Difference between revisions of "Team:Valencia UPV/Practices/Minecraft"

 
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<ul class="actions">
 
<ul class="actions">
 
<li><a href="#scroll1" class="button">Overview</a></li>
 
<li><a href="#scroll1" class="button">Overview</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Minecraft" class="button">SynBiocraft</a></li>
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<li><a href="#scroll2" class="button">DNA blocks</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety" class="button">Safety</a></li>
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<li><a href="#scroll3" class="button">Lab machines</a></li>
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<li><a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations" class="button">Collaboration</a></li>
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<li><a href="#scroll4" class="button">Reaching the next level</a></li>
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</ul>
 
</ul>
 
</section>
 
</section>
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<section class="box">
 
<section class="box">
 
<header class="major">
 
<header class="major">
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<h2>Minecraft<br />
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<h2>Overview<br />
 
</h2><hr>
 
</h2><hr>
 
</header>
 
</header>
−
+
<p><span style="color:red;font-weight:bold;">Breaking news!</span> We have a special webpage just for SynBiocraft! Click <a href="http://personales.alumno.upv.es/albarmou/">here</a> to visit it.</p><br>
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<p>The idea of Minecraft is simple. Create your own constructions using blocks by moving them from one site to another in a 3D virtual world.</p>
+
<p>The idea of Minecraft is simple. Create your own constructions using blocks by moving them from one site to another in a 3D virtual world.This idea has catch more than 34 million players that are moving around, manipulating their space in order to build everything that comes out from their imagination.</p>
  
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<p>This idea has catch more than 34 million players that are moving around, manipulating their space in order to build everything that comes out from their imagination.</p>
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<div><video style="width: 50em;margin-left: 4em;" poster="https://static.igem.org/mediawiki/2015/thumb/7/71/ValenciaUPV_minecraft_LABO.png/800px-ValenciaUPV_minecraft_LABO.png
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" controls>
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<p>We also wanted to create our dream: SynBiocraft mod</p>
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<source src="https://static.igem.org/mediawiki/2015/8/8e/Valencia_UPV_MineVideo.mp4" type='video/mp4'/>
 +
<img border="0" src="https://static.igem.org/mediawiki/2015/thumb/7/71/ValenciaUPV_minecraft_LABO.png/800px-ValenciaUPV_minecraft_LABO.png
 +
" alt="Click to view on Youtube" width="500" height="281.25"></a>
 +
<p style="font-style:italic;color:red;border-style:solid;border-width:2px;border-color:red">Your browser either does not support HTML5 or cannot handle MediaWiki open video formats. Please consider upgrading your browser, installing the appropriate plugin or switching to a Firefox or Chrome install.</p>
 +
</video>
  
 
<p>From an engineering point of view, Minecraft is just a huge 3D matrix where every cell can contain a lot of information. With a little knowledge of java language, the blocks inside the game can be modified; more kinds of blocks can be created, and the most important, more different traits can be implemented to those blocks. This allowed us to implement Synthetic Biology inside the game.</p>
 
<p>From an engineering point of view, Minecraft is just a huge 3D matrix where every cell can contain a lot of information. With a little knowledge of java language, the blocks inside the game can be modified; more kinds of blocks can be created, and the most important, more different traits can be implemented to those blocks. This allowed us to implement Synthetic Biology inside the game.</p>
  
 
<p>DNA pieces, machines, DNA ligation, Petri dishes… this powerful tool provides all possibilities to recreate the practices that can be done in a lab without spending material and without having to wait days in order to carry the experiment out. In fact, ligations always occur, no mistakes, no one opens your termocycler while the ligation is being carried out and plasmid insertions are always done correctly, there are always white colonies.</p>
 
<p>DNA pieces, machines, DNA ligation, Petri dishes… this powerful tool provides all possibilities to recreate the practices that can be done in a lab without spending material and without having to wait days in order to carry the experiment out. In fact, ligations always occur, no mistakes, no one opens your termocycler while the ligation is being carried out and plasmid insertions are always done correctly, there are always white colonies.</p>
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+
<div id="scroll2"></div>
 
<p>We implemented:</p>
 
<p>We implemented:</p>
  
 
<p>DNA blocks with the information of the FASTA files.</p>
 
<p>DNA blocks with the information of the FASTA files.</p>
 +
 +
<div style="text-align:center><img src="https://static.igem.org/mediawiki/2015/9/98/ValenciaUPV_minecraf_promoter.png"></div>
 +
<div style="text-align:center><img src="https://static.igem.org/mediawiki/2015/8/8e/VlaenciaUPV_minecraf_CDS.png"></div>
  
