Difference between revisions of "Team:NYMU-Taipei/Project-Model"

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     </div>
 
     </div>
  
 
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<div class="prototypeprototype">
 
<div id="wrap">
 
<div id="wrap">
 +
<div class="fund">
  
   
+
<h2 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Purpose</h2><hr />
  
<div class="fund">
+
<p style="font-size:16px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Our model aims to figure out the efficacy of the IOS system by comparing the population of B. dorsalis with and without this system. Written in NetLogo<sub>(1),</sub> , a software designed for modeling complex situations, the model combines both stochastic and deterministic methods. The stochastic part of the model was used to estimate the <em>Metarhizium Anisopliae</em> infection by our traps, whereas the deterministic part was used to simulate natural population growth of the flies. The efficiency of our IOS system predicted by this model is further used to analyze the cost-effectiveness of our prototype.</p>
<br>
+
<font size=36px>第一頁</font>
+
<hr>
+
<br>
+
<h2>Epidemic</h2><hr>
+
  
<p style="font-size:16px;">
+
<h2 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Rules</h2><hr />
B. dorsalis is a major cause of annual agricultural losses due to oviposition in fruits. We hereby introduce our prototype trap and M. anisopliae, our genetically engineered fungi, to address this issue. <br>
+
Our model aims to demonstrate that combining our prototype with the fungi can reduce the population of B. dorsalis. We selected and revised the SEIR model, which fits the ideal assumption in epidemiology, to make it more practical for our purpose.<br>
+
</p>
+
<div align="center">
+
<table border="1" cellpadding="0" cellspacing="0" align="center">
+
<tbody>
+
<tr>
+
<td style="width:92px;">
+
<p style="font-size:16px;">Symbol</p>
+
</td>
+
<td style="width:478px;">
+
                                <p style="font-size:16px;">Description</p>
+
</td>
+
</tr>
+
<tr>
+
<td style="width:92px;">
+
                                <p style="font-size:16px;">Susceptible</p>
+
</td>
+
<td style="width:478px;">
+
<p style="font-size:16px;">
+
<em>B. dorsalis</em> is slightly or moderately resistant to&nbsp;<em>M. anisopliae</em></p>
+
</td>
+
</tr>
+
<tr>
+
<td style="width:92px;">
+
<p style="font-size:16px;">Exposed</p>
+
</td>
+
<td style="width:478px;">
+
<p style="font-size:16px;">
+
<em>B. dorsalis</em> is exposed to a low amount of&nbsp;<em>M. anisopliae</em> in our trap; disease will be spread further during mating.</p>
+
</td>
+
</tr>
+
<tr>
+
<td style="width:92px;">
+
<p style="font-size:16px;">Infected</p>
+
</td>
+
<td style="width:478px;">
+
<p style="font-size:16px;">
+
<em>M. anisopliae </em>enters <em>B. dorsalis</em>&rsquo; hemolymph and initiates cell division.</p>
+
</td>
+
</tr>
+
<tr>
+
<td style="width:92px;">
+
<p style="font-size:16px;">Death</p>
+
</td>
+
<td style="width:478px;">
+
<p style="font-size:16px;">
+
<em>B. dorsalis </em>dies from the infection of <em>M. anisopliae</em>.</p>
+
</td>
+
</tr>
+
</tbody>
+
</table>
+
  
</div>
+
<h4 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Assumption</h4>
  
<p style="font-size:16px;">
+
<p style="font-size:16px;">This model follows the assumptions listed below:</p>
Based on our assumptions, we developed a set of differential equations that characterizes the nature of the epidemic in our model:<br><br>
+
<ol>
<img src="https://static.igem.org/mediawiki/2016/2/20/%E6%96%B9%E7%A8%8B%E5%BC%8F.png"/>
+
<li>The fly influx and efflux are always the same in the orchard.</li>
</p>
+
<li>The mortality caused by naturally existing <em>anisopliae</em> is considered as natural death while the death caused by <em>M.anisopliae</em> inside the traps and its infection afterward is regarded as IOS-caused deaths</li>
 +
<li>The fly population has already reached the stable stage before the start of the simulation.</li>
 +
</ol>
  
