Difference between revisions of "Team:Mingdao/Collaborations"

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{{Mingdao}}
 
 
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−
<h2> Collaborations</h2>
 
  
−
<p>
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−
Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.
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</p>
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−
<h4> Which other teams can we work with? </h4>
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#u5104
−
<p>
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{
−
You can work with any other team in the competition, including software, hardware, high school and other tracks. You can also work with non-iGEM research groups, but they do not count towards the <a hreef="https://2015.igem.org/Judging/Awards#Medals">iGEM team collaboration gold medal criterion</a>.
+
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<p>
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−
In order to meet the gold medal criteria on helping another team, you must complete this page and detail the nature of your collaboration with another iGEM team.
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min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5732:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5732:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5732.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5711
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5711:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5711:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5711.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5718
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5718:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5718:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5718.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5690
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5690:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5690:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5690.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5662
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5662:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5662:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5662.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5753
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5753:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5753:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5753.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5704
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5704:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5704:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5704.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5762
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5762:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5762:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5762.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5697
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5697:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5697:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5697.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5685
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5685:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5685:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5685.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5774
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5774:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5774:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5774.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5669
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5669:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5669:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5669.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5727
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5727:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5727:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5727.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5648
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5648:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5648:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5648.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5676
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 10px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5676:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5676:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5676.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5733-4,#u5712-4,#u5719-4,#u5693-4,#u5663-4,#u5776-4,#u5671-4,#u5679-4
 +
{
 +
width: 227px;
 +
min-height: 22px;
 +
line-height: 22px;
 +
color: #FFFFFF;
 +
font-size: 18px;
 +
text-align: right;
 +
position: relative;
 +
margin-right: -10000px;
 +
top: 5px;
 +
}
 +
 
 +
#u5769
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
background-color: rgba(255, 213, 121, 0.55);
 +
padding-bottom: 15px;
 +
position: relative;
 +
margin-right: -10000px;
 +
-pie-background: rgba(255, 213, 121, 0.55);
 +
}
 +
 
 +
#u5769:hover
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5769:active
 +
{
 +
background-color: #ADADAD;
 +
background-color: rgba(107, 107, 107, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(107, 107, 107, 0.55);
 +
}
 +
 
 +
#u5769.MuseMenuActive
 +
{
 +
background-color: #C6C6C6;
 +
background-color: rgba(153, 153, 153, 0.55);
 +
margin: 0px -10000px 0px 0px;
 +
-pie-background: rgba(153, 153, 153, 0.55);
 +
}
 +
 
 +
#u5755-4,#u5707-4,#u5764-4,#u5700-4,#u5686-4,#u5728-4,#u5649-4,#u5771-4
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
color: #FFFFFF;
 +
font-size: 14px;
 +
text-align: right;
 +
position: relative;
 +
margin-right: -10000px;
 +
top: 7px;
 +
}
 +
 
