Team:Aalto-Helsinki/Journal

From 2014.igem.org

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       <li>Chemical safety: working with different chemicals and how to dispose of them
       <li>Chemical safety: working with different chemicals and how to dispose of them
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       <li>GMO safety: putting all waste that has been in contact with bacteria (living or dead) to bacterial waste, aseptical working methods
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       <li>GMO safety: putting all waste that has been in contact with bacteria (living or dead) to bacterial waste, aseptic working methods
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         <p>Perfecting everything and admiring our wiki which is totally done at this point. All's well, we can just relax before the Jamboree.</p>
         <p>Perfecting everything and admiring our wiki which is totally done at this point. All's well, we can just relax before the Jamboree.</p>
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        <h4>Our New Biobricks Were Sequenced</h4>
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        <p><small class="text-muted"> 9.10.2014</small></p>
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        <p>We didn’t have time to sequence our new Biobricks before sending them to iGEM HQ but we wanted to sequence them anyway, just in case. The sequences were confirmed to be ok and we were really happy about this since we did have some doubts about synthesizing parts with PCR on our own.</p>
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        <h4>Our Biobricks Started Their Journey to Boston</h4>
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        <p><small class="text-muted"> 6.10.2014</small></p>
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        <p>Finally we got our own Biobricks ready to be sent to iGEM HQ. We put them in a box and wished them a safe journey.</p>
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      <img src="https://static.igem.org/mediawiki/2014/b/b3/AaltoHelsinki_shipment.JPG" class="img-responsive">
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         <p>Testing the first DNA constructs.</p>
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         <p>Testing the first DNA constructs. The results seemed promising.</p>
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         <p>We plan to go to an escape the room thing, but when all the suitable times are booked, Minttu takes us bowling instead.</p>
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         <p>We planned to go to an escape the room thing, but when all the suitable times are booked, Minttu took us bowling instead.</p>
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        <h4>The LEDrig Is Ready!</h4>
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        <p><small class="text-muted"> 22.8.2014</small></p>
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        <p>It’s like our bacteria got their own personalized disco!</p>
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        <p>KUVA TULOSSA!</p>
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        <h4>A Microscope That Can Almost Make You a Cup of Coffee</h4>
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        <p><small class="text-muted"> 21.8.2014</small></p>
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        <p>We got to try a super cool programmable microscope (worth 120 000€!). We wanted to see if our cells produced any GFP but unfortunately it turned out that all our cells were already dead so there was no GFP to be detected.</p>
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      <img src="https://static.igem.org/mediawiki/2014/3/3f/AaltoHelsinki_supermicroscope.jpg" class="img-responsive">
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         <p> We go visit the observatorium during the Night of the Arts event in Helsinki. There's also massive soap bubbles and a man with a whole band setup in a baby carriage.</p>
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         <p> We went to visit the observatorium during the Night of the Arts event in Helsinki. There were also massive soap bubbles and a man with a whole band setup in a baby carriage.</p>
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         <p> The next day we go back to playing pinball and Crash Team Racing because it was so much fun last week.</p>
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         <p> The next day we went back to playing pinball and Crash Team Racing because it was so much fun last week.</p>
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         <h4>Testing Starts!</h4>
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         <h4>Testing Started!</h4>
         <p><small class="text-muted">  19.8.2014</small></p>
         <p><small class="text-muted">  19.8.2014</small></p>
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         <p>We build the first part of the prototype and start testing!</p>
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         <p>We built the first part of the prototype and started testing!</p>
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         <h4>Our Synthetized Genes Arrive!</h4>
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         <h4>Our Synthetized Genes Arrived!</h4>
         <p><small class="text-muted">  18.8.2014</small></p>
         <p><small class="text-muted">  18.8.2014</small></p>
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         <p>After a long while, our genes finally arrive. Now we can take them and other parts we've assembled and the whole genetically engineered machine together.</p>
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         <p>After a long while, our genes finally arrived. Now we could take them and other parts we had assembled and put the whole genetically engineered machine together.</p>
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         <p>We meet the event manager and event organizer of Heureka and come up with a synthetic biology weekend workshop we could organize in Spring.</p>
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         <p>We met the event manager and event organizer of Heureka and came up with a synthetic biology weekend workshop we could organize in Spring.</p>
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         <p>They were very excited about us and everything we had to show and tell. They said that this is a perfect match from them and all the simulations, games, pictures fit perfectly into the workshop.</p>