<br/>
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Natural Condition</h3>
 +
<p style="font-size:16px;">The fly population obeys the discrete time logistic function:</p>
  
 +
<img src="https://static.igem.org/mediawiki/2016/2/22/T-NYMU-Taipei-photo-protocol-model-image001.png" alt="" width="212" height="60" />
  
<h1>Parameter</h1><hr /><br />
+
<p style="font-size:16px;">&nbsp;&nbsp;represents the population of fruit flies at time t.</p>
 +
<ol>
 +
<li>Population of next generation is proportional to that of this generation by the coefficient r.</li>
 +
<li>Population reaches a stable stage regulated by the number of capacity K.</li>
 +
<li>Death caused by naturally existing <em> anisopliae</em> is considered as a part of K.</li>
 +
</ol>
  
<div align="center" style="overflow-x:auto;">
 
<table border="1" cellpadding="0" cellspacing="0" align="center">
 
<tbody>
 
<tr>
 
<td style="width:73px;">
 
<p style="font-size:16px;">
 
Type</p>
 
</td>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
Name</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
Meaning (Value)</p>
 
</td>
 
<td style="width:179px;">
 
<p style="font-size:16px;">
 
Reference</p>
 
</td>
 
</tr>
 
<tr>
 
<td rowspan="5" style="width:73px;">
 
<p style="font-size:16px;">
 
Constant</p>
 
</td>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
Mating rate</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
0.8635</p>
 
</td>
 
<td style="width:179px;">
 
<p style="font-size:16px;">
 
&nbsp;</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
daily_capture</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
40</p>
 
</td>
 
<td style="width:179px;">
 
<p style="font-size:16px;">
 
&nbsp;</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
daily_move_in</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
0</p>
 
</td>
 
<td style="width:179px;">
 
<p style="font-size:16px;">
 
&nbsp;</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
K</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
adult death rate (0.05)</p>
 
</td>
 
<td style="width:179px;">
 
<p style="font-size:16px;">
 
[1]</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
k0</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
larval death rate (0.23)</p>
 
</td>
 
<td style="width:179px;">
 
<p style="font-size:16px;">
 
[2]</p>
 
</td>
 
</tr>
 
<tr>
 
<td rowspan="7" style="width:73px;">
 
<p style="font-size:16px;">
 
Variable</p>
 
</td>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
ms</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
susceptible male</p>
 
</td>
 
<td rowspan="7" style="width:179px;">
 
<p style="font-size:16px;">
 
&nbsp;</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
Fs</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
susceptible female</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
me</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
exposed male</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
Fe</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
exposed female</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
mi</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
infected male</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
Fi</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
infected female</p>
 
</td>
 
</tr>
 
<tr>
 
<td style="width:109px;">
 
<p style="font-size:16px;">
 
D</p>
 
</td>
 
<td style="width:220px;">
 
<p style="font-size:16px;">
 
Death</p>
 
</td>
 
</tr>
 
</tbody>
 
</table>
 
</div>
 
  
<br>
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">With IOS system</h3>
  
<h2>Result</h2><hr />
+
<p style="font-size:16px;">The addition of our IOS system leads to greater death rate caused by <em>M. anisopliae</em> in our traps and . The additional term is modified from SIR epidemic model:</p>
  
<img src="https://static.igem.org/mediawiki/2016/2/21/T--NYMU-Taipei--model_result.png" width=100% /><br>
+
<p style="font-size:16px;"><img src="https://static.igem.org/mediawiki/2016/0/0b/T-NYMU-Taipei-photo-protocol-model-image005.png" alt="" /></p>
 +
<ol>
 +
<li>Male flies within the attraction radius of the methyl eugenol from trap will be attracted to the trap by a certain probability.</li>
 +
<li>After being trapped, male flies will be infected by <em>anisopliae</em> and released later.</li>
 +
<li>Infected males are prone to spread <em>anisopliae</em> conidia to females while mating.</li>
 +
<li>Females are likely to re-mate and thus are likely to spread <em>anisopliae</em> conidia further.</li>
 +
<li>The overall lethality of the infection is described by the formula<img src="https://static.igem.org/mediawiki/2016/3/39/T-NYMU-Taipei-photo-protocol-model-image007.png" alt="" /> where &nbsp;represents the rate of infection spread, and <img src="https://static.igem.org/mediawiki/2016/3/3d/T-NYMU-Taipei-photo-protocol-model-image011.png" alt="" width="35" height="30" />and <img src="https://static.igem.org/mediawiki/2016/4/4b/T-NYMU-Taipei-photo-protocol-model-image013.png" alt="" />&nbsp;represents the population of susceptible and infected flies at &nbsp;units of time before.</li>
 +
</ol>
  