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<div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/8/81/Valencia_UPV_PCDSTTU.png ></div>
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<div style="text-align:center><img src="https://static.igem.org/mediawiki/2015/f/fa/ValenciaUPV_minecraft_TER.png"></div>
 +
<div style="text-align:center><img src="https://static.igem.org/mediawiki/2015/7/74/ValenciaUPV_minecraft_TU.png"></div>
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 +
<br/>
 +
 +
<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/2/28/ValenciaUPV_minecraft_BAdDNA.png"></div>
 +
 +
<p>Those transcription units can be joined in the different parts of our project</p>
  
 
<details>
 
<details>
−
<summary class="button fit">Promoters</summary>
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<summary class="button fit">DNA Constructions:</summary> <br/>
 +
 
<div class="clsPadding">
 
<div class="clsPadding">
−
<p>
 
−
<p>35s</p>
 
−
 
−
<p>Etr8</p>
 
−
 
−
<p>Gal4</p>
 
−
 
−
<p>LexA</p>
 
−
 
−
<p>LacI</p>
 
−
 
−
<p>BD1</p>
 
−
 
−
<p>BD2</p>
 
−
 
−
</p><br/>
 
−
</div>
 
−
</details>
 
−
 
−
<details>
 
−
<summary class="button fit">CDSs</summary>
 
−
<div class="clsPadding">
 
−
<p>
 
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<p>EPIF</p>
 
−
 
−
<p>Phy</p>
 
−
 
−
<p>Gal4Kdronpa</p>
 
−
 
−
<p>Ndronpa</p>
 
−
 
−
<p>LexAPIF</p>
 
−
 
−
<p>BD1Kdronpa</p>
 
−
 
−
<p>Recombinasa A</p>
 
−
 
−
<p>LACIPIF</p>
 
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<p>BD2KDronpa</p>
 
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<p>Recombinasa B</p>
 
−
 
−
<p>Azul</p>
 
−
 
−
<p>Amarillo</p>
 
−
 
−
<p>Rojo</p>
 
−
 
−
<p>Verde</p>
 
 
 
−
</p><br/>
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<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/0/06/ValenciaUPV_minecraft_constructions.png"></div>
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</div>
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−
</details>
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−
 
+
−
<details>
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−
<summary class="button fit">Terminator</summary>
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−
<div class="clsPadding">
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−
<p><p>Tnos</p></p><br/>
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−
</div>
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−
</details>
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−
 
+
−
<p>That can be joined in Transcription units (if the construction makes no sense they are transformed in a “BAD DNA block”). For the creation of the TU, it is needed the usage of a termocycler</p>
+
−
 
+
−
<details>
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−
<summary class="button fit">TU</summary>
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−
<div class="clsPadding">
+
−
 
+
−
<p>35s_EPIF_Tnos</p>
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−
 
+
−
<p>35s_Phy_Tnos</p>
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−
 
+
−
<p>35s_Gal4KDronpa_Tnos</p>
+
−
 
+
−
<p>35s_Ndronpa_Tnos</p>
+
−
 
+
−
<p>Etr8_LexPIF_Tnos</p>
+
−
 
+
−
<p>Etr8_BD1KDronpa_Tnos</p>
+
−
 
+
−
<p>Etr8_RecombinasaA_Tnos</p>
+
−
 
+
−
<p>Gal4_LacPIF_Tnos</p>
+
−
 
+
−
<p>Gal4_BD2Kdronpa_Tnos</p>
+
−
 
+
−
<p>Gal4_RecombinasaB_Tnos</p>
+
−
 
+
−
<p>LexA_azul_tnos</p>
+
−
 
+
−
<p>BD1_Amarillo_Tnos</p>
+
−
 
+
−
<p>LacI_Rojo_Tnos</p>
+
−
 
+
−
<p>BD2_Verde_Tnos</p>
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−
 
+
−
<p>Stuffer fragment</p>
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−
</p><br/>
+
−
+
−
</div>
+
−
</details>
+
−
 
+
−
<p style="text-align:center;font-weight:bold">Bad DNA block</b></p>
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−
<div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/0/0e/Valencia_UPV_ConstruccionBadDNA.png ></div>
+
−
 
