|
|
(75 intermediate revisions by 2 users not shown) |
Line 1: |
Line 1: |
| {{Nankai}} | | {{Nankai}} |
| <html> | | <html> |
− | | + | <title>Modeling</title> |
− | | + | |
− | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
| + | |
− | <title>Power House</title> | + | |
− | | + | |
− | <!--slidercss-->
| + | |
− | | + | |
− | | + | |
| <style type="text/css"> | | <style type="text/css"> |
| | | |
− | | + | .gap{ |
− | | + | margin-top:15px; |
− | body {
| + | |
− | | + | |
− | font-family: "myriad Pro",Constantia,Gotham,Consolas;
| + | |
− | background-image: url(https://static.igem.org/mediawiki/2015/7/79/Nankai_Model_Body_bg.png);
| + | |
− | background-position: 0 0;
| + | |
− | background-repeat: repeat;
| + | |
− | background-color: #F4F4F4;
| + | |
− | layer-background-color: white;
| + | |
| } | | } |
− |
| |
| | | |
| | | |
Line 28: |
Line 12: |
| min-width:880px; | | min-width:880px; |
| } | | } |
| + | |
| section { | | section { |
| width:80%; | | width:80%; |
Line 59: |
Line 44: |
| } | | } |
| .normalsection .title h3 { | | .normalsection .title h3 { |
| + | font-family: 'Segoe UI',Gill Sans,Lucida Sans,Consolas; |
| font-size:40px; | | font-size:40px; |
| color:#10A300; | | color:#10A300; |
Line 67: |
Line 53: |
| margin-top:10px; | | margin-top:10px; |
| margin-bottom:-80px; | | margin-bottom:-80px; |
− | background-color:#0200FF; | + | background-color:#53C94F; |
| + | |
| text-align:center; | | text-align:center; |
| + | padding-bottom:7px; |
| } | | } |
| .headsection h3{ | | .headsection h3{ |
| + | font-family: 'Segoe UI',Gill Sans,Lucida Sans,Consolas; |
| font-size:45px; | | font-size:45px; |
| + | line-height:49px; |
| font-weight:normal; | | font-weight:normal; |
| color:#FFF; | | color:#FFF; |
Line 78: |
Line 68: |
| font-size:30px; | | font-size:30px; |
| font-weight:bold; | | font-weight:bold; |
| + | line-height:35px; |
| + | font-family:"Constantia",Gotham,Consolas; |
| } | | } |
| .normalsection .box_1 .title h4 { | | .normalsection .box_1 .title h4 { |
Line 89: |
Line 81: |
| font-weight:normal; | | font-weight:normal; |
| line-height:30px; | | line-height:30px; |
| + | font-family:"Lucida Sans Unicode",Times New Roman,Constantia,Gotham,Consolas; |
| } | | } |
| .text { | | .text { |
Line 98: |
Line 91: |
| .text p{ | | .text p{ |
| font-size:20px; | | font-size:20px; |
| + | font-familt:"Lucida Sans Unicode",Times New Roman,Constantia,Gotham,Consolas; |
| + | text-align:justify; |
| } | | } |
| .normalsection .title img { | | .normalsection .title img { |
Line 113: |
Line 108: |
| #place a{ | | #place a{ |
| color: #00a8d6; | | color: #00a8d6; |
| + | } |
| + | #place a:hover{ |
| + | color:#C800FF; |
| + | } |
| + | .text .firstpic{ |
| + | float:left; |
| + | width:45%; |
| + | height:auto; |
| + | margin-left:0; |
| + | } |
| + | |
| + | .text .firstpic h6{ |
| + | font-size:15px; |
| + | margin-bottom:5px; |
| + | text-align:center; |
| + | font-weight:bold; |
| + | font-family:"Gill Sans MT",Consolas,Constantia; |
| + | line-height:17px; |
| + | } |
| + | .text .firstpic p{ |
| + | font-family:"Gill Sans MT",Consolas,Constantia; |
| + | font-size:18px; |
| + | line-height:18px; |
| + | text-indent:0px; |
| + | margin-left:40px; |
| + | text-align:left; |
| + | } |
| + | .text .secondpic{ |
| + | float:right; |
| + | width:45%; |
| + | height:auto; |
| + | margin-right:5%; |
| + | } |
| + | .text .secondpic p{ |
| + | font-family:"Gill Sans MT",Consolas,Constantia; |
| + | font-size:18px; |
| + | line-height:18px; |
| + | text-indent:0px; |
| + | margin-left:40px; |
| + | text-align:left; |
| + | } |
| + | .text .secondpic h6{ |
| + | font-size:15px; |
| + | text-align:center; |
| + | font-weight:bold; |
| + | font-family:"Gill Sans MT",Consolas,Constantia; |
| + | line-height:17px; |
| + | } |
| + | |