<p style="font-size:16px;">
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Parameters</h3>
The graph above shows the initial increase in population due to the attraction of B. dorsalis from the surrounding environment. However, the population subsequently drops when the M. anisopliae infection begin to spread. The results indicate that the use of prototype combined with the fungi yields a 70% decrease in the B. dorsalis population. Thus, we deduce that our product can be deployed in orchards and farms a few weeks prior to harvest to minimize crop damage.</p><br>
+
<p style="font-size:16px;">Model was a simulation of a one-hectare (100100m) orchard. Four traps and three counters (not shown) were deployed symmetrically in the orchard and their effective distance completely cover all the orchard.</p>
  
 +
<table>
 +
<tbody>
 +
<tr>
 +
<td width="230">
 +
<p><strong>Parameter</strong></p>
 +
</td>
 +
<td width="230">
 +
<p><strong>Value</strong></p>
 +
</td>
 +
<td width="231">
 +
<p><strong>Meaning</strong></p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>male-fly-color</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>blue</p>
 +
</td>
 +
<td width="231">
 +
<p>&nbsp;</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>female-fly-color</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>yellow</p>
 +
</td>
 +
<td width="231">
 +
<p>&nbsp;</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>counter-color</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>black</p>
 +
</td>
 +
<td width="231">
 +
<p>&nbsp;</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>r-value</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>0.17</p>
 +
</td>
 +
<td width="231">
 +
<p>Growth rate of fly. Calculated value from doubling time<sub>(2)</sub>.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>Infection-rate</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>0.42</p>
 +
</td>
 +
<td width="231">
 +
<p>M. anisopliae infection spread rate. Calculated value from mating frequency<sub>(3)</sub>.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>average-flies-per-day</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>Depending on simulation conditions</p>
 +
</td>
 +
<td width="231">
 +
<p>The average population of fly per day.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>max-fly-stride</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>8</p>
 +
</td>
 +
<td width="231">
 +
<p>The distance a fly flies per day. Assumed value.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>M.A.switch </strong></p>
 +
</td>
 +
<td width="230">
 +
<p>On/off</p>
 +
</td>
 +
<td width="231">
 +
<p>Our IOS system is implemented when its value is &ldquo;on&rdquo;, and the original state is presented when its value is &ldquo;off&rdquo;.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>fly-initial-amount</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>360</p>
 +
</td>
 +
<td width="231">
 +
<p>The initial population of oriental fruit fly in a hectare of orchard. Estimation based on this report<sub>(4)</sub>.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>Infective-distance</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>50</p>
 +
</td>
 +
<td width="231">
 +
<p>The distance that methyl eugenol in a trap is attractive to a fly.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>attraction-rate</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>0.7</p>
 +
</td>
 +
<td width="231">
 +
<p>The probability that a male fly within the infective-distance will be attracted toward the closest trap.</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="230">
 +
<p><strong>base</strong></p>
 +
</td>
 +
<td width="230">
 +
<p>360</p>
 +
</td>
 +
<td width="231">
 +
<p>The upper limit of the population in the model orchard environment. Since we presume the population already reached stable state before modeling, its value is exactly the same as fly-initial-amount.</p>
 +
</td>
 +
</tr>
 +
</tbody>
 +
</table>
  
 +
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Results</h3>
  
 +
<p style="font-size:16px;">Population of both original state and IOS implementing conditions has been modeled and is shown below.</p>
 +
<p style="font-size:16px;"><strong>Scenario 1: the original state of fruit fly population</strong></p>
  
 +
<video src="https://static.igem.org/mediawiki/2016/b/bc/T-NYMU-Taipei-model-movie.mp4"
 +
controls
 +
autoplay
 +
width="100%">
 +
</video><br><br>
  
