Difference between revisions of "Team:USTC/Software"
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{{USTC}} | {{USTC}} | ||
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| − | + | <ul class="tabs tabs-wrapper transparent"> | |
| − | + | <li class="tab col s2"> | |
| − | + | <a href="#Overview" class="blue-text active waves-effect waves-light">Overview</a> | |
| − | + | </li> | |
| − | + | <li class="tab col s2"> | |
| − | + | <a href="#fringes-analysis" class="blue-text active waves-effect waves-light">Fringes Analysis</a> | |
| − | + | </li> | |
| − | + | <li class="tab col s2"> | |
| − | + | <a href="#adhesion-dynamics" class="blue-text active waves-effect waves-light">Adhesion Dynamics</a> | |
| − | + | </li> | |
| − | + | <li class="tab col s2"> | |
| − | + | <a href="#rose-dynamics" class="blue-text active waves-effect waves-light">ROSE Dynamics</a> | |
| − | + | </li> | |
| − | + | </ul> | |
</div> | </div> | ||
</div> | </div> | ||
<ul id='Nav-dropdown' class='dropdown-content'> | <ul id='Nav-dropdown' class='dropdown-content'> | ||
| − | + | <li><a href="https://2015.igem.org/Team:USTC" class="waves-effect waves-light">Home</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Description" class="waves-effect waves-light">Project</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Modeling" class="waves-effect waves-light">Modeling</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Results" class="waves-effect waves-light">Results</a></li> | |
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| − | + | <li><a href="https://2015.igem.org/Team:USTC/Measurement" class="waves-effect waves-light">Measurement</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Software" class="waves-effect waves-light">Software</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Parts" class="waves-effect waves-light">Parts</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Tutorials" class="waves-effect waves-light">Tutorials</a></li> | |
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| − | + | <li><a href="https://2015.igem.org/Team:USTC/Safety" class="waves-effect waves-light">Safety</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Practices" class="waves-effect waves-light">Policy&Practices</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Team" class="waves-effect waves-light">Team</a></li> | |
| − | + | <li><a href="https://2015.igem.org/Team:USTC/Attributions" class="waves-effect waves-light">Attributions</a></li> | |
</ul> | </ul> | ||
<div class="row"> | <div class="row"> | ||
| − | + | <div class="col offset-m1 offset-l2 s12 m10 l8"> | |
| − | + | <div id="Overview" class="row"> | |
| − | + | <div class="card hoverable"> | |
| − | + | <div class="col s12 m9"> | |
| − | + | <div class="card-content"> | |
| − | <p>In this section, we will introduce all the software program we used when processing our modeling and experimental data. Through our modeling, many complicated processdures are simply omitted by our convenient programs.</p> | + | <p>In this section, we will introduce all the software program we used when processing our |
| − | <p>In general, our software programs are used in several sections,</p> | + | modeling and experimental data. Through our modeling, many complicated processdures are |
| − | <ul> | + | simply omitted by our convenient programs.</p> |
| − | + | ||
| − | + | <p>In general, our software programs are used in several sections,</p> | |
| − | + | <ul> | |
| − | </ul> | + | <li><strong>Fringes Analysis</strong>, analysis of interference pattern.</li> |
