x"></i></a> 
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                    <a href="https://instagram.com/iGEMCambridge" target="_blank"><i class="fa fa-instagram fa-3x"></i></a> 
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                </div>
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                <div class="col-md-3">
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                    <h4> <strong>LOCATION</strong> </h4>
+
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                    <p>
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                    Department of Plant Sciences, <br>
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                    University of Cambridge <br>
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                    Downing Street <br>
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                    CB2 3EA
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                    </p>
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                </div>
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                <div class="col-md-3">
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                    <h4> <strong>CONTACT US</strong> </h4>
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                    <p>
+
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                    Email: <a href="mailto:&#105;&#103;&#101;&#109;&#99;&#97;&#109;&#98;&#114;&#105;&#100;&#103;&#101;&#50;&#48;&#49;&#53;&#64;&#103;&#109;&#97;&#105;&#108;&#46;&#99;&#111;&#109;">&#105;&#103;&#101;&#109;&#99;&#97;&#109;&#98;&#114;&#105;&#100;&#103;&#101;&#50;&#48;&#49;&#53;&#64;&#103;&#109;&#97;&#105;&#108;&#46;&#99;&#111;&#109;</a> <br>
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                    Tel: <a href="tel:+447721944314">+447721944314</a>
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            <a href="http://www.bbsrc.ac.uk"><img src="//2015.igem.org/wiki/images/8/81/CamJIC-Sponsors-BBSRC.png" class="sponsor"></a>
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Latest revision as of 03:01, 20 October 2016

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Increased production of fragrance for new food preservation method E.coli

ABSTRACT

To innovate the refrigerator without electricity, we invented a prototype of FRAVORATOR that is possible to preserve food by antibacterial volatiles synthesized by Escherichia coli. For the high-efficiency synthetic process of preservation flavor, farnesol, we focused on improving its synthetic pathway. First, 1-deoxy-D-xylulose 5-phosphate（DXP）synthase, Dxs, is down-regulated when its downstream material has been produced to some extent. So, we tried to over-express, another DXP synthase, nDXP, that rarely has been used in normal conditions. Also, we created fusion gene for ispC-ribB protein for enzymatic function. Second, to avoid recombinant in the real usage, we tried to knock out synthase that produces unnecessary byproduct by genome editing.

TRACK

Food Nutrition

We certainly achieved GOLD Medal Criteria!

Bronze Medal

1 Register for iGEM, have a great summer, and attend the Giant Jamboree. Yes, we are looking forward to taking part in the Giant Jamboree.
2 Meet all deliverables on the Requirements page (section 3). We meet all requirements.
3 Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services. Please check Here.
4 Document at least one new standard BioBrick Part or Device central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). You may also document a new application of a BioBrick part from a previous iGEM year, adding that documentation to the part's main page. Please check Here.

Silver Medal

1 Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected. Document the characterization of this part in the Main Page section of the Registry entry for that Part/Device. This working part must be different from the part you documented in Bronze medal criterion #4. Submit this part to the iGEM Parts Registry. We created 3 new BioBrick devices for silver medal criterion. Please look at [http://parts.igem.org/wiki/index.php?title=Part:BBa_K1950010 BBa_K1950010] , [http://parts.igem.org/wiki/index.php?title=Part:BBa_K1950008 BBa_K1950008], and [http://parts.igem.org/wiki/index.php?title=Part:BBa_K1950007 BBa_K1950007].
2 Convince the judges you have helped any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synthetic biology problem. Please check here.
3 iGEM projects involve important questions beyond the lab bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. Demonstrate how your team has identified, investigated, and addressed one or more of these issues in the context of your project. Your activity could center around education, public engagement, public policy issues, public perception, or other activities (see the human practices hub for more information and examples of previous teams' exemplary work). Please check here.

Gold Medal

1 Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the design and/or execution of your project. Please check here.
2 Improve the function OR characterization of an existing BioBrick Part or Device and enter this information in the Registry. Please see the Registry help page on how to document a contribution to an existing part. This part must NOT be from your 2016 part number range. Please check [http://parts.igem.org/Part:BBa_K1230000 here].
3 Demonstrate a functional proof of concept of your project. Your proof of concept must consist of a BioBrick device; a single BioBrick part cannot constitute a proof of concept. (Remember, biological materials may not be taken outside the lab.) Please check here.
4 Show your project working under real-world conditions. To achieve this criterion, you should demonstrate your whole system, or a functional proof of concept working under simulated conditions in the lab (Remember, biological materials may not be taken outside the lab.) Please check here.