<h2>Reference</h2><hr />
+
<p style="font-size:16px;"><strong>Scenario 2: fruit fly population after IOS implementation</strong></p>
 +
<video src="https://static.igem.org/mediawiki/2016/d/d4/T-NYMU-Taipei-photo-model1mb.mp4"
 +
controls
 +
autoplay
 +
width="100%">
 +
</video><br>
  
<p style="font-size:16px;">1. Life History and Demographic Parameters of Three Laboratory-reared Tephritids (Diptera: Tephritidae)
+
<p style="font-size:16px;">The original population of fly per day is 355 and this number decreased to 231 after implementation of our IOS system. The population decreased by 35% when our IOS system is implemented, suggesting the high efficiency of our system.</p>
R. Vargas - D. Miyashita - T. Nishida - Annals of the Entomological Society of America - 1984</p>
+
 
<p style="font-size:16px;">2. Effect of Temperature on the Development and Survival of Immature Stages of the Carambola Fruit Fly,Bactrocera carambolae, and the Asian Papaya Fruit Fly,Bactrocera papayae, Reared On Guava Diet
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Code</h3>
Solomon Danjuma - Narit Thaochan - Surakrai Permkam - Chutamas Satasook - Journal of Insect Science - 2014</p>
+
<p style="font-size:16px;"><a href="https://static.igem.org/mediawiki/2016/4/48/T-NYMU-Taipei-photo-model-code.pdf">code.pdf</a></p>
 +
 
 +
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Reference</h3>
 +
 
 +
<p style="font-size:16px;">1. Wilensky, U. (1999). NetLogo.<a href="http://ccl.northwestern.edu/netlogo/">http://ccl.northwestern.edu/netlogo/</a>. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.</p>
 +
<p style="font-size:16px;">2. Vargas, R. I., Walsh, W. A., Kanehisa, D., Jang, E. B., &amp; Armstrong, J. W. (1997). Demography of Four Hawaiian Fruit Flies (Diptera: Tephritidae) Reared at Five Constant Temperatures.<em>Annals of the Entomological Society of America,</em>&nbsp;<em>90</em>(2), 162-168. doi:10.1093/aesa/90.2.162</p>
 +
<p style="font-size:16px;">3. Ji, Q. E., Chen, J. H., Mcinnis, D. O., &amp; Guo, Q. L. (2011). The effect of methyl eugenol exposure on subsequent mating performance of sterile males ofBactrocera dorsalis. <em>Journal of Applied Entomology,</em> <em>137</em>, 238-243. doi:10.1111/j.1439-0418.2011.01686.x</p>
 +
<p style="font-size:16px;">4. 鄭明發.&rdquo;東方果實蠅防治策略&rdquo;.台灣柑橘產業發展研究會專刊.</p>
 +
<p style="font-size:16px;">&nbsp;</p>
  
 
</div>
 
</div>
<br>
+
</div>
 +
</div>
 +
 
 +
<div class="prototypeprototypesp">
 +
<div id="wrap">
 
<div class="fund">
 
<div class="fund">
<font size=36px>另一頁</font>
 
  
<h2>Purpose</h2><hr />
+
<h2 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Purpose</h2><hr />
  
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Our model aims to figure out the efficacy of the IOS system by comparing the population of B. dorsalis with and without this system. Written in NetLogo<sub>(1),</sub> , a software designed for modeling complex situations, the model combines both stochastic and deterministic methods. The stochastic part of the model was used to estimate the <em>Metarhizium Anisopliae</em> infection by our traps, whereas the deterministic part was used to simulate natural population growth of the flies. The efficiency of our IOS system predicted by this model is further used to analyze the cost-effectiveness of our prototype.</p>
+
<p style="font-size:16px;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Our model aims to figure out the efficacy of the IOS system by comparing the population of B. dorsalis with and without this system. Written in NetLogo<sub>(1),</sub> , a software designed for modeling complex situations, the model combines both stochastic and deterministic methods. The stochastic part of the model was used to estimate the <em>Metarhizium Anisopliae</em> infection by our traps, whereas the deterministic part was used to simulate natural population growth of the flies. The efficiency of our IOS system predicted by this model is further used to analyze the cost-effectiveness of our prototype.</p>
  