| − | <p>All software of our project, you can download them at <a href="https://github.com/Cintau/2015USTCiGEM" target="_blank">Github:2015USTCiGEM</a>. All codes are based on </p> | + | <li><strong>Adhesion Dynamics</strong>, a series of programs relating to bacteria adhesion |
| − | + | dynamics. | |
| + | </li> | ||
| + | <li><strong>Rose Prediction</strong>, which calculate the advantages of our ROSE | ||
| + | improvement. | ||
| + | </li> | ||
| + | </ul> | ||
| + | <p>All software of our project, you can download them at <a | ||
| + | href="https://github.com/Cintau/2015USTCiGEM" target="_blank">Github:2015USTCiGEM</a>. | ||
| + | All codes are based on </p> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
</div> | </div> | ||
| − | |||
| − | |||
| − | + | <div id="fringes-analysis" class="row"> | |
| − | + | <div class="card hoverable"> | |
| − | + | <div class="col s12 m9"> | |
| − | + | <div class="card-content"> | |
| − | <h4 id="Fringes-Pattern-Simulation-Film-I" class="scrollspy">Fringes Pattern Simulation-Film I</h4> | + | <h4 id="Fringes-Pattern-Simulation-Film-I" class="scrollspy">Fringes Pattern Simulation-Film |
| − | <p>This program is used to simulate fringes pattern deliverd by film I.</p> | + | I</h4> |
| − | + | ||
| − | <p>Code:</p> | + | <p>This program is used to simulate fringes pattern deliverd by film I.</p> |
| − | <div><textarea id="code" name="code">function drawndh(r,h,t,n) %r is radius of film，h is the distance of deformation，t is the drift angle of film，n is pixel number | + | |
| + | <p>Code:</p> | ||
| + | |||
| + | <div><textarea id="code" name="code">function drawndh(r,h,t,n) %r is radius of film，h is the distance of deformation，t is the drift angle of film，n is pixel number | ||
wl=6.5e-7; %wave length | wl=6.5e-7; %wave length | ||
R=r.^2/(2*h); | R=r.^2/(2*h); | ||
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imshow(I); | imshow(I); | ||
end | end | ||
| − | </textarea></div><p>Demo<br><img src="https://static.igem.org/mediawiki/2015/c/cd/0.02-5e-6-5e-4.jpg" alt="Figure 1: Film II deformation simulation result"></p> | + | </textarea></div> |
| − | <p>After the formation of demo, we are able to recongize the real situation in our pre-experiment.</p> | + | <p>Demo<br><img src="https://static.igem.org/mediawiki/2015/c/cd/0.02-5e-6-5e-4.jpg" |
| − | <div class="divider"></div> | + | alt="Figure 1: Film II deformation simulation result"></p> |
| + | |||
| + | <p>After the formation of demo, we are able to recongize the real situation in our | ||
| + | pre-experiment.</p> | ||
| + | |||
| + | <div class="divider"></div> | ||
| + | |||
| + | <h4 id="Fringes-Pattern-Simulation-Film-II" class="scrollspy">Fringes Pattern Simulation-Film | ||
| + | II</h4> | ||
| + | |||
| + | <p>This program is used to simulate fringes pattern deliverd by film II.</p> | ||
| + | |||
| + | <p>Code</p> | ||
| − | + | <div><textarea id="code1" name="code">function drawfr(a,b,h,n)%a is the angle between film and x axis, b is the angle between film and y axis, h is the distance of film deformation, n is the pixel number | |
| − | + | ||
| − | + | ||
| − | <div><textarea id="code1" name="code">function drawfr(a,b,h,n)%a is the angle between film and x axis, b is the angle between film and y axis, h is the distance of film deformation, n is the pixel number | + | |
[X,Y]=meshgrid(linspace(-0.003,0.003,n),linspace(-0.003,0.003,n)); | [X,Y]=meshgrid(linspace(-0.003,0.003,n),linspace(-0.003,0.003,n)); | ||
wl=6.5e-7; | wl=6.5e-7; | ||
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imshow(I) | imshow(I) | ||