+
−
<p>Those transcription units can be joined in the different parts of our project</p>
+
−
 
+
−
<details>
+
−
<summary class="button fit">DNA Constructions:</summary>
+
−
<div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/5/50/Valencia_UPV_Construccion.png></div>
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−
<div class="clsPadding">
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−
+
−
<p>Toggle Rojo</p>
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−
 
+
−
<p>Toggle Azul</p>
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−
 
+
−
<p>Producto Toggle rojo 1</p>
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−
 
+
−
<p>Producto toggle rojo 2</p>
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−
 
+
−
<p>Producto Toggle Rojo</p>
+
−
 
+
−
<p>Producto Toggle azul 1</p>
+
−
 
+
−
<p>Producto Toggle azul 2</p>
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−
 
+
−
<p>Producto Toggle azul</p>
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−
 
+
−
<p>Pack Colores 1</p>
+
−
 
+
−
<p>Pack colores 2</p>
+
−
 
+
−
<p>Pack colores</p>
+
−
 
+
−
<p>Circuito 1</p>
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−
 
+
−
<p>Circuito 2</p>
+
−
 
+
−
<p>Circuito 3</p>
+
−
 
+
−
<p>Circuito semifinal</p>
+
−
 
+
−
<p>Circuito semifinal 2</p>
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−
 
+
−
<div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/4/42/Valencia_UPV_ConstruccionFinal.png></div>
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−
 
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−
<p>Circuito Final Final: This is our final circuit, needs to be electroporated and cell cultured in a Petri dish in order to infiltrate it into a plant.</p>
+
 
 
 
</p><br/>
 
</p><br/>
 
</div>
 
</div>
 
</details>
 
</details>
 +
<br/>
 +
<br/>
 +
<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/9/91/ValenciaUPV_minecraft_finalconstruct.png"></div>
 
 
 +
<div id="scroll3"></div>
 +
<br/>
 +
<br/>
 +
<br/>
 +
 
<p>Lab machines implemented are:</p>
 
<p>Lab machines implemented are:</p>
 
 
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<summary class="button fit">Electroporator at 1440 mW</summary>
 
<summary class="button fit">Electroporator at 1440 mW</summary>
 
<div class="clsPadding">
 
<div class="clsPadding">
−
<p>This is the intensity needed in order to insert plasmids in <i><i>Agrobacterium</i> tumefaciens</i>.</p>
+
<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/8/82/ValenciaUPV_minecraft_ELECTROPORATOR.png"></div>
−
<img src=https://static.igem.org/mediawiki/2015/0/06/Valencia_UPV_Electroporator.png >
+
 
</div>
 
</div>
 
</details>
 
</details>
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<summary class="button fit">BioBricks termocycler</summary>
 
<summary class="button fit">BioBricks termocycler</summary>
 
<div class="clsPadding">
 
<div class="clsPadding">
−
<p> Standard for iGEM DNA assembly. It allows binary joining in the DNA.</p>
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<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/6/6d/ValenciaUPV_minecraft_BIOBRICK.png"></div>
−
<img src=https://static.igem.org/mediawiki/2015/9/9b/Valencia_UPV_BioBricks.png >
+
 
</div>
 
</div>
 
</details>
 
</details>
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<summary class="button fit">Golden Gate termocycler</summary>
 
<summary class="button fit">Golden Gate termocycler</summary>
 
<div class="clsPadding">
 
<div class="clsPadding">
−
<p> Standard for DNA assembly in plants. It allows joining promoter, CDS and terminator.</p>
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<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/6/6c/ValenciaUPV_minecraft_GOLDENGATE.png"></div>
−
<img src=https://static.igem.org/mediawiki/2015/b/b1/Valencia_UPV_GoldenGate.png >
+
 
</div>
 
</div>
 
</details>
 
</details>
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<summary class="button fit">Golden Braid termocycler</summary>
 
<summary class="button fit">Golden Braid termocycler</summary>
 
<div class="clsPadding">
 
<div class="clsPadding">
−
<p> Standard for DNA assembly in plants. It allows the union of transcription units and constructions. </p>
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<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/2/26/ValenciaUPV_minecraft_GOLDENBRAID.png"></div>
−
<img src=https://static.igem.org/mediawiki/2015/b/ba/Valencia_UPV_GoldenBraid.png >
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</div>
 