 +
#u5741
 +
{
 +
width: 227px;
 +
min-height: 17px;
 +
background-color: #FFE7B5;
 +
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−
<p>
+
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−
Here are some suggestions for projects you could work on with other teams:
+
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−
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+
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+
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−
<li> Mentor a high-school team</li>
+
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<body>
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<div id="all">
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        <a class="anchor_item colelem" id="collaboration"></a>
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        <img class="colelem" id="u4039-4" alt="Collaboration" width="815" height="102" src="https://static.igem.org/mediawiki/2015/3/31/Mingdao-u4039-4.png"/><!-- rasterized frame -->
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        <a class="anchor_item colelem" id="data-mining"></a>
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          <img class="grpelem" id="u4044-4" alt="Data mining" width="266" height="48" src="https://static.igem.org/mediawiki/2015/4/45/Mingdao-u4044-4.png"/><!-- rasterized frame -->
 +
          <div class="clearfix grpelem" id="u4045-4"><!-- content -->
 +
          <p>*</p>
 +
          </div>
 +
        </div>
 +
        <div class="clearfix grpelem" id="u4042-4"><!-- content -->
 +
          <p>*</p>
 +
        </div>
 +
        </div>
 +
        <div class="clearfix colelem" id="u4046-13"><!-- content -->
 +
        <p>After understanding of protein composition required for fire retardant effectiveness, we would like to find a novel protein candiate with fire retardant properties. We decided to use protein data mining approach in bioinformatics for our purpose.</p>
 +
        <p>&nbsp;</p>
 +
        <p>We contacted&nbsp;and asked iGEM team, NCTU&#45;Formosa for collaboration with data mining and programming. Chao&#45;Di Chang, who is an advisor of team <a class="nonblock" href="https://2014.igem.org/Team:NCTU_Formosa/team">NCTU&#45;Formosa</a>&nbsp;in 2014, taught us a lot in the field of bioinformatics and protein databases such as NCBI, UniProtKB and dbPTM. The super advisor, Prof. Wen&#45;Liang Chen gave us many great advices and shared experiences in the previous iGEM projects and Jamboree.</p>
 +
        <p>&nbsp;</p>
 +
        <p>This year, the members of NCTU&#45;Formosa helped us finding out the fire retardant target in the protein data bank. And Yi&#45;Ru Liu of team Mingdao wrote a programming code (see here) and NCTU&#45;Formosa gave us a lot of comments on the code. With the thanks of NCTU&#45;Formosa, we found the ideal target with high serine and arginine contents in protein composition from Uniprot database (see the result).</p>
 +
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 +
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 +
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      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5732" href="https://2015.igem.org/Team:Mingdao/Project#abstract"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5733-4"><!-- content --><p id="u5733-2">Abstract&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1</p></div></a>
 +
    </div>
 +
    <div class="MenuItemContainer clearfix colelem" id="u5710"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5711" href="https://2015.igem.org/Team:Mingdao/Project#motivation"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5712-4"><!-- content --><p id="u5712-2">Motivation&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2</p></div></a>
 +
    </div>
 +
    <div class="MenuItemContainer clearfix colelem" id="u5717"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5718" href="https://2015.igem.org/Team:Mingdao/Project#background"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5719-4"><!-- content --><p id="u5719-2">Background&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3</p></div></a>
 +
    </div>
 +
    <div class="MenuItemContainer clearfix colelem" id="u5689"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5690" href="https://2015.igem.org/Team:Mingdao/Project#approach"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5693-4"><!-- content --><p id="u5693-2">Approach&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4</p></div></a>
 +
    </div>
 +
    <div class="MenuItemContainer clearfix colelem" id="u5661"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5662" href="https://2015.igem.org/Team:Mingdao/Project#result"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5663-4"><!-- content --><p id="u5663-2">Results&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5</p></div></a>
 +
    </div>
 +
    <div class="MenuItemContainer clearfix colelem" id="u5773"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5774" href="https://2015.igem.org/Team:Mingdao/Project#summary-discussion"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5776-4"><!-- content --><p id="u5776-2">Summary &amp; Discussion&nbsp;&nbsp;&nbsp; 6</p></div></a>
 +
    </div>
 +
    <div class="MenuItemContainer clearfix colelem" id="u5668"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5669" href="https://2015.igem.org/Team:Mingdao/Design#prototype"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5671-4"><!-- content --><p id="u5671-2">Prototype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7</p></div></a>
 +
    </div>
 +
          <div class="MenuItemContainer clearfix colelem" id="u5675"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu rgba-background clearfix grpelem" id="u5676" href="https://2015.igem.org/Team:Mingdao/Application#application"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5679-4"><!-- content --><p id="u5679-2">Application&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8</p></div></a>
 +
    </div>
 +
          <div class="MenuItemContainer clearfix colelem" id="u5780"><!-- horizontal box -->
 +
      <a class="nonblock nontext MenuItem MenuItemWithSubMenu MuseMenuActive rgba-background clearfix grpelem" id="u5781" href="https://2015.igem.org/Team:Mingdao/Collaborations"><!-- horizontal box --><div class="MenuItemLabel clearfix grpelem" id="u5784-4"><!-- content --><p id="u5784-2">Collaborations&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9</p></div></a>
 +
    </div>
 +
    </nav>
 +
    <div class="clearfix colelem" id="pu4059"><!-- group -->
 +
    <div class="clip_frame grpelem" id="u4059"><!-- image -->
 +
      <img class="block" id="u4059_img" src="https://static.igem.org/mediawiki/2015/5/56/Mingdao-37-3.jpeg" alt="" width="556" height="417"/>
 +
    </div>
 +
    <div class="clip_frame grpelem" id="u4065"><!-- image -->
 +
      <img class="block" id="u4065_img" src="https://static.igem.org/mediawiki/2015/0/01/Mingdao-38-1.jpeg" alt="" width="556" height="417"/>
 +
    </div>
 +
    </div>
 +
    <img class="colelem" id="u4072-4" alt="Code data for data mining of fire retardant protein" width="1124" height="43" src="https://static.igem.org/mediawiki/2015/2/2c/Mingdao-u4072-4.png"/><!-- rasterized frame -->
 +
      <div class="colelem" id="u4076"><textarea readonly="readonly" style="width:1120px; height:614px;">//
 +
//  main.c
 +
//  sequence_read
 +
//
 +
//  Created by Daniel Yi-Ru, Liu on 2/13/15.
 +
//  Copyright (c) 2015 iGEM Mingdao. All rights reserved.
 +
//
 +
#include <stdio.h>
 +
#include <string.h>
 +
#include <time.h>
  