end | end | ||
| − | </textarea></div><p>Demo<br><img src="https://static.igem.org/mediawiki/2015/f/f8/20150917061.jpg" alt="Figure 2 :Film II deformation simulation result"></p> | + | </textarea></div> |
| − | <div class="divider"></div> | + | <p>Demo<br><img src="https://static.igem.org/mediawiki/2015/f/f8/20150917061.jpg" |
| + | alt="Figure 2 :Film II deformation simulation result"></p> | ||
| + | |||
| + | <div class="divider"></div> | ||
| + | |||
| + | <h4 id="Film I Fringes Analysis" class="scrollspy">Film I Fringes Analysis</h4> | ||
| + | |||
| + | <p>Using this code, we are able to capture some important parameters in Film I.</p> | ||
| + | |||
| + | <p>Code</p> | ||
| − | + | <div><textarea id="code2" name="code">function ms3=solvendh(X,nx,ny,n,dx,dy)%nx is the number of fringes on x axis,ny is the number of fringes on y axis,n is the number of fringes on diag,dx is the x length of CCD,dx is the x length of CCD. | |
| − | + | ||
| − | + | ||
| − | <div><textarea id="code2" name="code">function ms3=solvendh(X,nx,ny,n,dx,dy)%nx is the number of fringes on x axis,ny is the number of fringes on y axis,n is the number of fringes on diag,dx is the x length of CCD,dx is the x length of CCD. | + | |
x=X(1); | x=X(1); | ||
y=X(2); | y=X(2); | ||
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ms3(2)=(2*(z+ny)*l)^0.5-(2*z*l)^0.5-(x^2+(y+dy)^2)^0.5+(x^2+y^2)^0.5; | ms3(2)=(2*(z+ny)*l)^0.5-(2*z*l)^0.5-(x^2+(y+dy)^2)^0.5+(x^2+y^2)^0.5; | ||
ms3(3)=(2*(z+n)*l)^0.5-(2*z*l)^0.5-((x+dx)^2+(y+dy)^2)^0.5+(x^2+y^2)^0.5; | ms3(3)=(2*(z+n)*l)^0.5-(2*z*l)^0.5-((x+dx)^2+(y+dy)^2)^0.5+(x^2+y^2)^0.5; | ||
| − | </textarea></div><p>Demo<br><img src="https://static.igem.org/mediawiki/2015/0/0d/20150919071.png" alt="Figure 3 : Film I Fringes analysis running result"></p> | + | </textarea></div> |
| − | <div class="divider"></div> | + | <p>Demo<br><img src="https://static.igem.org/mediawiki/2015/0/0d/20150919071.png" |
| + | alt="Figure 3 : Film I Fringes analysis running result"></p> | ||
| + | |||
| + | <div class="divider"></div> | ||
| + | |||
| + | <h4 id="Film-II-Fringes-Analysis-Fringes-number-analysis" class="scrollspy">Film II Fringes | ||
| + | Analysis-Fringes number analysis</h4> | ||
| + | |||
| + | <p>This is the final program used to get our NDM calibration. Based on this software program, we | ||
| + | are able to count the number of bright fringes. As a matter of fact, the variation of bright | ||
| + | fringes is the key breakthrough to antibiotic analysis.</p> | ||
| + | |||
| + | <p>Code</p> | ||
| − | + | <div><textarea id="code3" name="code">function seeim(i) | |
| − | + | ||
| − | + | ||
| − | <div><textarea id="code3" name="code">function seeim(i) | + | |
name=num2str(i); | name=num2str(i); | ||
I=imread(name,'pnm'); | I=imread(name,'pnm'); | ||
G=rgb2gray(I); | G=rgb2gray(I); | ||
imshow(G); | imshow(G); | ||
| − | </textarea></div><p>Demo<br><img src="https://static.igem.org/mediawiki/2015/2/2d/20150919072.png" alt="Figure 4: Checking figure program"></p> | + | </textarea></div> |
| − | <div><textarea id="code4" name="code">function A=getfr(i) | + | <p>Demo<br><img src="https://static.igem.org/mediawiki/2015/2/2d/20150919072.png" |
| + | alt="Figure 4: Checking figure program"></p> | ||
| + | |||
| + | <div><textarea id="code4" name="code">function A=getfr(i) | ||
name=num2str(i); | name=num2str(i); | ||
I=imread(name,'pnm'); | I=imread(name,'pnm'); | ||
| Line 137: | Line 178: | ||
end | end | ||
A=r; | A=r; | ||
| − | </textarea></div><div><textarea id="code5" name="code">function M=getfrs(i) | + | </textarea></div> |