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         <p>They were very excited about us and everything we had to show and tell. They said that this is a perfect match for them and all the simulations, games, pictures fit perfectly into the workshop.</p>
         <p>We hope to inspire young people to study synthetic biology in the future and let the older people know it exists. This will also be a perfect opportunity for the next year's iGEM Team to get involved and organize something together.</p>
         <p>We hope to inspire young people to study synthetic biology in the future and let the older people know it exists. This will also be a perfect opportunity for the next year's iGEM Team to get involved and organize something together.</p>
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         <p>Lassi takes us to play pinball. It's surprisingly fun. We play a ton of Crash Team Racing too.</p>
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         <p>Lassi took us to play pinball. It was surprisingly fun. We played a ton of Crash Team Racing too.</p>
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        <h4>Early Version of the LEDrig is ready!</h4>
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        <p><small class="text-muted"> 14.8.2014</small></p>
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        <p>Pietu had been busy making the LEDrig inspired by Tabor Lab. This is what the early version looked like. The LEDrig would be the tool to control our light sensitive bacteria.</p>
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      <img src="https://static.igem.org/mediawiki/2014/7/73/AaltoHelsinki_earlyLEDrig.jpg" class="img-responsive">
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         <h4>HYBER Takes Interest In Us!</h4>
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         <h4>HYBER Took Interest In Us!</h4>
         <p><small class="text-muted"> 8.8.2014</small></p>
         <p><small class="text-muted"> 8.8.2014</small></p>
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         <p>We meet with The Academy of Finland's Center of Excellence HYBER 2014-2019. They want us to talk in their conference and support us. </p>
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         <p>We met with The Academy of Finland's Center of Excellence HYBER 2014-2019. They wanted us to talk in their conference and support us. </p>
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         <p>In the evening Oskari takes us to play laser tag! He is way better at it than anyone else.</p>
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         <p>In the evening Oskari took us to play laser tag! He was way better at it than anyone else.</p>
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         <h4>The First Sequencing Results Arrive!</h4>
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         <h4>The First Sequencing Results Arrived!</h4>
         <p><small class="text-muted"> 5.8.2014</small></p>
         <p><small class="text-muted"> 5.8.2014</small></p>
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         <p>We get our first sequencing results that are in confusing .ab1-files. Then it turns out that Geneious makes analysing them incredibly easy. Most of the sequences look good, some not so much.</p>
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         <p>We got our first sequencing results that were in confusing .ab1-files. Then it turned out that Geneious makes analysing them incredibly easy. Most of the sequences looked good, some not so much.</p>
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         <p>Instead of staying in our HQ and eating in the cafeteria next to it, Laura takes us to eat fancy sushi. It's delicious and fun.</p>
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         <p>Instead of staying in our HQ and eating in the cafeteria next to it, Laura took us to eat fancy sushi. It was delicious and fun.</p>
         <p>SUSHIKUVA?</p>
         <p>SUSHIKUVA?</p>
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         <p>We build the sequences to synthetize from scratch. They include the lambda repressor <em>O</em><sub>R</sub> sites that we designed. We find out that the synthetisizing costs the same for 0-1000 nucleotides, so we include a few surrounding BioBricks to save on lab time. (The <em>O</em><sub>R</sub> sites are fairly small.)</p>
+
         <p>We built the sequences to synthetize from scratch. They included the lambda repressor <em>O</em><sub>R</sub> sites that we designed. We found out that the synthetisizing costs the same for 0-1000 nucleotides, so we include a few surrounding BioBricks to save on lab time. (The <em>O</em><sub>R</sub> sites are fairly small.)</p>
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         <h4>The First Ligations Are Sent to Be Sequenced</h4>
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         <h4>The First Ligations Were Sent to Be Sequenced</h4>
         <p><small class="text-muted"> 28.7.2014</small></p>
         <p><small class="text-muted"> 28.7.2014</small></p>
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         <p>We have a number of ligations ready for assembling and it turns out there's a sequencing place like 5 kilometers away.</p>
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         <p>We had a number of ligations ready for assembling and it turned out there was a sequencing lab like 5 kilometers away.</p>
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         <p>We seal 16 samples into tubes and send them off. We are left eagerly waiting to see if the work this far has succeeded.</p>
+
         <p>We sealed 16 samples into tubes and sent them off. We were left eagerly awaiting to see if the work this far had succeeded.</p>
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         <p> We meet Tania, an ex-iGEMer from the <a href=""> one 2012 Amsterdam team.</a> It's a great meeting and we finally get some validation that we're doing some things right.</p>
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         <p> We meet Tania, an ex-iGEMer from the <a href=""> one 2012 Amsterdam team.</a> It was a great meeting and we finally got some validation that we're doing some things right.</p>
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         <p>In the evening Martina takes us geocaching! It is amazing what can be hidden in completely plain sight.</p>
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         <p>In the evening Martina took us geocaching! It is amazing what can be hidden in completely plain sight.</p>