</div>
 
</details>
 
</details>
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<div class="clsPadding">
 
<div class="clsPadding">
 
<p> And do not forget the Petri dishes! If you have done it correctly and the piece of DNA is electroporated, you will obtain white colonies that can be taken with a syringe and inserted into one of our plants in order to create a light sensitive GMO. By using our light sticks, it will change to one color or another. </p>
 
<p> And do not forget the Petri dishes! If you have done it correctly and the piece of DNA is electroporated, you will obtain white colonies that can be taken with a syringe and inserted into one of our plants in order to create a light sensitive GMO. By using our light sticks, it will change to one color or another. </p>
−
<img src=https://static.igem.org/mediawiki/2015/e/e4/Valencia_UPV_PlacasPetri.png >
+
<div style="text-align:center"><img src=https://static.igem.org/mediawiki/2015/e/e4/Valencia_UPV_PlacasPetri.png ></div>
 
</div>
 
</div>
 
</details>
 
</details>
 +
<br/>
 +
<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2015/thumb/1/11/ValenciaUPV_minecraft_CPI.png/800px-ValenciaUPV_minecraft_CPI.png
 +
"></div>
 
 
−
<div style="text-align:center"><img style="width: 35em;" src=https://static.igem.org/mediawiki/2015/e/ea/Valencia_UPV_Flowers.png ></div>
 
−
 
 
<p>And it does not stop there!</p>
 
<p>And it does not stop there!</p>
−
 
+
<div id="scroll4"></div>
 
<p>We have also implemented Cholerae in Minecraft, and the only method to obtain the vaccine is by creating the green flower. </p>
 
<p>We have also implemented Cholerae in Minecraft, and the only method to obtain the vaccine is by creating the green flower. </p>
  
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<ul class="actions" style="text-align:right">
 
<ul class="actions" style="text-align:right">
−
<li><a href="scroll1" class="button alt">Safety</a></li>
+
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Practices/Safety" class="button alt">Safety</a></li>
−
<li><a href="scroll3" class="button alt">Collaborations</a></li>
+
<li><a href="https://2015.igem.org/Team:Valencia_UPV/Collaborations" class="button alt">Collaborations</a></li>
 
</ul>
 
</ul>
 
 

Latest revision as of 09:35, 20 November 2015

Valencia UPV iGEM 2015

Overview

Breaking news! We have a special webpage just for SynBiocraft! Click here to visit it.


The idea of Minecraft is simple. Create your own constructions using blocks by moving them from one site to another in a 3D virtual world.This idea has catch more than 34 million players that are moving around, manipulating their space in order to build everything that comes out from their imagination.

From an engineering point of view, Minecraft is just a huge 3D matrix where every cell can contain a lot of information. With a little knowledge of java language, the blocks inside the game can be modified; more kinds of blocks can be created, and the most important, more different traits can be implemented to those blocks. This allowed us to implement Synthetic Biology inside the game.

DNA pieces, machines, DNA ligation, Petri dishes… this powerful tool provides all possibilities to recreate the practices that can be done in a lab without spending material and without having to wait days in order to carry the experiment out. In fact, ligations always occur, no mistakes, no one opens your termocycler while the ligation is being carried out and plasmid insertions are always done correctly, there are always white colonies.

We implemented:

DNA blocks with the information of the FASTA files.


Those transcription units can be joined in the different parts of our project

DNA Constructions:







Lab machines implemented are:

Electroporator at 1440 mW
BioBricks termocycler
Golden Gate termocycler
Golden Braid termocycler
Petri dishes

And do not forget the Petri dishes! If you have done it correctly and the piece of DNA is electroporated, you will obtain white colonies that can be taken with a syringe and inserted into one of our plants in order to create a light sensitive GMO. By using our light sticks, it will change to one color or another.


And it does not stop there!

We have also implemented Cholerae in Minecraft, and the only method to obtain the vaccine is by creating the green flower.

Will you survive this new challenge?

Reaching the next level

Implementing our project inside the game has not been easy, but it has taught us that Minecraft is more powerful than we expected. So, why should we stop there?

By using a DNA database and BioBricks assembly method, we have reached the next level, we have recreated a represilator that was created by Elowitz & Liebler in 2000 and also the SEXY Plant project (Valencia_UPV 2014). But this can be expanded to all BioBricks database. We expect that, in the future, you will be able to replicate all the projects that have already been done in iGEM competition.