| + | <div><textarea id="code5" name="code">function M=getfrs(i) | ||
A=getfr(i); | A=getfr(i); | ||
t=1:480; | t=1:480; | ||
| Line 143: | Line 185: | ||
[a,k]=size(pksa); | [a,k]=size(pksa); | ||
M=a; | M=a; | ||
| − | </textarea></div><p>Running result<br>ans =<br> | + | </textarea></div> |
| − | <p><img src="https://static.igem.org/mediawiki/2015/c/c1/20150919073.png" alt="Figure 5: Fringes counting program running result"></p> | + | <p>Running result<br>ans =<br> 78</p> |
| − | <p>To get a series of results, this program is required.</p> | + | |
| − | + | <p><img src="https://static.igem.org/mediawiki/2015/c/c1/20150919073.png" | |
| + | alt="Figure 5: Fringes counting program running result"></p> | ||
| + | |||
| + | <p>To get a series of results, this program is required.</p> | ||
| + | |||
| + | <div><textarea id="code6" name="code">function N=getpkss(i,j) | ||
B=zeros(j-i+1,1); | B=zeros(j-i+1,1); | ||
for m=i:j | for m=i:j | ||
| Line 155: | Line 202: | ||
end | end | ||
N=B; | N=B; | ||
| − | </textarea></div><p>Demo</p> | + | </textarea></div> |
| − | <p>ans =</p> | + | <p>Demo</p> |
| − | <div><textarea id="code7" name="code">78 | + | |
| + | <p>ans =</p> | ||
| + | |||
| + | <div><textarea id="code7" name="code">78 | ||
80 | 80 | ||
77 | 77 | ||
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</textarea></div> | </textarea></div> | ||
| − | + | </div> | |
| + | </div> | ||
| + | <div class="col hide-on-small-only m3"> | ||
| + | <div class="toc-wrapper pinned"> | ||
| + | <ul class="section table-of-contents"> | ||
| + | <li> | ||
| + | <a href="#Fringes-Pattern-Simulation-Film-I">Fringes Pattern Simulation-Film I</a> | ||
| + | </li> | ||
| + | <li> | ||
| + | <a href="#Fringes-Pattern-Simulation-Film-II">Fringes Pattern Simulation-Film II</a> | ||
| + | </li> | ||
| + | <li> | ||
| + | <a href="#Film-I-Fringes-Analysis">Film I Fringes Analysis</a> | ||
| + | </li> | ||
| + | <li> | ||
| + | <a href="#Film-II-Fringes-Analysis-Fringes-number-analysis">Film II Fringes Analysis-Fringes | ||
| + | number analysis</a> | ||
| + | </li> | ||
| + | </ul> | ||
| + | </div> | ||
| + | </div> | ||
</div> | </div> | ||
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</div> | </div> | ||
<div id="adhesion-dynamics" class="row"> | <div id="adhesion-dynamics" class="row"> | ||
| − | + | <div class="card hoverable"> | |
| − | + | <div class="col s12 m9"> | |
| − | + | <div class="card-content"> | |
| − | <p>During analysis of ahdesion assay results, we are quite annoyed about counting total bacteria number and moving bacteria number, which is really important for mechanism analysis and results determination. Consequently, this part explains how we efficiently accomplished these tough work based on our software.</p> | + | <p>During analysis of ahdesion assay results, we are quite annoyed about counting total bacteria |
| − | <h4 id="Bacteria-counting-program" class="scrollspy">Bacteria counting program</h4> | + | number and moving bacteria number, which is really important for mechanism analysis and results |
| − | <p>This program is used to count the total number of bacteria.</p> | + | determination. Consequently, this part explains how we efficiently accomplished these tough work |
| − | <p>Code</p> | + | based on our software.</p> |
| − | <div><textarea id="code8" name="code">function a=shujun(i) | + | <h4 id="Bacteria-counting-program" class="scrollspy">Bacteria counting program</h4> |
| + | |||
| + | <p>This program is used to count the total number of bacteria.</p> | ||
| + | |||
| + | <p>Code</p> | ||