| + | .text img{ |
| + | max-width:100%; |
| + | width:auto; |
| + | height:auto; |
| + | } |
| + | .downtext{ |
| + | clear:both; |
| } | | } |
| </style> | | </style> |
Line 130: |
Line 181: |
| <section class="normalsection"> | | <section class="normalsection"> |
| <div class="box_1"> | | <div class="box_1"> |
− | <img src="https://static.igem.org/mediawiki/2015/5/52/Nankai_Model_1_img.png" class="img0" alt=""/> | + | <img src="https://static.igem.org/mediawiki/2015/5/52/Nankai_Model_1_img.png" class="img0"> |
| <div class="title"> | | <div class="title"> |
| <h3>Bacteria scale</h3> | | <h3>Bacteria scale</h3> |
Line 139: |
Line 190: |
| <p>In this equation, ‘X’ means the bacteria scale, it’s the function of‘t’, time. 'Vmax' represents the possible max relative growth speed of the bacteria . 'Xmax' is the upper limit of the growth. In this function, we can find out that the instantaneous growth speed is determined by the relative growth speed, upper limit of the growth, and the instantaneous scale. With time passing by, the scale grows larger, while the speed turns down. | | <p>In this equation, ‘X’ means the bacteria scale, it’s the function of‘t’, time. 'Vmax' represents the possible max relative growth speed of the bacteria . 'Xmax' is the upper limit of the growth. In this function, we can find out that the instantaneous growth speed is determined by the relative growth speed, upper limit of the growth, and the instantaneous scale. With time passing by, the scale grows larger, while the speed turns down. |
| </p> | | </p> |
− | <img src="https://static.igem.org/mediawiki/2015/1/1f/Nankai_Model_Box_3.png" alt="" class="main_img0" /> | + | <div class="firstpic"> |
| + | <img src="https://static.igem.org/mediawiki/2015/c/c6/Nankai_modchar1.png"> |
| + | </div> |
| + | <div class="secondpic"> |
| + | <img src="https://static.igem.org/mediawiki/2015/b/b2/Nankai_modpic1.jpg"> |
| + | <h6>Fig.1 The fitting curve of the growth of bacteria cells.</h6> |
| + | <p>1. Fit Results:</br> |
| + | (1)General model:</br> |
| + | f(x) = X/(exp(-X*(C3 + V*x)) + 1)</br> |
| + | (2)Coefficients (with 95% confidence bounds):</br> |
| + | C3 = -1.248 (-1.962, -0.5334)</br> |
| + | V = 0.07547 (0.02994, 0.121)</br> |
| + | X = 3.055 (2.717, 3.393)</p> |
| + | |
| + | <p class="gap">2. Goodness of fit:</br> |
| + | SSE: 1.99</br> |
| + | R-square: 0.9164</br> |
| + | Adjusted R-square: 0.9045</br> |
| + | RMSE: 0.3771</p> |
| + | </div> |
| + | <p class="downtext">As the foundation of our modeling, the logistic model fits quite well with our data. It takes about 30 hours for the bacteria to reach the upper limit. According to the growth law, we can say that the highest growth speed is around 15h, when the scale is half of the maximum.</p> |
| </div> | | </div> |
| + | |
| </div> | | </div> |
| | | |
| <div class="box_2"> | | <div class="box_2"> |
− | <img src="https://static.igem.org/mediawiki/2015/a/a7/Nankai_Model_2_img.png" class="img0" alt=""/> | + | <img src="https://static.igem.org/mediawiki/2015/a/a7/Nankai_Model_2_img.png" class="img0"> |
| <div class="title"> | | <div class="title"> |
| <h3>Product scale</h3> | | <h3>Product scale</h3> |
Line 151: |
Line 223: |
| </div> | | </div> |
| <div class="text"> | | <div class="text"> |
− | <p> | + | <p>In this equation, ‘X’ and ‘t’ are the bacteria scale and time. ‘P’ means the product. We can see the familiar ‘X’ and ‘t’, that is how we base the production on the bacteria growth. 'α' and 'β' indicates the proportion of the two processes. With these parameters, we can find out when is the most important part of time in the whole fermentation process. This is quite useful, because we can decide the length of fermentation and decide the timing to do some changes. |