 +
int aaAnalization(char aa);
 +
/*
 +
fasta file format:
 +
 +
item  Serial Number  space Protein Name          New Line Mark
 +
example >sp|Q6GZX4|001R_FRG3G  Putative transcription factor 001R OS=Frog virus 3  \n
 +
format  %s        %[^\n]            %*c
 +
saves at serialNumber  ignore proteinName            ignore
 +
 +
item  Sequence
 +
example MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPS
 +
        EKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLD
 +
        AKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHL
 +
        EKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDD
 +
        SFRKIYTDLGWKFTPL
 +
format  %[^>]
 +
saves at sequence
 +
*/
 +
char serialNumber [50];
 +
int sequenceLength;
 +
char proteinName [1000];
 +
char sequence [100000];
 +
int aaCount [27];  //times of each amino acid appear in a protein
 +
float aaRate;    //"amino acid/sequenceLength" content of amino acid in each protein
 +
int sequenceCount;  //scans the string "sequence"
 +
int aaCode;    //code for amino acid, sees at amino_acid.txt
 +
int sequenceLengthCheck; //check the length of a sequence with "sequenceLength"
 +
int printScan;    //scans array "aaCount" for printing out
 +
float proteinMass;
 +
float proteinNitrogenRate;
 +
int completeMount = 0;
 +
clock_t start, end;
 +
const char aminoAcid [][30] = {
 +
{"Alanine"},  {"Cysteine"},  {"Aspartic acid"}, {"Glutamic acid"},
 +
{"Phenylalanine"}, {"Glycine"},  {"Histidine"},  {"Isoleucine"},
 +
{"Lysine"},  {"Leucine"},  {"Methionine"},  {"Asparagine"},
 +
{"Proline"},  {"Glutamine"},  {"Arginine"},  {"Serine"},
 +
{"Threonine"},  {"Valine"},  {"Tryptophan"},  {"Tyrosine"},
 +
{"Selenocysteine"}, {"Pyrrolysine"}, {"Glutamine or Glutamic acid"},
 +
{"Aspartic acid or Asparagine"},  {"Unknow"},  {"New line mark"}
 +
};
 +
const float aaNitrogenContain [] = {
 +
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 3.0, 1.0, 2.0, 1.0, 1.0, 2.0, 1.0, 2.0, 4.0, 1.0,
 +
1.0, 1.0, 2.0, 1.0, 1.0, 3.0, 1.5, 1.5
 +
};
 +
const float aaMass [] = {
 +
89.09404, 121.15404, 133.10384, 147.13074, 165.19184, 75.06714, 155.15634, 131.17464,
 +
146.18934, 131.17464, 149.20784, 132.11904, 115.13194, 146.14594, 174.20274, 105.09344,
 +
119.12034, 117.14784, 204.22844, 181.19124, 168.053, 255.31, 146.63834, 132.61144
 +
};
 +
const int aaConvert [] ={
 +
//  A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z
 +
    1, 24, 2, 3, 4, 5, 6, 7, 8, 0, 9, 10, 11, 12, 22, 13, 14, 15, 16, 17, 21, 18, 19, 25, 20, 23
 +
};
  