| + | |||
| + | <div><textarea id="code8" name="code">function a=shujun(i) | ||
name=num2str(i); | name=num2str(i); | ||
I=imread(name,'jpg'); | I=imread(name,'jpg'); | ||
| Line 223: | Line 280: | ||
a=num; | a=num; | ||
end | end | ||
| − | </textarea></div><p>Demo</p> | + | </textarea></div> |
| − | <p>input image:<br><img src="https://static.igem.org/mediawiki/2015/0/0e/20150919074.jpg" alt="Figure 6: Adhesion Assay image"><br>output result<br>ans =<br> | + | <p>Demo</p> |
| − | <div><textarea id=" | + | |
| + | <p>input image:<br><img src="https://static.igem.org/mediawiki/2015/0/0e/20150919074.jpg" | ||
| + | alt="Figure 6: Adhesion Assay image"><br>output result<br>ans =<br> 865</p> | ||
| + | |||
| + | <div><textarea id="code13" name="code">function A=mulshu(m) | ||
A=zeros(m,1); | A=zeros(m,1); | ||
for i=1:m | for i=1:m | ||
| Line 231: | Line 292: | ||
end | end | ||
</textarea></div> | </textarea></div> | ||
| − | <div class="divider"></div> | + | <div class="divider"></div> |
| − | <h4 id="Moving-Bacteria-Counting-Program" class="scrollspy">Moving Bacteria Counting Program</h4> | + | <h4 id="Moving-Bacteria-Counting-Program" class="scrollspy">Moving Bacteria Counting Program</h4> |
| − | <p>This program is used to count the total number of moving bacteria. Along with bacterial counting program, we finally got the mechanism of polylysine interaction.</p> | + | |
| − | <p>Code</p> | + | <p>This program is used to count the total number of moving bacteria. Along with bacterial counting |
| − | <div><textarea id="code9" name="code">function b=act(m,n) | + | program, we finally got the mechanism of polylysine interaction.</p> |
| + | |||
| + | <p>Code</p> | ||
| + | |||
| + | <div><textarea id="code9" name="code">function b=act(m,n) | ||
s1=num2str(m); | s1=num2str(m); | ||
s2=num2str(n); | s2=num2str(n); | ||
| Line 244: | Line 309: | ||
b=shujun(G); | b=shujun(G); | ||
end | end | ||
| − | </textarea></div><div><textarea id=" | + | </textarea></div> |
| + | <div><textarea id="code14" name="code">function A=mulact(m) | ||
A=zeros(m,1); | A=zeros(m,1); | ||
for i=1:m | for i=1:m | ||
| Line 254: | Line 320: | ||
A(i,1)=c; | A(i,1)=c; | ||
end | end | ||
| − | </textarea></div><p>Demo</p> | + | </textarea></div> |
| − | <p>ans =<br> | + | <p>Demo</p> |
| − | <div class="divider"></div> | + | |
| + | <p>ans =<br> 405 </p> | ||
| + | |||
| + | <div class="divider"></div> | ||
| + | |||
| + | <h4 id="Bacteria-total-number-time-curve" class="scrollspy">Bacteria total number-time curve</h4> | ||
| − | + | <p>Coding</p> | |
| − | <p>Coding</p> | + | |
| − | + | <div><textarea id="code10" name="code">function drawBT1(Ka,Kd,C,Vz,sigma0)%Ka is the adhesive rate of bacteria, Kd is the drop rate of bacteria, C is the density of bacteria solution,Vz is the velocity of bacteria,sigma0 is the maximum density of baacteria on surface | |
t=linspace(0,100,101); | t=linspace(0,100,101); | ||
K=Ka*C*Vz/(Kd*sigma0+Ka*C*Vz); | K=Ka*C*Vz/(Kd*sigma0+Ka*C*Vz); | ||
| Line 266: | Line 337: | ||
plot(t,sigma) | plot(t,sigma) | ||
end | end | ||
| − | </textarea></div><p>Running result<br><img src="https://static.igem.org/mediawiki/2015/9/99/20150901024.png" alt="Figure 7: Movement number simulation result"></p> | + | </textarea></div> |
| − | <div class="divider"></div> | + | <p>Running result<br><img src="https://static.igem.org/mediawiki/2015/9/99/20150901024.png" |
| + | alt="Figure 7: Movement number simulation result"></p> | ||
| + | |||
| + | <div class="divider"></div> | ||
| + | |||