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         <p>We present our idea to hundreds of people and hold a booth for 6 hours.</p>
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         <p>We presented our idea to hundreds of people and held a booth for 6 hours.</p>
         <img src="https://static.igem.org/mediawiki/2014/0/06/Aalto_Helsinki_Demoday.jpg" class="img-responsive">
         <img src="https://static.igem.org/mediawiki/2014/0/06/Aalto_Helsinki_Demoday.jpg" class="img-responsive">
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         <p>In the evening Mikko takes us to watch The Skin I Live In, Scott Pilgrim vs. The World and The Grand Budapest Hotel.</p>
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         <p>In the evening Mikko took us to watch The Skin I Live In, Scott Pilgrim vs. The World and The Grand Budapest Hotel.</p>
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         <h4>The Gene Circuit Is Finished</h4>
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         <h4>The Gene Circuit Was Finished</h4>
         <p><small class="text-muted"> 14.7.2014</small></p>
         <p><small class="text-muted"> 14.7.2014</small></p>
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         <p>We have the lambda repressor figured out and integrated into our system. We start planning for the parts to be synthesized.</p>
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         <p>We had the lambda repressor figured out and integrated into our system. We started planning for the parts to be synthesized.</p>
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         <img src="https://static.igem.org/mediawiki/2014/2/2d/Aalto_Helsinki_Genecircus.jpg" class="img-responsive">
         <img src="https://static.igem.org/mediawiki/2014/2/2d/Aalto_Helsinki_Genecircus.jpg" class="img-responsive">
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         <p>Summer of Startups takes us to visit the Startup people of Tallinn. We decide this is a practice trip for Boston, so we planned to have as much fun as possible. It was a great success and an unforgettable experience.</p>
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         <p>Summer of Startups took us to visit the Startup people of Tallinn. We decided this was a practice trip for Boston, so we planned to have as much fun as possible. It was a great success and an unforgettable experience.</p>
       </div>
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       <img src="https://static.igem.org/mediawiki/2014/f/f9/Aalto_Helsinki_Tallinna.jpg" class="img-responsive">
       <img src="https://static.igem.org/mediawiki/2014/f/f9/Aalto_Helsinki_Tallinna.jpg" class="img-responsive">
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         <p> We find out that the lambda repressor system would be perfect for our three-way switch idea. We figure out how it works and how to include it in our gene circuit.</p>
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         <p> We found out that the lambda repressor system would be perfect for our three-way switch idea. We figured out how it worked and how to include it in our gene circuit.</p>
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         <h4>The "Fun Master" System Begins</h4>
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         <h4>The "Fun Master" System Began</h4>
         <p><small class="text-muted"> 4.7.2014</small></p>
         <p><small class="text-muted"> 4.7.2014</small></p>
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         <p>We decided that we should do something fun every week as a group that has nothing to do with iGEM. Every team member has their own week to plan an activity and pull the team to the mandatory weekly having-fun moment.</p>
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         <p>We decided that as a group we should do something fun every week that has nothing to do with iGEM. Every team member had their own week to plan an activity and pull the team to the mandatory weekly having-fun moment.</p>
         <p>So, Otto surprised us with a fruit juicer and a ton of fresh fruit. We spent the early morning happily drinking smoothies while working intensely on our project.</p>
         <p>So, Otto surprised us with a fruit juicer and a ton of fresh fruit. We spent the early morning happily drinking smoothies while working intensely on our project.</p>
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         <h4>Brian Is Born</h4>
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         <h4>Brian Was Born</h4>
         <p><small class="text-muted">1.7.2014, 2.7.2014</small></p>
         <p><small class="text-muted">1.7.2014, 2.7.2014</small></p>
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         <p>We get the idea of explaining synthetic biology as turning bacteria into superheroes from a meeting with ???. We start working on a new pitch based on that.</p>
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         <p>We got the idea of explaining synthetic biology as turning bacteria into superheroes from a meeting with ???. We started working on a new pitch based on that.</p>
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         <p>Pietu finishes the pitch the next day and presents it at Summer of Startups. It seems to go over very well. People finally understand what we are doing.</p>
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         <p>Pietu finished the pitch the next day and presented it at Summer of Startups. It seemed to go over very well. People finally understood what we were doing.</p>
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         <p>Our BioBrick Seeker has been mentioned on the official help page for a while. We only noticed it now.</p>
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         <p>Our BioBrick Seeker had been mentioned on the official help page for a while. We only noticed it now.</p>
         <p>We also wrote a small advertisement text for the Community page and got the Seekers featured there.</p>
         <p>We also wrote a small advertisement text for the Community page and got the Seekers featured there.</p>
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         <h4>The First BioBrick Ligation Combo Works</h4>
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         <h4>The First BioBrick Ligation Combo Worked</h4>
         <p><small class="text-muted"> 24.6.2014</small></p>
         <p><small class="text-muted"> 24.6.2014</small></p>
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         <p>We even checked it with a gel.</p>
         <p>We even checked it with a gel.</p>
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        <p>KUVA??</p>
 