<h2>Rules</h2><hr />
+
<h2 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Rules</h2><hr />
  
<h4>Assumption</h4>
+
<h4 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Assumption</h4>
<p>This model follows the assumptions listed below:</p>
+
 
 +
<p style="font-size:16px;">This model follows the assumptions listed below:</p>
 
<ol>
 
<ol>
 
<li>The fly influx and efflux are always the same in the orchard.</li>
 
<li>The fly influx and efflux are always the same in the orchard.</li>
Line 320: Line 276:
 
</ol>
 
</ol>
  
<h3>Natural Condition</h3>
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Natural Condition</h3>
<p>The fly population obeys the discrete time logistic function:</p>
+
<p style="font-size:16px;">The fly population obeys the discrete time logistic function:</p>
<p><img src="https://static.igem.org/mediawiki/2016/2/22/T-NYMU-Taipei-photo-protocol-model-image001.png" alt="" width="212" height="60" /></p>
+
 
<p>&nbsp;&nbsp;represents the population of fruit flies at time t.</p>
+
<img src="https://static.igem.org/mediawiki/2016/2/22/T-NYMU-Taipei-photo-protocol-model-image001.png" alt="" width="212" height="60" />
 +
 
 +
<p style="font-size:16px;">&nbsp;&nbsp;represents the population of fruit flies at time t.</p>
 
<ol>
 
<ol>
 
<li>Population of next generation is proportional to that of this generation by the coefficient r.</li>
 
<li>Population of next generation is proportional to that of this generation by the coefficient r.</li>
Line 331: Line 289:
  
  
<h3>With IOS system</h3>
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">With IOS system</h3>
<p>The addition of our IOS system leads to greater death rate caused by <em>M. anisopliae</em> in our traps and . The additional term is modified from SIR epidemic model:</p>
+
 
<p><img src="https://static.igem.org/mediawiki/2016/0/0b/T-NYMU-Taipei-photo-protocol-model-image005.png" alt="" /></p>
+
<p style="font-size:16px;">The addition of our IOS system leads to greater death rate caused by <em>M. anisopliae</em> in our traps and . The additional term is modified from SIR epidemic model:</p>
 +
 
 +
<p style="font-size:16px;"><img src="https://static.igem.org/mediawiki/2016/0/0b/T-NYMU-Taipei-photo-protocol-model-image005.png" alt="" /></p>
 
<ol>
 
<ol>
 
<li>Male flies within the attraction radius of the methyl eugenol from trap will be attracted to the trap by a certain probability.</li>
 
<li>Male flies within the attraction radius of the methyl eugenol from trap will be attracted to the trap by a certain probability.</li>
Line 342: Line 302:
 
</ol>
 
</ol>
  
<h3>Parameters</h3>
+
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Parameters</h3>
<p>Model was a simulation of a one-hectare (100100m) orchard. Four traps and three counters (not shown) were deployed symmetrically in the orchard and their effective distance completely cover all the orchard.</p>
+
<p style="font-size:16px;">Model was a simulation of a one-hectare (100100m) orchard. Four traps and three counters (not shown) were deployed symmetrically in the orchard and their effective distance completely cover all the orchard.</p>
  
 
<table>
 
<table>
Line 493: Line 453:
 
</table>
 
</table>
  
 +
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Results</h3>
  
 +
<p style="font-size:16px;">Population of both original state and IOS implementing conditions has been modeled and is shown below.</p>
 +
<p style="font-size:16px;"><strong>Scenario 1: the original state of fruit fly population</strong></p>
  
<h3>Results</h3>
 
 
<p>Population of both original state and IOS implementing conditions has been modeled and is shown below.</p>
 
<p><strong>Scenario 1: the original state of fruit fly population</strong></p>
 
 
<video src="https://static.igem.org/mediawiki/2016/b/bc/T-NYMU-Taipei-model-movie.mp4"
 
<video src="https://static.igem.org/mediawiki/2016/b/bc/T-NYMU-Taipei-model-movie.mp4"
 
controls
 
controls
Line 504: Line 463:
 
width="100%">
 
width="100%">
 
</video><br><br>
 
</video><br><br>
<p><strong>Scenario 2: fruit fly population after IOS implementation</strong></p>
+
 