| + | <h4 id="Bacteria-movement-number-Time-curve" class="scrollspy">Bacteria movement number-Time curve</h4> | ||
| − | + | <p>Coding</p> | |
| − | <p>Coding</p> | + | |
<textarea id="code11" name="code">function drawBMT(c,b,m0,k) | <textarea id="code11" name="code">function drawBMT(c,b,m0,k) | ||
t=linspace(0,100,101); | t=linspace(0,100,101); | ||
| Line 279: | Line 354: | ||
title('PAO1-PLL-0 Movement number-time'); | title('PAO1-PLL-0 Movement number-time'); | ||
end | end | ||
| − | </textarea></div><p>Running result<br><img src="https://static.igem.org/mediawiki/2015/8/88/20150907052.png" alt="Figure8:Bacteria movement number-Time simulation result"></p | + | </textarea></div> |
| − | + | <p>Running result<br><img src="https://static.igem.org/mediawiki/2015/8/88/20150907052.png" | |
| + | alt="Figure8:Bacteria movement number-Time simulation result"></p> | ||
</div> | </div> | ||
| − | + | </div> | |
| − | + | <div class="col hide-on-small-only m3"> | |
| + | <div class="toc-wrapper pinned"> | ||
<ul class="section table-of-contents"> | <ul class="section table-of-contents"> | ||
| − | + | <li> | |
| − | + | <a href="#Bacteria-counting-program">Bacteria Counting Program</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Moving-Bacteria-Counting-Program">Moving Bacteria Counting Program</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Bacteria-total-number-time-curve">Bacteria Total Number-Time Curve</a> | |
| − | + | </li> | |
| − | + | <li> | |
| − | + | <a href="#Bacteria-movement-number-Time-curve">Bacteria Movement Number-Time Curve</a> | |
| − | + | </li> | |
</ul> | </ul> | ||
| − | |||
</div> | </div> | ||
| − | |||
</div> | </div> | ||
| + | </div> | ||
| + | </div> | ||
| − | + | <div id="rose-dynamics" class="row"> | |
| − | + | <div class="card hoverable"> | |
<div class="col s12 m9"> | <div class="col s12 m9"> | ||
| − | + | <div class="card-content"> | |
| − | <p>This program is used to predict the advantages of ROSE construction. We successfully demonstrate our ROSE will be able to amplify fluorescence siganl.</p> | + | <p>This program is used to predict the advantages of ROSE construction. We successfully demonstrate our |
| − | <p>Code</p> | + | ROSE will be able to amplify fluorescence siganl.</p> |
| + | |||
| + | <p>Code</p> | ||
<textarea id="code12" name="code">clear all | <textarea id="code12" name="code">clear all | ||
R=R,k=k,k1=k1,k2=k2,k3=k3,k4=k4,k5=k5,k6=k6,k7=k7,k0=k0; %define the constant | R=R,k=k,k1=k1,k2=k2,k3=k3,k4=k4,k5=k5,k6=k6,k7=k7,k0=k0; %define the constant | ||
| Line 328: | Line 407: | ||
hold on | hold on | ||
plot(k0*t,t); %print the traditional strategy result in the same image | plot(k0*t,t); %print the traditional strategy result in the same image | ||
| − | </textarea></div><p>Demo</p> | + | </textarea></div> |
| − | <p><img src="https://static.igem.org/mediawiki/2015/1/1b/20150906Circuit.jpg" alt="Figure 9: ROSE Dynamics simulation result" data-image-src="https://static.igem.org/mediawiki/2015/1/1b/20150906Circuit.jpg"></p | + | <p>Demo</p> |
| − | + | ||
| + | <p><img src="https://static.igem.org/mediawiki/2015/1/1b/20150906Circuit.jpg" | ||
| + | alt="Figure 9: ROSE Dynamics simulation result" | ||
| + | data-image-src="https://static.igem.org/mediawiki/2015/1/1b/20150906Circuit.jpg"></p> | ||
</div> | </div> | ||
| − | |||
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| − | |||
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| + | </div> | ||
| + | |||
| + | |||
| − | <script type="text/javascript" src="https://2015.igem.org/Template:USTC/js/codemirror?action=raw&ctype=text/javascript"></script> | + | <script type="text/javascript" |