 +
void main(){
 +
 +
printf("Analization Start...\n");
 +
 +
start = clock();
 +
 +
FILE *input, *output;
 +
 +
//input = fopen("uniprot_sprot_test.fasta","r");
 +
input = fopen("uniprot_sprot.fasta","r");
 +
 +
if(input == NULL){
 +
    printf("Fail To Open File: uniprot_sprot.fasta!");
 +
    return;
 +
}
 +
 +
output = fopen("output_uniport_N_rate.txt","w+");
 +
 +
if(output == NULL){
 +
    printf("Fail To Open File: output_uniport_N_rate.txt!");
 +
    return;
 +
}
 +
 +
fprintf(output, "Serial Number\t");
 +
fprintf(output, "Protein Name\t");
 +
 +
int i;
 +
for(i = 0; i < 26; i++){
 +
    fprintf(output, "%s\t", aminoAcid[i]);
 +
}
 +
 +
for(i = 0; i < 26; i++){
 +
    fprintf(output, "%s rate\t", aminoAcid[i]);
 +
}
 +
 +
fprintf(output, "Protein Mass (Da)\t");
 +
fprintf(output, "Nitrogen rate");
 +
 +
fprintf(output, "\n");
 +
 +
 +
while(!feof(input)){
 +
   
 +
    completeMount++;
 +
   
 +
    for (i=0; i<99999; i++) {
 +
        sequence[i] = '\0' ;
 +
    }
 +
   
 +
   
 +
    fscanf(input, "%s%*c%[^\n]%*c%[^>]", &serialNumber, &proteinName, &sequence);
 +
    //http://blog.csdn.net/u011478505/article/details/25399721
 +
   
 +
    if(serialNumber[0]!='>'){
 +
        printf("ERROR: Overflow! Line %d", completeMount);
 +
        return;
 +
    }
 +
   
 +
    //printf("%s %s %s\n", serialNumber, proteinName, sequence);
 +
    //printf("%s\n", serialNumber);
 +
    //printf("%s\n", proteinName);
 +
    //printf("%s\n", sequence);
 +
   
 +
    //fprintf(output, "%s %s %s\n", serialNumber, proteinName, sequence);
 +
    fprintf(output, "%s\t", serialNumber);
 +
    fprintf(output, "%s\t", proteinName);
 +
    //fprintf(output, "%s\n", sequence);
 +
   
 +
   
 +
    for( i = 0; i < 27; i++){
 +
        aaCount[i] = 0;
 +
    }
 +
   
 +
   
 +
    for(sequenceCount = 0; sequenceCount < strlen(sequence); sequenceCount++){
 +
        aaCode = aaAnalization(sequence [sequenceCount]);
 +
       
 +
        if(aaCode == 0){
 +
            printf("ERROR: Amino acid code unknow! Code:%c", sequence [sequenceCount]);
 +
            return;
 +
        }
 +
       
 +
        aaCount[aaCode]++;
 +
    }
 +
   
 +
    sequenceLengthCheck = 0;
 +
   
 +
   
 +
    for(printScan = 1; printScan < 27; printScan++){
 +
       
 +
        //printf("%d\t", aaCount[printScan]);
 +
        fprintf(output, "%d\t", aaCount[printScan]);
 +
        sequenceLengthCheck += aaCount[printScan];
 +
       
 +
    }
 +
   
 +
    sequenceLength = (int)strlen(sequence) - aaCount[26];
 +
    sequenceLengthCheck -= aaCount[26];
 +
   
 +
    for(printScan = 1; printScan < 27; printScan++){
 +
       
 +
        aaRate = (float)aaCount[printScan]/(float)sequenceLength;
 +
        //printf("%f\t", aaRate);
 +
        fprintf(output, "%f\t", aaRate);
 +
       
 +
    }
 +
   
 +
    proteinMass = 0;
 +
    for(printScan = 1; printScan < 25; printScan++){
 +
       
 +
        proteinMass += aaCount[printScan]*aaMass[printScan-1];
 +
       
 +
    }
 +
   
 +
    //printf("%f\t", proteinMass);
 +
    fprintf(output, "%f\t", proteinMass);
 +
   
 +
    proteinNitrogenRate = 0;
 +
    for(printScan = 1; printScan < 25; printScan++){
 +
       
 +
        proteinNitrogenRate += aaCount[printScan]*aaNitrogenContain[printScan-1]*14;
 +
       
 +
    }
 +
    proteinNitrogenRate /= proteinMass;
 +
    //printf("%f\t", proteinNitrogenRate);
 +
    fprintf(output, "%f\t", proteinNitrogenRate);
 +
   
