Difference between revisions of "Team:SMMU-China/Software"

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<h3>★  ALERT! </h3>
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<h1><a href="https://2018.igem.org/Team:SMMU-China">Ca<sup>2+</sup>RTIN</a></h1>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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              <h1><a href="https://2018.igem.org/Team:SMMU-China">Ca<sup>2+</sup>RTIN</a></h1>
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<h3>Best Software Tool Special Prize</h3>
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          <li><a href="https://2018.igem.org/Team:SMMU-China/Demonstrate">Demonstrate</a></li>
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
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          <li><a href="https://2018.igem.org/Team:SMMU-China/Safety">Safety</a></li>
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<br><br>
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          <li><a href="https://2018.igem.org/Team:SMMU-China/Notebook">Notebook</a></li>
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You must also delete the message box on the top of this page to be eligible for this prize.
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          <li><a href="https://2018.igem.org/Team:SMMU-China/InterLab">Interlab</a></li>
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</p>
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<div class="highlight decoration_A_full">
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          <li><a href="https://2018.igem.org/Team:SMMU-China/Team">Team Members</a></li>
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<h3> Inspiration </h3>
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          <li><a href="https://2018.igem.org/Team:SMMU-China/Attributions">Attributions</a></li>
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<p>
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        </ul>
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Here are a few examples from previous teams:
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      </li>
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    </ul>
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  </nav>
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<li><a href="https://2016.igem.org/Team:BostonU_HW">2016 BostonU HW</a></li>
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<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">2014 Aachen</a></li>
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</ul>
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</div>
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</div>
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</section>
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<!-- Main -->
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<section id="main">
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<div class="container">
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<!-- Content -->
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<article class="box post">
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<header>
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<h2 class="inner-h">Software</h2>
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</header>
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<section>
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<h3 class="inner-h">Introduction</h3>
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<p class="inner-text">
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Although the calcium leakage plays a notable role in the development of Heart Failure (HF), it is hard to detect with noninvasive methods in clinical practice. The severity of HF can also be estimated by the level of calcium leakage, which in turn helps the clinical investors to determine the dosage and methodology of AAV based gene therapy. Therefore, we invented a software which can adopt the BNP expression level in patients' blood to reckon the level of calcium leakage, to choose of different AAVs and the to discriminate of expressing promoters.
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</p>
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</section>
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<section>
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<h3 class="inner-h">Instruction</h3>
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<h4 class="inner-h">Objective</h4>
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<p class="inner-text">
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To provide a guiding dosage of composite AAV that carries functional intrabody sequencing according to advanced set-up mathematical modeling and data.
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</p>
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<h4 class="inner-h">Content</h4>
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<h5 class="inner-h">1. Calcium leakage trending module</h5>
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<p class="inner-text">
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Based on the parameters of calcium iron (number of calcium sparkles, calcium stored in SR, the extent of calcium transient) to predict the trending of calcium leakage over time.
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</p>
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<h5 class="inner-h">2. Treatment plan assisting module</h5>
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<p class="inner-text">
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Provide different treatment plans (titer of AAV, promoter, treatment time) for different objectives of therapeutic effect (such as reducing 90 percent calcium leakage, or 60 percent, etc.).
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</p>
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<h5 class="inner-h">3. The custom setting assessment module</h5>
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<p class="inner-text">
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Evaluate the therapeutic effect according to the severity of disease and the selection of treatment plans.
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</p>
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<h4 class="inner-h">Guilding</h4>
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<h5 class="inner-h">1. Calcium leakage trending module</h5>
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<p class="inner-text">
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a) Input: calcium iron parameters: including intervals between onset of heart failure and detection, the number of calcium sparkles, calcium storage of SR and the extent of calcium transient.
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<br>
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b) At least three groups data required.
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<br>
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c) Calculation: based on the calcium leakage predicting model, it could calculate the expectation of calcium leakage in a few days.
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<br>
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d) Output: provide a trend graph from attacking of heart failure.
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</p>
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<center><img src="https://static.igem.org/mediawiki/2018/5/5e/T--SMMU-China--b1.png" width="800px"></center>
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<center><img src="https://static.igem.org/mediawiki/2018/5/58/T--SMMU-China--b2.png" width="600px"></center>
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<h5 class="inner-h">2. Treatment plan assisting module</h5>
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<p class="inner-text">
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a)Input: select the target value of reducing calcium leakage;
 +
<br>
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b)Output: based on your combination of virus serotype, promoter, and serum BNP value to calculate the titer of the therapeutic virus required for treatment.
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 +
</p>
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<center><img src="https://static.igem.org/mediawiki/2018/f/f9/T--SMMU-China--b3.png" width="600px"></center>
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<h5 class="inner-h">3. The custom setting assessment module </h5>
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 +
<p class="inner-text">
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a) Input: user can select serotype of virus and promoter, etc.
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<br>
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b) Calculation: based on the custom setting above, this function could calculate the expectation of reduced calcium leakage fitting the model built before.
 +
<br>
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c) Output: the expectation of calcium leakage reduction.
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</p>
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 +
<center><img src="https://static.igem.org/mediawiki/2018/2/2d/T--SMMU-China--b4.png" width="600px"></center>
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<h3 class="inner-h">Github</h3>
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 +
<p class="inner-text">
 +
You can download and use our software from <a href=" https://github.com/igemsoftware2018/Team_SMMU_China">Github</a>.
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</p>
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</section>
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</article>
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</div>
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</section>
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<section id="footer">
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<div class="container">
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<div class="row">
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<div class="col-7 col-12-medium">
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<section>
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<header>
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<h2>Brief report</h2>
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</header>
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<ul class="dates">
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<li>
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<span class="date">Sept <strong>27</strong></span>
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<h3><a href="#">Mathematical modeling</a></h3>
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<p>We have finished mathematical modeling for our project.</p>
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</li>
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<li>
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<span class="date">Sept <strong>7</strong></span>
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<h3><a href="#">CCiC conference</a></h3>
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<p>We attended the conference of China iGEMer community this week.</p>
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</li>
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<li>
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<span class="date">Sept <strong>1</strong></span>
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<h3><a href="#">Wiki online</a></h3>
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<p>Start building our Wiki Website.</p>
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</li>
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</ul>
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</section>
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</div>
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<div class="col-5 col-12-medium">
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<section>
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<header>
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<h2>Wanna contact us?</h2>
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</header>
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<ul class="contact">
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<li>
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<h3>Address</h3>
 +
<p>
 +
3rd floor, Library building<br />
 +
Second Military Medical University<br />
 +
800 Xiangyin Road, Yangpu, Shanghai, China
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</p>
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</li>
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Latest revision as of 16:12, 20 November 2018