 +
<p style="font-size:16px;"><strong>Scenario 2: fruit fly population after IOS implementation</strong></p>
 
<video src="https://static.igem.org/mediawiki/2016/d/d4/T-NYMU-Taipei-photo-model1mb.mp4"
 
<video src="https://static.igem.org/mediawiki/2016/d/d4/T-NYMU-Taipei-photo-model1mb.mp4"
 
controls
 
controls
Line 511: Line 471:
 
</video><br>
 
</video><br>
  
<p>The original population of fly per day is 355 and this number decreased to 231 after implementation of our IOS system. The population decreased by 35% when our IOS system is implemented, suggesting the high efficiency of our system.</p>
+
<p style="font-size:16px;">The original population of fly per day is 355 and this number decreased to 231 after implementation of our IOS system. The population decreased by 35% when our IOS system is implemented, suggesting the high efficiency of our system.</p>
  
 +
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Code</h3>
 +
<p style="font-size:16px;"><a href="https://static.igem.org/mediawiki/2016/4/48/T-NYMU-Taipei-photo-model-code.pdf">code.pdf</a></p>
  
 +
<h3 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Reference</h3>
  
<h3>Code</h3>
+
<p style="font-size:16px;">1. Wilensky, U. (1999). NetLogo.<a href="http://ccl.northwestern.edu/netlogo/">http://ccl.northwestern.edu/netlogo/</a>. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.</p>
<p><a href="https://static.igem.org/mediawiki/2016/4/48/T-NYMU-Taipei-photo-model-code.pdf">code.pdf</a></p>
+
<p style="font-size:16px;">2. Vargas, R. I., Walsh, W. A., Kanehisa, D., Jang, E. B., &amp; Armstrong, J. W. (1997). Demography of Four Hawaiian Fruit Flies (Diptera: Tephritidae) Reared at Five Constant Temperatures.<em>Annals of the Entomological Society of America,</em>&nbsp;<em>90</em>(2), 162-168. doi:10.1093/aesa/90.2.162</p>
 
+
<p style="font-size:16px;">3. Ji, Q. E., Chen, J. H., Mcinnis, D. O., &amp; Guo, Q. L. (2011). The effect of methyl eugenol exposure on subsequent mating performance of sterile males ofBactrocera dorsalis. <em>Journal of Applied Entomology,</em> <em>137</em>, 238-243. doi:10.1111/j.1439-0418.2011.01686.x</p>
<h3>Reference</h3>
+
<p style="font-size:16px;">4. 鄭明發.&rdquo;東方果實蠅防治策略&rdquo;.台灣柑橘產業發展研究會專刊.</p>
<p>1. Wilensky, U. (1999). NetLogo.<a href="http://ccl.northwestern.edu/netlogo/">http://ccl.northwestern.edu/netlogo/</a>. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.</p>
+
<p style="font-size:16px;">&nbsp;</p>
<p>2. Vargas, R. I., Walsh, W. A., Kanehisa, D., Jang, E. B., &amp; Armstrong, J. W. (1997). Demography of Four Hawaiian Fruit Flies (Diptera: Tephritidae) Reared at Five Constant Temperatures.<em>Annals of the Entomological Society of America,</em>&nbsp;<em>90</em>(2), 162-168. doi:10.1093/aesa/90.2.162</p>
+
<p>3. Ji, Q. E., Chen, J. H., Mcinnis, D. O., &amp; Guo, Q. L. (2011). The effect of methyl eugenol exposure on subsequent mating performance of sterile males ofBactrocera dorsalis. <em>Journal of Applied Entomology,</em> <em>137</em>, 238-243. doi:10.1111/j.1439-0418.2011.01686.x</p>
+
<p>4. 鄭明發.&rdquo;東方果實蠅防治策略&rdquo;.台灣柑橘產業發展研究會專刊.</p>
+
<p>&nbsp;</p>
+
  
 
</div>
 
</div>
 
+
</div>
 
+
</div>
  
 
</body>
 
</body>
  
 
</html>
 
</html>

Revision as of 00:39, 20 October 2016

Purpose


        Our model aims to figure out the efficacy of the IOS system by comparing the population of B. dorsalis with and without this system. Written in NetLogo(1), , a software designed for modeling complex situations, the model combines both stochastic and deterministic methods. The stochastic part of the model was used to estimate the Metarhizium Anisopliae infection by our traps, whereas the deterministic part was used to simulate natural population growth of the flies. The efficiency of our IOS system predicted by this model is further used to analyze the cost-effectiveness of our prototype.