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        <img src="https://static.igem.org/mediawiki/2014/c/cd/AaltoHelsinki_ligationgel.jpg" class="img-responsive">
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        <h4>We Had Visitors in the Lab</h4>
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        <p><small class="text-muted"> 23.6.2014</small></p>
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        <p>The Summer of Startups people came to visit our lab and see what we’re actually doing.</p>
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        <img src="https://static.igem.org/mediawiki/2014/0/0a/AaltoHelsinki_SoSLab.JPG" class="img-responsive">
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 +
        <h4>Backbones</h4>
 +
        <p><small class="text-muted"> 13.6.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We found out that the Registry provides BBa_J04450 parts in different backbones, which could be used as destination plasmids. The red fluorescent protein insert makes it easier to screen out the background.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/7/7f/AaltoHelsinki_RFPbackbone.JPG" class="img-responsive">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Gradient PCR</h4>
 +
        <p><small class="text-muted"> 12.6.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We kept getting weird results from PCR so we tried to solve the issue by doing a gradient PCR with different annealing temperatures. Seemed like 55 °C would be the answer to our problems.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/2/27/AaltoHelsinki_gradientPCR.jpg" class="img-responsive">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>First Colony PCR - no succesful ligations</h4>
 +
        <p><small class="text-muted"> 11.6.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We made our first colony PCR to test if the ligations seemed right. Unfortunately they didn’t. We decided to make linearized plasmid backbones to increase the efficiency.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/3/31/AaltoHelsinki_firstPCR.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We're trying to advertise ourselves and get some kind of financial help and support for this project. It feels really difficult and time consuming. We also took some new pictures, a new group photo, for example.</p>
+
         <p>We were trying to advertise ourselves and get some kind of financial help and support for this project. It felt really difficult and time consuming. We also took some new pictures, a new group photo, for example.</p>
         <p><img src="http://aaltohelsinki.com/img/igem_aalto_helsinki_2014.jpg" class="img-responsive"></img></p>
         <p><img src="http://aaltohelsinki.com/img/igem_aalto_helsinki_2014.jpg" class="img-responsive"></img></p>
       </div>
       </div>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Trouble in the Lab</h4>
         <h4>Trouble in the Lab</h4>
-
         <p><small class="text-muted">  8.6.2014</small></p>
+
         <p><small class="text-muted">  9.6.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>The backbones don't seem to be working right and the negative control keeps growing. Not good.</p>
+
         <p>The backbones did't seem to be working right and the negative control kept growing. Not good.</p>
 +
        <p>The reason seemed to be that we hadn’t gel purified the backbone and it kept religating with itself.</p>
       </div>
       </div>
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>The Ligation Calculator</h4>
 +
        <p><small class="text-muted"> 5.6.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We made a ligation calculator to help us estimate the amounts of different plasmids to be digested. The calculator calculates how many microliters of miniprepped plasmid is needed to be digested in order to pipet 4 ul of each digestion mix to the ligation mix. Insert-plasmid ratio as well as vector mass fields could be changed if needed. Taking these two variables into account, the appropriate molar amount and then the mass amount of inserts are calculated using the information of their lengths. This tiny little excel tool really saved time in the lab during the summer.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/4/4d/AaltoHelsinki_ligationcalculator.png" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>BioBrick Seeker spreading</h4>
+
         <h4>BioBrick Seeker Spreading</h4>
         <p><small class="text-muted">  2.6.2014</small></p>
         <p><small class="text-muted">  2.6.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We've received tons of mentions on Twitter. People really seem to like the tool.</p>
+
         <p>We've received tons of mentions on Twitter. People really seemed to like the tool.</p>
       </div>
       </div>
     </div>
     </div>
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       </div>
       </div>
     </div>
     </div>
 +
  </li>
   <li class="entry timeline-inverted">
   <li class="entry timeline-inverted">
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>The First BioBrick Transformation in Finland</h4>
         <h4>The First BioBrick Transformation in Finland</h4>
-
         <p><small class="text-muted">26.5.2014</small></p>
+
         <p><small class="text-muted"> 27.5.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>Cooool. Here it is!</p>
+
         <p>Cooool. There it was!</p>
         <img src="https://static.igem.org/mediawiki/2014/3/30/Aalto_Helsinki_First_Transformation.jpg" class="img-responsive">