 +
    if(sequenceLengthCheck !=sequenceLength){
 +
        printf("\nERROR: Sequence length not match! Length:%d LengthCheck:%d", sequenceLength, sequenceLengthCheck);
 +
        return;
 +
    }
 +
   
 +
    //printf("\n");
 +
    fprintf(output, "\n");
 +
   
 +
   
 +
    int completeRate = completeMount * 10000/ 547599;
 +
    int oldCompleteRate;
 +
   
 +
    if(completeRate != oldCompleteRate){
 +
        printf("\rProcessing...\t%.2lf%%", completeMount * 100.0/ 547599);
 +
        oldCompleteRate = completeRate;
 +
    }
 +
   
 +
   
 +
}
 +
 +
 +
fclose(input);
 +
fclose(output);
 +
 +
end = clock();
 +
 +
printf("\n\nComplete in %.2lf seconds.\t(%.2lf proteins/sec)\n",(end-start)/(double)(CLOCKS_PER_SEC), completeMount/((end-start)/(double)(CLOCKS_PER_SEC)));
 +
printf("%d Proteins Read\n", completeMount);
 +
 +
}
  
 +
int aaAnalization(char aa){
 +
int i;
 +
 +
if(aa=='\n'){
 +
    return(26);
 +
}
 +
else{
 +
    i=(int)aa-65;
 +
    return(aaConvert[i]);
 +
}
 +
 +
}
 +
</textarea></div>
 +
    <a class="anchor_item colelem" id="biobrick-parts-validation"></a>
 +
    <div class="clearfix colelem" id="u4077"><!-- group -->
 +
    <div class="clearfix grpelem" id="u4079"><!-- group -->
 +
      <img class="grpelem" id="u4080-4" alt="BioBrick parts validation" width="607" height="48" src="https://static.igem.org/mediawiki/2015/9/92/Mingdao-u4080-4.png"/><!-- rasterized frame -->
 +
      <div class="clearfix grpelem" id="u4081-4"><!-- content -->
 +
      <p>*</p>
 +
      </div>
 +
    </div>
 +
    <div class="clearfix grpelem" id="u4078-4"><!-- content -->
 +
      <p>*</p>
 +
    </div>
 +
    </div>
 +
    <div class="clearfix colelem" id="u4082-10"><!-- content -->
 +
    <p>We’ve created BioBricks of SR/pSB1C3 (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1608000">BBa_K1608000</a>), SRPK/pSB1C3 (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1608001">BBa_K1608001</a>) and cloned the genes to the commercial expression vectors, i.e., SR/pGEX&#45;2T and SRPK/pET&#45;29b.</p>
 +
    </div>
 +
    <div class="clip_frame colelem" id="u4083"><!-- image -->
 +
    <img class="block" id="u4083_img" src="https://static.igem.org/mediawiki/2015/3/34/Mingdao-44-1.jpeg" alt="" width="948" height="532"/>
 +
    </div>
 +
    <div class="clearfix colelem" id="u4089-6"><!-- content -->
 +
    <p>Credit: <a class="nonblock" href="https://2012.igem.org/Team:Uppsala_University/Chromoproteins">iGEM Team Uppsala 2012</a></p>
 +
    </div>
 +
    <div class="clearfix colelem" id="u4090-34"><!-- content -->
 +
    <p>In order to test the expression system, we request some BioBricks carrying the genes (amajLime, <a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033915">BBa_K1033915</a>; asPink, <a class="nonblock" href="http://parts.igem.org/wiki/index.php/Part:BBa_K1033933">BBa_K1033933</a>; eforRed, <a class="nonblock" href="http://parts.igem.org/Part:BBa_K592012">BBa_K592012</a>&nbsp;tsPurple, <a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033905">BBa_K1033905</a>) of chromoproteins from iGEM Team <a class="nonblock" href="https://2015.igem.org/Team:Uppsala">Uppsala</a>. The work was done in 2012.</p>
 +
    <p>We transferred the parts to pGEX&#45;2T followed by transforming E. coli BL21. Color proteins seen by naked eyes are the indicator of success of protein induction and expression system. In addition to validation of BioBricks created previously, it also can be used to optimize the condition of protein induction system.</p>
 +
    <p>&nbsp;</p>
 +
    <p>The experiment procedure was described briefly as follows:</p>
 +
    <p>↓ Culture E. coli BL21 O/N, which carry indicated BioBricks from the stocks at &#45;80°C.</p>
 +
    <p>&nbsp;↓ Dilute 100X in the fresh media (LB with 100 ug/ml Ampicillin) for 2 hr</p>
 +
    <p>↓ Till OD600 = 06~1.0, 1mM IPTG was added and incubate for 4~5 hr at 37°C</p>
 +
    <p>↓ Transfer 1 ml of bacteria and centrifuge for 1.5 min</p>
 +
    <p>↓ Observe color expression</p>
 +
    </div>
 +
    <div class="clip_frame colelem" id="u4091"><!-- image -->
 +
    <img class="block" id="u4091_img" src="https://static.igem.org/mediawiki/2015/2/22/Mingdao-45-1.jpeg" alt="" width="960" height="720"/>
 +
    </div>
 +
    <div class="clearfix colelem" id="u4097-16"><!-- content -->
 +
    <p>The expression of color genes after IPTG induction in pGEX&#45;2T system. Left to right: amajLime (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033915">BBa_K1033915</a>), asPink (<a class="nonblock" href="http://parts.igem.org/wiki/index.php/Part:BBa_K1033933">BBa_K1033933</a>), eforRed ( <a class="nonblock" href="http://parts.igem.org/Part:BBa_K592012">BBa_K592012</a>), tsPurple (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033905">BBa_K1033905</a>), BL21 (pGEX&#45;2T empty vector)</p>
 +
    </div>
 +
    <div class="verticalspacer"></div>
 +
  </div>
 +
  </div>
 
