Difference between revisions of "Team:DTU-Denmark/Software"

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<h3>★  ALERT! </h3>
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    <link rel="stylesheet" type="text/css" href="https://2017.igem.org/Team:DTU-Denmark/stylesheetsub?action=raw&ctype=text/css&?ver=6">
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1>Software</h1>
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<h3>Best Software Tool Special Prize</h3>
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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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          <h1 id="app" class="bottomborder">The SV Detector App</h1>
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          <div class="row">
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              <div class="colp-4 rmvpadmarg">
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<figure style="margin-top:0;">
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                  <img src="https://static.igem.org/mediawiki/2017/6/6c/T--DTU-Denmark--software-1.jpeg" alt="App in use" width=270>
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                  <figcaption>Figure 1: The app on an Android phone (Sony M4A).</figcaption>
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</figure>
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              </div>
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              <div class="colp-6 rmvpadmarg">
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                  <p>The SV Detector app was developed to work with the spectrophotometer. The purpose of the spectrophotometer was to quantify the results by creating a controlled uniform environment for every test. The app is the spectrophotometer’s brain – the idea was to create a simple app so that even operators with little specialized knowledge of snake venom could still utilise it. The app is compatible with Android 5.0 meaning that it can run on hardware from 2014 and up.</p><br><br>
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<p>The SV Detector allows the operator to simply test the incubated samples for the relative amount of colour that is present in every sample.</p><br><br>
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</p>
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              </div>
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<figure>
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                  <img src="https://static.igem.org/mediawiki/2017/6/69/T--DTU-Denmark--software-2.png" alt="App front page" width=270>
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                  <figcaption>Figure 2: The start-up screen of the SV Detector.</figcaption>
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</figure>
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              </div>
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              <div class="colp-6 rmvpadmarg">
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                  <p><br />The workflow is simple. The app is launched and the operator selects start measuring when ready. The next screen presented shows the instructions. These are extremely simple and numbered to increase the readability as well as eliminate misunderstanding.
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                  </p>
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              </div>
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<br><br>
 
<br><br>
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To compete for the <a href="https://2017.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://2017.igem.org/Judging/Judging_Form">judging form</a>.
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          <div class="colp-4 rmvpadmarg">
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<figure>
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            <img src="https://static.igem.org/mediawiki/2017/4/48/T--DTU-Denmark--software-3.jpeg" alt="App instructions page" width=270>
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<figcaption>Figure 3: The instructions screen of the app.</figcaption>
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</figure>
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          </div>
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          <div class="colp-6 rmvpadmarg">
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            <p><br>The instructions are also simplified by calling the three different substrates as 1, 2, and 3. These substrates were chosen from the peptide screening as they enable us to use logic in order to distinguish between the three chosen snakes. One substrate will react with the three venoms, and the other two will react with two different ones. Thus if the first substrate reacts and the remaining two do not, one can exclude all but the <i>Naja nigricollis</i>. If either of the other substrates react it is respectively either <i>Bitis arietans</i> or <i>Bitis gabonica</i>. <br><br>
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 +
Once the operator selects the continue button the app launches the camera of the operator’s phone. The default camera interface was used to increase user-friendliness thus ensuring that the operator does not have to acquaint themselves with a new interface. <br><br>
 +
 
 +
The pictures are analysed based on RGB histograms. The difference in colours and similarities measures are accounted for and is how either the match or no match is ensured.
 +
 
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<br><br>
 
<br><br>
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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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</p>
 
  
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          <div class="row">
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          <div class="colp-4 rmvpadmarg">
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<figure>
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            <img src="https://static.igem.org/mediawiki/2017/4/4a/T--DTU-Denmark--software-4.jpeg" alt="App results screen" width=270>
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<figcaption>Figure 4: The final screen with results and a link to the database.</figcaption>
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</figure>
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          </div>
  