         <img src="https://static.igem.org/mediawiki/2014/3/30/Aalto_Helsinki_First_Transformation.jpg" class="img-responsive">
       </div>
       </div>
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>The First Biobrick Out of the Plate</h4>
 +
        <p><small class="text-muted"> 26.5.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We got our hands on the Biobrick plates and took the first piece out. This is where it all started.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/2/2f/Aalto_Helsinki_Distribkit.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>Website Is Done</h4>
+
         <h4>Website Was Done</h4>
         <p><small class="text-muted"> 23.5.2014</small></p>
         <p><small class="text-muted"> 23.5.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>This time it does actually look cool! The actual website might still be available on <a href="http://aaltohelsinki.com/index_en.html">http://aaltohelsinki.com/index_en.html</a>: check it out!</p>
+
         <p>This time it did actually look cool! The actual website might still be available on <a href="http://aaltohelsinki.com/index_en.html">http://aaltohelsinki.com/index_en.html</a>: check it out!</p>
       </div>
       </div>
     </div>
     </div>
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     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>Lab Kicks Off!</h4>
+
         <h4>Lab Kicked Off!</h4>
         <p><small class="text-muted">  20.5.2014</small></p>
         <p><small class="text-muted">  20.5.2014</small></p>
       </div>
       </div>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We get one desk from the laboratory. and there's still someone else's stuff on it, but it's ours and we are going to do amazing things there.</p>
+
         <p>We got one desk from the laboratory. and there was still someone else's stuff on it, but it was ours and we were going to do amazing things there.</p>
       </div>
       </div>
     </div>
     </div>
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     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>The iGEM 2014 Distribution Kit Arrives</h4>
+
         <h4>The iGEM 2014 Distribution Kit Arrived</h4>
         <p><small class="text-muted"> 9.5.2014</small></p>
         <p><small class="text-muted"> 9.5.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>The competition starts to feel real.</p>
+
         <p>We got the eagerly awaited box from iGEM and the competition started to feel real. In the box we found plates full of Biobricks and other cool stuff like these pins!</p>
       </div>
       </div>
-
       <img src="https://static.igem.org/mediawiki/2014/2/2f/Aalto_Helsinki_Distribkit.jpg" class="img-responsive">
+
       <img src="https://static.igem.org/mediawiki/2014/0/05/AaltoHelsinki_pinssi.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We meet a few times to go over what we will say to the Summer of Startups panel, so that they will accept us to the program. This culminates on the 28th, when we have the interview. Our team leader tries to attend through Skype, but the panel doesn't like it. We manage to pull through anyway, and the panel is very excited about us at the end.</p>
+
         <p>We met a few times to go over what we would say to the Summer of Startups panel, so that they would accept us to the program. This culminated on the 28th, when we had the interview. Our team leader tried to attend through Skype, but the panel didn't like it. We managed to pull through anyway, and the panel was very excited about us at the end.</p>
         <p>They accepted us in the program.</p>
         <p>They accepted us in the program.</p>
       </div>
       </div>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We presented our initial ideas to our advisor, Markus, in preparation for the expert meet. We discussed what direction to go and what kind of idea to pick.</p>
+
         <p>We presented our initial ideas to our advisor, Markus, in preparation for the expert meeting. We discussed what direction to go and what kind of an idea to pick.</p>
       </div>
       </div>
     </div>
     </div>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>Oskari is in the first job interview in his life, as the interviewer. He holds 19 more interviews during the week. Nine people are chosen to be in the final team.</p>
+
         <p>Oskari was in the first job interview in his life, as the interviewer. He hoeld 19 more interviews during the week. Nine people were chosen to be in the final team.</p>
       </div>
       </div>
     </div>
     </div>
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         </div>
         </div>
         <div class="tl-body">
         <div class="tl-body">
-
           <p>It seems like the universities are into the idea.</p>
+
           <p>It seemed like the universities were into the idea.</p>
         </div>
         </div>
       </div>
       </div>
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     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>The Idea of a Finnish iGEM Team Forms</h4>
+
         <h4>The Idea of a Finnish iGEM Team Was Formed</h4>
         <p><small class="text-muted"></i>28.8.2013</small></p>
         <p><small class="text-muted"></i>28.8.2013</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>First e-mails about the idea are sent.</p>
+
         <p>First e-mails about the idea were sent.</p>
       </div>
       </div>
     </div>
     </div>