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Latest revision as of 04:01, 18 September 2015

Collaboration

Collaboration
Data mining

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After understanding of protein composition required for fire retardant effectiveness, we would like to find a novel protein candiate with fire retardant properties. We decided to use protein data mining approach in bioinformatics for our purpose.

 

We contacted and asked iGEM team, NCTU-Formosa for collaboration with data mining and programming. Chao-Di Chang, who is an advisor of team NCTU-Formosa in 2014, taught us a lot in the field of bioinformatics and protein databases such as NCBI, UniProtKB and dbPTM. The super advisor, Prof. Wen-Liang Chen gave us many great advices and shared experiences in the previous iGEM projects and Jamboree.

 

This year, the members of NCTU-Formosa helped us finding out the fire retardant target in the protein data bank. And Yi-Ru Liu of team Mingdao wrote a programming code (see here) and NCTU-Formosa gave us a lot of comments on the code. With the thanks of NCTU-Formosa, we found the ideal target with high serine and arginine contents in protein composition from Uniprot database (see the result).

Code data for data mining of fire retardant protein
BioBrick parts validation

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We’ve created BioBricks of SR/pSB1C3 (BBa_K1608000), SRPK/pSB1C3 (BBa_K1608001) and cloned the genes to the commercial expression vectors, i.e., SR/pGEX-2T and SRPK/pET-29b.

In order to test the expression system, we request some BioBricks carrying the genes (amajLime, BBa_K1033915; asPink, BBa_K1033933; eforRed, BBa_K592012 tsPurple, BBa_K1033905) of chromoproteins from iGEM Team Uppsala. The work was done in 2012.

We transferred the parts to pGEX-2T followed by transforming E. coli BL21. Color proteins seen by naked eyes are the indicator of success of protein induction and expression system. In addition to validation of BioBricks created previously, it also can be used to optimize the condition of protein induction system.

 

The experiment procedure was described briefly as follows:

↓ Culture E. coli BL21 O/N, which carry indicated BioBricks from the stocks at -80°C.

 ↓ Dilute 100X in the fresh media (LB with 100 ug/ml Ampicillin) for 2 hr

↓ Till OD600 = 06~1.0, 1mM IPTG was added and incubate for 4~5 hr at 37°C

↓ Transfer 1 ml of bacteria and centrifuge for 1.5 min

↓ Observe color expression

The expression of color genes after IPTG induction in pGEX-2T system. Left to right: amajLime (BBa_K1033915), asPink (BBa_K1033933), eforRed ( BBa_K592012), tsPurple (BBa_K1033905), BL21 (pGEX-2T empty vector)