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          <div class="colp-6 rmvpadmarg">
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            <p><br>The last screen displays the results. We aimed to make the results screen as simple as possible. The operator can instantly see the detected venom, if there is one. An elaborated 1x3 matrix-table shows the operator the substrates and the relative amount of color, if they are interested in the results or wish to double check them. The only other option apart from closing results is <a href="http://apps.who.int/bloodproducts/snakeantivenoms/database/">clicking</a> to go to WHO’s venomous snakes and antivenoms search interface. This was advised by Gernot J. Abel, the science manager at Novozymes Discovery and UNICEF team representative. <br><br>
 +
The database’s search is useful in exploring the global distributions of venomous snake species. The operator can access information on antivenom products and their manufacturers. The operator can search by region, subregion, country, territory or other geographical areas. It is also possible to search for a specific snake, like the <i>Naja nigricollis</i> and go directly to that entry. The database also has Information on antivenoms and their manufacturers [1].
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            </p>
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          </div>
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          </div>
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          <h1 id="ref" class="bottomborder">References</h1>
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          <p><font size="1">
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          [1] WHO (2017). <a href="http://apps.who.int/bloodproducts/snakeantivenoms/database/">Venomous snakes distribution and species risk categories</a></font></p>
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<h5> Inspiration </h5>
 
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<p>
 
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Here are a few examples from previous teams:
 
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</p>
 
 
<ul>
 
<ul>
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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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<li  class="rightnavbarbtn">
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<a href="#app">The SV <br>Detector App</a>
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</li>
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<li  class="rightnavbarbtn">
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<a href="#ref">References</a>
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</li>
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</ul>
 
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                    <span>DTU BIOBUILDERS</span><br />
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                    <span>DENMARK</span><br />
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                    <span>DTU - SØLTOFTS PLADS, BYGN. 221/006</span><br />
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Latest revision as of 00:15, 2 November 2017

The SV Detector App

App in use
Figure 1: The app on an Android phone (Sony M4A).

The SV Detector app was developed to work with the spectrophotometer. The purpose of the spectrophotometer was to quantify the results by creating a controlled uniform environment for every test. The app is the spectrophotometer’s brain – the idea was to create a simple app so that even operators with little specialized knowledge of snake venom could still utilise it. The app is compatible with Android 5.0 meaning that it can run on hardware from 2014 and up.



The SV Detector allows the operator to simply test the incubated samples for the relative amount of colour that is present in every sample.



App front page
Figure 2: The start-up screen of the SV Detector.


The workflow is simple. The app is launched and the operator selects start measuring when ready. The next screen presented shows the instructions. These are extremely simple and numbered to increase the readability as well as eliminate misunderstanding.



App instructions page
Figure 3: The instructions screen of the app.


The instructions are also simplified by calling the three different substrates as 1, 2, and 3. These substrates were chosen from the peptide screening as they enable us to use logic in order to distinguish between the three chosen snakes. One substrate will react with the three venoms, and the other two will react with two different ones. Thus if the first substrate reacts and the remaining two do not, one can exclude all but the Naja nigricollis. If either of the other substrates react it is respectively either Bitis arietans or Bitis gabonica.

Once the operator selects the continue button the app launches the camera of the operator’s phone. The default camera interface was used to increase user-friendliness thus ensuring that the operator does not have to acquaint themselves with a new interface.

The pictures are analysed based on RGB histograms. The difference in colours and similarities measures are accounted for and is how either the match or no match is ensured.



App results screen
Figure 4: The final screen with results and a link to the database.


The last screen displays the results. We aimed to make the results screen as simple as possible. The operator can instantly see the detected venom, if there is one. An elaborated 1x3 matrix-table shows the operator the substrates and the relative amount of color, if they are interested in the results or wish to double check them. The only other option apart from closing results is clicking to go to WHO’s venomous snakes and antivenoms search interface. This was advised by Gernot J. Abel, the science manager at Novozymes Discovery and UNICEF team representative.

The database’s search is useful in exploring the global distributions of venomous snake species. The operator can access information on antivenom products and their manufacturers. The operator can search by region, subregion, country, territory or other geographical areas. It is also possible to search for a specific snake, like the Naja nigricollis and go directly to that entry. The database also has Information on antivenoms and their manufacturers [1].

References

[1] WHO (2017). Venomous snakes distribution and species risk categories

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