Revision as of 00:40, 11 October 2014

Journal

The summer was full of exciting new experiences and a lot of hard work. You can browse through our sweat and tears here.

There and Back Again
an iGEM team's tale by Aalto-Helsinki

We worked hard but it all paid off. We had fun, we made new friends. We did something new, we learned something new. It was an amazing journey.

We also have more details to share, if you have the interest to read it all (pdf files inc)!

A Scientist discovers that which exists; an Engineer creates that which never was. Theodore von Karmen

Safety

General Safety Matters

All members of our team, who work in the lab, have had a safety training as a part of their studies. The training covered the following topics:

  • Personal protective wear: safety goggles, lab coats and gloves
  • General safety: acting in case of an accident, where to find emergency showers and fire extinguishers, understanding safety labels
  • Chemical safety: working with different chemicals and how to dispose of them
  • GMO safety: putting all waste that has been in contact with bacteria (living or dead) to bacterial waste, aseptic working methods

In our iGEM work we have only worked with non-toxic E. coli (K12 derivatives) and all the protein coding sequences that we have used in our project are non-hazardous. We did not create new protein coding sequences but instead we used sequences that are already available as Biobricks.

Our Laboratory

We got to work in the Bioprocess Technology lab of Aalto University. We had our own table and we got to use all the instruments in the department. We also did some measurements in the labs of VTT Technical Research Centre of Finland.

Here are some pictures of our journey. Enjoy!


Lab Close-Ups

Our Office

Vuori HUB <3

Timeline

Being the first team in Finland, we wanted to make sure that we documented everything we did as closely as possible. Below you can find a nice pictured timeline with the biggest events and other fun things we did during the project.

We borrowed a convention from the software development framework, Scrum. Every day, all the team members answered three question: "What did you do yesterday?", "What will you do today?" and "What is stopping you from doing that?". We wrote the answers down in our online team tool and made a detailed description of every single working day during the summer. So if you really really want to read exactly what we did, here's 30 pages of text for you to check out:

  • October 2014
  • Jamboree Bootcamp at Mikkeli Summer Cottage

    25.10.2014

    Perfecting everything and admiring our wiki which is totally done at this point. All's well, we can just relax before the Jamboree.

  • Our New Biobricks Were Sequenced

    9.10.2014

    We didn’t have time to sequence our new Biobricks before sending them to iGEM HQ but we wanted to sequence them anyway, just in case. The sequences were confirmed to be ok and we were really happy about this since we did have some doubts about synthesizing parts with PCR on our own.

  • Our Biobricks Started Their Journey to Boston

    6.10.2014

    Finally we got our own Biobricks ready to be sent to iGEM HQ. We put them in a box and wished them a safe journey.

  • September 2014
  • August 2014
  • Testing the DNA Constructs

    28.8.2014

    Testing the first DNA constructs. The results seemed promising.

  • Bowling

    26.8.2014

    We planned to go to an escape the room thing, but when all the suitable times are booked, Minttu took us bowling instead.

  • The LEDrig Is Ready!

    22.8.2014

    It’s like our bacteria got their own personalized disco!

    KUVA TULOSSA!

  • A Microscope That Can Almost Make You a Cup of Coffee

    21.8.2014

    We got to try a super cool programmable microscope (worth 120 000€!). We wanted to see if our cells produced any GFP but unfortunately it turned out that all our cells were already dead so there was no GFP to be detected.

  • The Night of the Arts in Helsinki and More Pinball

    21.8.2014, 22.8.2014

    We went to visit the observatorium during the Night of the Arts event in Helsinki. There were also massive soap bubbles and a man with a whole band setup in a baby carriage.

    The next day we went back to playing pinball and Crash Team Racing because it was so much fun last week.

  • Testing Started!

    19.8.2014

    We built the first part of the prototype and started testing!

  • Our Synthetized Genes Arrived!

    18.8.2014

    After a long while, our genes finally arrived. Now we could take them and other parts we had assembled and put the whole genetically engineered machine together.

  • Meeting at Heureka Science Center!

    18.8.2014

    We met the event manager and event organizer of Heureka and came up with a synthetic biology weekend workshop we could organize in Spring.

    They were very excited about us and everything we had to show and tell. They said that this is a perfect match for them and all the simulations, games, pictures fit perfectly into the workshop.

    We hope to inspire young people to study synthetic biology in the future and let the older people know it exists. This will also be a perfect opportunity for the next year's iGEM Team to get involved and organize something together.

  • Pinball Night

    14.8.2014

    Lassi took us to play pinball. It was surprisingly fun. We played a ton of Crash Team Racing too.