| − | <script type="text/javascript" src="https://2015.igem.org/Template:USTC/js/octave?action=raw&ctype=text/javascript"></script> | + | src="https://2015.igem.org/Template:USTC/js/codemirror?action=raw&ctype=text/javascript"></script> |
| + | <script type="text/javascript" | ||
| + | src="https://2015.igem.org/Template:USTC/js/octave?action=raw&ctype=text/javascript"></script> | ||
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var editor = CodeMirror.fromTextArea(document.getElementById("code"), { | var editor = CodeMirror.fromTextArea(document.getElementById("code"), { | ||
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| + | singleLineStringErrors: false}, | ||
| + | lineNumbers: true, | ||
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| + | matchBrackets: true | ||
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| − | </script> | + | var editor = CodeMirror.fromTextArea(document.getElementById("code14"), { |
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| + | singleLineStringErrors: false}, | ||
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</html> | </html> | ||
{{USTC/footer}} | {{USTC/footer}} | ||
Revision as of 00:00, 19 September 2015
In this section, we will introduce all the software program we used when processing our modeling and experimental data. Through our modeling, many complicated processdures are simply omitted by our convenient programs.
In general, our software programs are used in several sections,
- Fringes Analysis, analysis of interference pattern.
- Adhesion Dynamics, a series of programs relating to bacteria adhesion dynamics.
- Rose Prediction, which calculate the advantages of our ROSE improvement.
All software of our project, you can download them at Github:2015USTCiGEM. All codes are based on
Fringes Pattern Simulation-Film I
This program is used to simulate fringes pattern deliverd by film I.
Code:
Demo
After the formation of demo, we are able to recongize the real situation in our pre-experiment.
Fringes Pattern Simulation-Film II
This program is used to simulate fringes pattern deliverd by film II.
Code
Demo
Film I Fringes Analysis
Using this code, we are able to capture some important parameters in Film I.
Code
Demo
Film II Fringes Analysis-Fringes number analysis
This is the final program used to get our NDM calibration. Based on this software program, we are able to count the number of bright fringes. As a matter of fact, the variation of bright fringes is the key breakthrough to antibiotic analysis.
Code
Demo
Running result
ans =
78
To get a series of results, this program is required.
Demo
ans =
During analysis of ahdesion assay results, we are quite annoyed about counting total bacteria number and moving bacteria number, which is really important for mechanism analysis and results determination. Consequently, this part explains how we efficiently accomplished these tough work based on our software.
Bacteria counting program
This program is used to count the total number of bacteria.
Code
Demo
input image:
output result
ans =
865
Moving Bacteria Counting Program
This program is used to count the total number of moving bacteria. Along with bacterial counting program, we finally got the mechanism of polylysine interaction.
Code
Demo
ans =
405
Bacteria total number-time curve
Coding
Running result
Bacteria movement number-Time curve
Coding
Running result
This program is used to predict the advantages of ROSE construction. We successfully demonstrate our ROSE will be able to amplify fluorescence siganl.
Code
Demo