Rules


Assumption

This model follows the assumptions listed below:

  1. The fly influx and efflux are always the same in the orchard.
  2. The mortality caused by naturally existing anisopliae is considered as natural death while the death caused by M.anisopliae inside the traps and its infection afterward is regarded as IOS-caused deaths
  3. The fly population has already reached the stable stage before the start of the simulation.

Natural Condition

The fly population obeys the discrete time logistic function:

  represents the population of fruit flies at time t.

  1. Population of next generation is proportional to that of this generation by the coefficient r.
  2. Population reaches a stable stage regulated by the number of capacity K.
  3. Death caused by naturally existing anisopliae is considered as a part of K.

With IOS system

The addition of our IOS system leads to greater death rate caused by M. anisopliae in our traps and . The additional term is modified from SIR epidemic model:

  1. Male flies within the attraction radius of the methyl eugenol from trap will be attracted to the trap by a certain probability.
  2. After being trapped, male flies will be infected by anisopliae and released later.
  3. Infected males are prone to spread anisopliae conidia to females while mating.
  4. Females are likely to re-mate and thus are likely to spread anisopliae conidia further.
  5. The overall lethality of the infection is described by the formula where  represents the rate of infection spread, and and  represents the population of susceptible and infected flies at  units of time before.

Parameters

Model was a simulation of a one-hectare (100100m) orchard. Four traps and three counters (not shown) were deployed symmetrically in the orchard and their effective distance completely cover all the orchard.

Parameter

Value

Meaning

male-fly-color

blue

 

female-fly-color

yellow

 

counter-color

black

 

r-value

0.17

Growth rate of fly. Calculated value from doubling time(2).

Infection-rate

0.42

M. anisopliae infection spread rate. Calculated value from mating frequency(3).

average-flies-per-day

Depending on simulation conditions

The average population of fly per day.

max-fly-stride

8

The distance a fly flies per day. Assumed value.

M.A.switch

On/off

Our IOS system is implemented when its value is “on”, and the original state is presented when its value is “off”.

fly-initial-amount

360

The initial population of oriental fruit fly in a hectare of orchard. Estimation based on this report(4).

Infective-distance

50

The distance that methyl eugenol in a trap is attractive to a fly.

attraction-rate

0.7

The probability that a male fly within the infective-distance will be attracted toward the closest trap.

base

360

The upper limit of the population in the model orchard environment. Since we presume the population already reached stable state before modeling, its value is exactly the same as fly-initial-amount.

Results

Population of both original state and IOS implementing conditions has been modeled and is shown below.

Scenario 1: the original state of fruit fly population



Scenario 2: fruit fly population after IOS implementation


The original population of fly per day is 355 and this number decreased to 231 after implementation of our IOS system. The population decreased by 35% when our IOS system is implemented, suggesting the high efficiency of our system.

Code

code.pdf

Reference

1. Wilensky, U. (1999). NetLogo.http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

2. Vargas, R. I., Walsh, W. A., Kanehisa, D., Jang, E. B., & Armstrong, J. W. (1997). Demography of Four Hawaiian Fruit Flies (Diptera: Tephritidae) Reared at Five Constant Temperatures.Annals of the Entomological Society of America, 90(2), 162-168. doi:10.1093/aesa/90.2.162

3. Ji, Q. E., Chen, J. H., Mcinnis, D. O., & Guo, Q. L. (2011). The effect of methyl eugenol exposure on subsequent mating performance of sterile males ofBactrocera dorsalis. Journal of Applied Entomology, 137, 238-243. doi:10.1111/j.1439-0418.2011.01686.x

4. 鄭明發.”東方果實蠅防治策略”.台灣柑橘產業發展研究會專刊.