  • Early Version of the LEDrig is ready!

    14.8.2014

    Pietu had been busy making the LEDrig inspired by Tabor Lab. This is what the early version looked like. The LEDrig would be the tool to control our light sensitive bacteria.

  • HYBER Took Interest In Us!

    8.8.2014

    We met with The Academy of Finland's Center of Excellence HYBER 2014-2019. They wanted us to talk in their conference and support us.

    In the evening Oskari took us to play laser tag! He was way better at it than anyone else.

  • The First Sequencing Results Arrived!

    5.8.2014

    We got our first sequencing results that were in confusing .ab1-files. Then it turned out that Geneious makes analysing them incredibly easy. Most of the sequences looked good, some not so much.

  • Friday Sushi Lunch

    1.8.2014

    Instead of staying in our HQ and eating in the cafeteria next to it, Laura took us to eat fancy sushi. It was delicious and fun.

    SUSHIKUVA?

  • July 2014
  • Building the Synthesizable Sequences

    31.7.2014

    We built the sequences to synthetize from scratch. They included the lambda repressor OR sites that we designed. We found out that the synthetisizing costs the same for 0-1000 nucleotides, so we include a few surrounding BioBricks to save on lab time. (The OR sites are fairly small.)

  • The First Ligations Were Sent to Be Sequenced

    28.7.2014

    We had a number of ligations ready for assembling and it turned out there was a sequencing lab like 5 kilometers away.

    We sealed 16 samples into tubes and sent them off. We were left eagerly awaiting to see if the work this far had succeeded.

  • Meeting with Tania

    22.7.2014

    We meet Tania, an ex-iGEMer from the one 2012 Amsterdam team. It was a great meeting and we finally got some validation that we're doing some things right.

    In the evening Martina took us geocaching! It is amazing what can be hidden in completely plain sight.

  • Demo Day

    15.7.2014

    We presented our idea to hundreds of people and held a booth for 6 hours.

  • A Movie Night with the Team

    14.7.2014

    In the evening Mikko took us to watch The Skin I Live In, Scott Pilgrim vs. The World and The Grand Budapest Hotel.

  • The Gene Circuit Was Finished

    14.7.2014

    We had the lambda repressor figured out and integrated into our system. We started planning for the parts to be synthesized.

  • Summer of Startups Tallinn Trip!

    10-11.7.2014

    Summer of Startups took us to visit the Startup people of Tallinn. We decided this was a practice trip for Boston, so we planned to have as much fun as possible. It was a great success and an unforgettable experience.

  • Extensive Research on the Lambda Repressor

    8.7.2014

    We found out that the lambda repressor system would be perfect for our three-way switch idea. We figured out how it worked and how to include it in our gene circuit.

  • The "Fun Master" System Began

    4.7.2014

    We decided that as a group we should do something fun every week that has nothing to do with iGEM. Every team member had their own week to plan an activity and pull the team to the mandatory weekly having-fun moment.

    So, Otto surprised us with a fruit juicer and a ton of fresh fruit. We spent the early morning happily drinking smoothies while working intensely on our project.

  • The First Team Member Chimera

    2.7.2014

    Because chimera is a term both in gene techonology and mythology, Laura decided (and others immediately agreed) that drawing a chimera for each member would be a cool idea. Everyone could decide three animals and a chimera would be drawn based on those.

    To read more about the chimeras, head to "chimeras" section on the Outreach page.

  • Brian Was Born

    1.7.2014, 2.7.2014

    We got the idea of explaining synthetic biology as turning bacteria into superheroes from a meeting with ???. We started working on a new pitch based on that.

    Pietu finished the pitch the next day and presented it at Summer of Startups. It seemed to go over very well. People finally understood what we were doing.

  • June 2014
  • BioBrick Seeker on the iGEM Help and Community Pages

    25.6.2014

    Our BioBrick Seeker had been mentioned on the official help page for a while. We only noticed it now.

    We also wrote a small advertisement text for the Community page and got the Seekers featured there.

  • The First BioBrick Ligation Combo Worked

    24.6.2014

    We even checked it with a gel.

  • We Had Visitors in the Lab

    23.6.2014

    The Summer of Startups people came to visit our lab and see what we’re actually doing.

  • Backbones

    13.6.2014

    We found out that the Registry provides BBa_J04450 parts in different backbones, which could be used as destination plasmids. The red fluorescent protein insert makes it easier to screen out the background.

  • Gradient PCR

    12.6.2014

    We kept getting weird results from PCR so we tried to solve the issue by doing a gradient PCR with different annealing temperatures. Seemed like 55 °C would be the answer to our problems.