− | In this equation, ‘X’ and ‘t’ are the bacteria scale and time. ‘P’ means the product. We can see the familiar ‘X’ and ‘t’, that is how we base the production on the bacteria growth. 'α' and 'β' indicates the proportion of the two processes. With these parameters, we can find out when is the most important part of time in the whole fermentation process. This is quite useful, because we can decide the length of fermentation and decide the timing to do some changes. | + | |
| </p> | | </p> |
− | <img src="https://static.igem.org/mediawiki/2015/1/1f/Nankai_Model_Box_3.png" alt="" class="main_img0" /> | + | <div class="firstpic"> |
| + | <img src="https://static.igem.org/mediawiki/2015/f/fc/Nankai_modpic2.jpg"> |
| + | <h6>Fig.2 The original fitting curve of product formation</h6> |
| + | <p>1. Fit Results:</br> |
| + | (1)General model:</br> |
| + | f(x) = C+(A*0.0255*3.055*exp(0.0754*x))/(3.055-0.0255+0.0255*exp(0.0754*x))+B*3.055/0.0754*log((3.055-0.0255+0.0255*exp(0.0754*x))/3.055)</br> |
| + | (2)Coefficients (with 95% confidence bounds):</br> |
| + | A = 8392 (4254, 1.253e+04)</br> |
| + | B = -588.1 (-885.2, -291)</br> |
| + | C = -201.6 (-312.1, -91.16)</p> |
| + | |
| + | <p class="gap">2. Goodness of fit:</br> |
| + | SSE: 344.8</br> |
| + | R-square: 0.9165</br> |
| + | Adjusted R-square: 0.898</br> |
| + | RMSE: 6.19</p> |
| + | </div> |
| + | <div class="secondpic"> |
| + | <img src="https://static.igem.org/mediawiki/2015/9/97/Nankai_modchar2.png"> |
| + | </div> |
| + | <p class="downtext">Although this can reach a better R-square, our parameter β meet a negative number which should not happen. However, it can show that the product is mainly synthesized from the first part. Then we fit the data again with only the first part of our equation.</p> |
| </div> | | </div> |
| </div> | | </div> |
| | | |
| <div class="box_1"> | | <div class="box_1"> |
− | <img src="https://static.igem.org/mediawiki/2015/9/99/Nankai_Model_3_img.png" class="img0" alt=""/> | + | <img src="https://static.igem.org/mediawiki/2015/9/99/Nankai_Model_3_img.png" class="img0"> |
| <div class="title"> | | <div class="title"> |
| <h3>Substrate scale</h3> | | <h3>Substrate scale</h3> |
Line 169: |
Line 260: |
| In this equation, 'S' is the substrate, 'γ', 'δ',and 'ε' are the ratio of the three outlets. Our genetic operation is aimed to make the bacteria put more energy into the product. In a way, these parameters can show whether our strategies are effective or not. | | In this equation, 'S' is the substrate, 'γ', 'δ',and 'ε' are the ratio of the three outlets. Our genetic operation is aimed to make the bacteria put more energy into the product. In a way, these parameters can show whether our strategies are effective or not. |
| </p> | | </p> |
− | <img src="https://static.igem.org/mediawiki/2015/1/1f/Nankai_Model_Box_3.png" alt="" class="main_img0" />
| + | <div class="firstpic"> |
| + | <img src="https://static.igem.org/mediawiki/2015/3/33/Nankai_modchar3.png"> |
| + | </div> |
| + | <div class="secondpic"> |
| + | <img src="https://static.igem.org/mediawiki/2015/2/25/Nankai_modpic3.jpg"> |
| + | <h6>Fig.3 The altered fitting curve of product formation</h6> |
| + | <p>1. Fit Results:</br> |
| + | (1)General model:</br> |
| + | f(x) = C+(A*0.0255*3.055*exp(0.0754*x))/(3.055-0.0255+0.0255*exp(0.0754*x))</br> |
| + | (2)Coefficients (with 95% confidence bounds):</br> |
| + | A = 204 (115.1, 292.9)</br> |
| + | C = 16.45 (4.215, 28.68)</p> |
| + | <p class="gap"> |
| + | 2. Goodness of fit:</br> |
| + | SSE: 344.8</br> |
| + | R-square: 0.9165</br> |
| + | Adjusted R-square: 0.898</br> |
| + | RMSE: 6.19</p> |
| + | </div> |
| + | <p class="downtext">This one loses some goodness of fit, but the data is reasonable. Anyway, it shows that our product mainly comes from the growth process.</p> |
| </div> | | </div> |
| </div> | | </div> |