 

Purpose


        Our model aims to figure out the efficacy of the IOS system by comparing the population of B. dorsalis with and without this system. Written in NetLogo(1), , a software designed for modeling complex situations, the model combines both stochastic and deterministic methods. The stochastic part of the model was used to estimate the Metarhizium Anisopliae infection by our traps, whereas the deterministic part was used to simulate natural population growth of the flies. The efficiency of our IOS system predicted by this model is further used to analyze the cost-effectiveness of our prototype.

Rules


Assumption

This model follows the assumptions listed below:

  1. The fly influx and efflux are always the same in the orchard.
  2. The mortality caused by naturally existing anisopliae is considered as natural death while the death caused by M.anisopliae inside the traps and its infection afterward is regarded as IOS-caused deaths
  3. The fly population has already reached the stable stage before the start of the simulation.

Natural Condition

The fly population obeys the discrete time logistic function:

  represents the population of fruit flies at time t.

  1. Population of next generation is proportional to that of this generation by the coefficient r.
  2. Population reaches a stable stage regulated by the number of capacity K.
  3. Death caused by naturally existing anisopliae is considered as a part of K.

With IOS system

The addition of our IOS system leads to greater death rate caused by M. anisopliae in our traps and . The additional term is modified from SIR epidemic model:

  1. Male flies within the attraction radius of the methyl eugenol from trap will be attracted to the trap by a certain probability.
  2. After being trapped, male flies will be infected by anisopliae and released later.
  3. Infected males are prone to spread anisopliae conidia to females while mating.
  4. Females are likely to re-mate and thus are likely to spread anisopliae conidia further.
  5. The overall lethality of the infection is described by the formula where  represents the rate of infection spread, and and  represents the population of susceptible and infected flies at  units of time before.

Parameters

Model was a simulation of a one-hectare (100100m) orchard. Four traps and three counters (not shown) were deployed symmetrically in the orchard and their effective distance completely cover all the orchard.

Parameter

Value

Meaning

male-fly-color

blue

 

female-fly-color

yellow

 

counter-color

black

 

r-value

0.17

Growth rate of fly. Calculated value from doubling time(2).

Infection-rate

0.42

M. anisopliae infection spread rate. Calculated value from mating frequency(3).

average-flies-per-day

Depending on simulation conditions

The average population of fly per day.

max-fly-stride

8

The distance a fly flies per day. Assumed value.

M.A.switch

On/off

Our IOS system is implemented when its value is “on”, and the original state is presented when its value is “off”.

fly-initial-amount

360

The initial population of oriental fruit fly in a hectare of orchard. Estimation based on this report(4).

Infective-distance

50

The distance that methyl eugenol in a trap is attractive to a fly.

attraction-rate

0.7

The probability that a male fly within the infective-distance will be attracted toward the closest trap.

base

360

The upper limit of the population in the model orchard environment. Since we presume the population already reached stable state before modeling, its value is exactly the same as fly-initial-amount.

Results

Population of both original state and IOS implementing conditions has been modeled and is shown below.

Scenario 1: the original state of fruit fly population



Scenario 2: fruit fly population after IOS implementation


The original population of fly per day is 355 and this number decreased to 231 after implementation of our IOS system. The population decreased by 35% when our IOS system is implemented, suggesting the high efficiency of our system.

Code

code.pdf

Reference

1. Wilensky, U. (1999). NetLogo.http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

2. Vargas, R. I., Walsh, W. A., Kanehisa, D., Jang, E. B., & Armstrong, J. W. (1997). Demography of Four Hawaiian Fruit Flies (Diptera: Tephritidae) Reared at Five Constant Temperatures.Annals of the Entomological Society of America, 90(2), 162-168. doi:10.1093/aesa/90.2.162

3. Ji, Q. E., Chen, J. H., Mcinnis, D. O., & Guo, Q. L. (2011). The effect of methyl eugenol exposure on subsequent mating performance of sterile males ofBactrocera dorsalis. Journal of Applied Entomology, 137, 238-243. doi:10.1111/j.1439-0418.2011.01686.x

4. 鄭明發.”東方果實蠅防治策略”.台灣柑橘產業發展研究會專刊.