  • First Colony PCR - no succesful ligations

    11.6.2014

    We made our first colony PCR to test if the ligations seemed right. Unfortunately they didn’t. We decided to make linearized plasmid backbones to increase the efficiency.

  • Writing Sponsorship Applications

    10.6.2014

    We were trying to advertise ourselves and get some kind of financial help and support for this project. It felt really difficult and time consuming. We also took some new pictures, a new group photo, for example.

  • Trouble in the Lab

    9.6.2014

    The backbones did't seem to be working right and the negative control kept growing. Not good.

    The reason seemed to be that we hadn’t gel purified the backbone and it kept religating with itself.

  • The Ligation Calculator

    5.6.2014

    We made a ligation calculator to help us estimate the amounts of different plasmids to be digested. The calculator calculates how many microliters of miniprepped plasmid is needed to be digested in order to pipet 4 ul of each digestion mix to the ligation mix. Insert-plasmid ratio as well as vector mass fields could be changed if needed. Taking these two variables into account, the appropriate molar amount and then the mass amount of inserts are calculated using the information of their lengths. This tiny little excel tool really saved time in the lab during the summer.

  • BioBrick Seeker Spreading

    2.6.2014

    We've received tons of mentions on Twitter. People really seemed to like the tool.

  • May 2014
  • Precipitation of the Cell Membranes

    30.5.2014

    This process would be repeated about 50 times during the summer, but this was the first. Video link: http://www.youtube.com/watch?v=TI_EuzNIaPg.

  • The First Version of BioBrick Seeker

    30.5.2014

    It started from the mild inconvenience of searching for BioBricks in the lab. Now we could search through this year's distribution effortlessly. Because it was so useful for us, we decided to share it to others, too.

  • The First BioBrick Transformation in Finland

    27.5.2014

    Cooool. There it was!

  • The First Biobrick Out of the Plate

    26.5.2014

    We got our hands on the Biobrick plates and took the first piece out. This is where it all started.

  • Website Was Done

    23.5.2014

    This time it did actually look cool! The actual website might still be available on http://aaltohelsinki.com/index_en.html: check it out!

  • Lab Kicked Off!

    20.5.2014

    ...by making plates. Not that mind-blowing, but very important.

  • A Tour in the Lab

    19.5.2014

    We got one desk from the laboratory. and there was still someone else's stuff on it, but it was ours and we were going to do amazing things there.

  • The iGEM 2014 Distribution Kit Arrived

    9.5.2014

    We got the eagerly awaited box from iGEM and the competition started to feel real. In the box we found plates full of Biobricks and other cool stuff like these pins!

  • April 2014
  • Getting Ready for the Summer of Startups

    22.4.2014, 25.4.2014, 28.4.2014

    We met a few times to go over what we would say to the Summer of Startups panel, so that they would accept us to the program. This culminated on the 28th, when we had the interview. Our team leader tried to attend through Skype, but the panel didn't like it. We managed to pull through anyway, and the panel was very excited about us at the end.

    They accepted us in the program.

  • Expert Meeting at Aalto University

    10.4.2014

    We presented ourselves and our initial ideas to a panel of experts, mostly researchers from VTT and the Viikki biocampus. The occasion went very well and there was a lot of interesting discussion. We noticed that we really can do cool things as a group.

  • Meeting with Markus at Helsinki Think Company

    10.4.2014

    We presented our initial ideas to our advisor, Markus, in preparation for the expert meeting. We discussed what direction to go and what kind of an idea to pick.

  • March 2014
  • Making an Introduction Video

    30.3.2014

    We made an introduction video of us so we could apply to Summer of Startups. It turned out pretty good! Video link: http://www.youtube.com/watch?v=LJX21WthZQg.

  • Hackathon

    23.3.2014

    The first version of our website was built. We wanted it to look cool. It didn't.

  • Coming up with Ideas

    18.3.2014, 25.3.2014

    Some brainstorming. Wild ideas. Rating the ideas. Then an unbelievably cool post-it gradient of all the ideas.

  • The First Meeting

    14.3.2014

    The first team meeting was held on a Friday afternoon. Some of us met each other for the first time ever, some had met before already. We talked about the project and got to know each other.

  • Picking the Team

    5.3.2014 - 12.3.2014

    Oskari was in the first job interview in his life, as the interviewer. He hoeld 19 more interviews during the week. Nine people were chosen to be in the final team.

  • The Beginning
  • Meetings with Aalto University and University of Helsinki

    31.1.2014, 5.2.2014

    It seemed like the universities were into the idea.

  • The Idea of a Finnish iGEM Team Was Formed

    28.8.2013

    First e-mails about the idea were sent.