Software

Introduction

Although the calcium leakage plays a notable role in the development of Heart Failure (HF), it is hard to detect with noninvasive methods in clinical practice. The severity of HF can also be estimated by the level of calcium leakage, which in turn helps the clinical investors to determine the dosage and methodology of AAV based gene therapy. Therefore, we invented a software which can adopt the BNP expression level in patients' blood to reckon the level of calcium leakage, to choose of different AAVs and the to discriminate of expressing promoters.

Instruction

Objective

To provide a guiding dosage of composite AAV that carries functional intrabody sequencing according to advanced set-up mathematical modeling and data.

Content

1. Calcium leakage trending module

Based on the parameters of calcium iron (number of calcium sparkles, calcium stored in SR, the extent of calcium transient) to predict the trending of calcium leakage over time.

2. Treatment plan assisting module

Provide different treatment plans (titer of AAV, promoter, treatment time) for different objectives of therapeutic effect (such as reducing 90 percent calcium leakage, or 60 percent, etc.).

3. The custom setting assessment module

Evaluate the therapeutic effect according to the severity of disease and the selection of treatment plans.

Guilding

1. Calcium leakage trending module

a) Input: calcium iron parameters: including intervals between onset of heart failure and detection, the number of calcium sparkles, calcium storage of SR and the extent of calcium transient.
b) At least three groups data required.
c) Calculation: based on the calcium leakage predicting model, it could calculate the expectation of calcium leakage in a few days.
d) Output: provide a trend graph from attacking of heart failure.

2. Treatment plan assisting module

a)Input: select the target value of reducing calcium leakage;
b)Output: based on your combination of virus serotype, promoter, and serum BNP value to calculate the titer of the therapeutic virus required for treatment.

3. The custom setting assessment module

a) Input: user can select serotype of virus and promoter, etc.
b) Calculation: based on the custom setting above, this function could calculate the expectation of reduced calcium leakage fitting the model built before.
c) Output: the expectation of calcium leakage reduction.

Github

You can download and use our software from Github.

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