Team:Aalto-Helsinki/Journal

From 2014.igem.org

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       <h1>Journal</h1>
       <h1>Journal</h1>
       <p class="bigsplashtext">
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         We made sure we documented everything important. The summer was full of different experiences and a lot of hard work. You can browse through our work flow here.
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         The summer was full of exciting new experiences and a lot of hard work. You can browse through our sweat and tears here.
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     <small>an iGEM team's tale by Aalto-Helsinki</small></h2>
     <small>an iGEM team's tale by Aalto-Helsinki</small></h2>
     <p>
     <p>
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        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.
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      In March, we had 9 students who were excited about a new field of science that was hardly known in Finland. No experience, some studies, but a lot of excitement.
     </p>
     </p>
     <p>
     <p>
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         We also have more details to share, if you have the interest to read it all (pdf files inc)!
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      In October, we had developed a genetically engineered machine from scratch, made a mathematical model and a simulation based on it, ran our own research lab for five months, designed web applications to make research easier, built a pitch explaining synthetic biology to the general public, figured out a new way to do business and built a massive wiki documenting all of this. How did that happen? Check it out here.
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    </p>
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      <p>
 +
      Our priorities during the summer were:
 +
      <ol>
 +
         <li>Have Fun</li>
 +
        <li>Learn New Things</li>
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        <li>Work Hard</li>
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        <li>Make Something New</li>
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      </ol>
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      </p>
 +
    <p>
 +
      We worked at least 8 hours a day from the middle of May until the end of August in Aalto University's science campus in Otaniemi. There was a huge learning hub/living room in the building adjacent to our lab, so we made it our HQ during the summer. Then we kept on working as much as possible in the autumn while continuing our studies. Some managed to pull off the same hours as before while still keeping up with their studies!
     </p>
     </p>
     <blockquote>
     <blockquote>
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       A Scientist discovers that which exists; an Engineer creates that which never was.
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       It's a dangerous business, Frodo, going out your door. You step onto the road, and if you don't keep your feet, there's no knowing where you might be swept off to.
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       <cite>Theodore von Karmen</cite>
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       <cite>J.R.R. Tolkien, The Lord of the Rings</cite>
     </blockquote>
     </blockquote>
</article>
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     <h2>Safety</h2>
     <h2>Safety</h2>
     <h3>General Safety Matters</h3>
     <h3>General Safety Matters</h3>
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     <p>
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         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:
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    </p>
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            <p>
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    <ul>
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                All of our team members who worked in the lab have had safety training as a part of their studies. The training covered the following topics:
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      <li>Personal protective wear: safety goggles, lab coats and gloves
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            </p>
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      </li>
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            <ul>
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      <li>General safety: acting in case of an accident, where to find emergency showers and fire extinguishers, understanding safety labels
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              <li>Personal protective wear: safety goggles, lab coats and gloves
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      </li>
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              </li>
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      <li>Chemical safety: working with different chemicals and how to dispose of them
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              <li>General safety: acting in case of an accident, where to find emergency showers and fire extinguishers, understanding safety labels
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      </li>
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              </li>
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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>Chemical safety: working with different chemicals and how to dispose of them
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      </li>
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              </li>
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    </ul>
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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
 +
              </li>
 +
            </ul>
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    <p>
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            <p>
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      In our iGEM work we have only worked with non-toxic <i>E. coli</i> (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.
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              In our iGEM work we have only worked with non-toxic <i>E. coli</i> (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.
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    </p>
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            </p>
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    <h3>Our Laboratory</h3>
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            <h3>Our Laboratory</h3>
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    <p>
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            <p>
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      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.
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              We got to work in the Bioprocess Technology lab of Aalto University. We had our own lab bench and we got to use all the instruments and equipment in the department. We also did some measurements in the labs of the VTT Technical Research Centre of Finland.
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    </p>
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            </p>
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    <p>
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        </div>
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      Here are some pictures of our journey. Enjoy!
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        <div class="col-md-6 img-100">
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    </p>
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            <img src="https://static.igem.org/mediawiki/2014/7/78/Aalto_Helsinki_Lab_Apple.jpg" class="img-responsive"></img>
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            <p class="kuvateksti">
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                Oskari, Martina and Minttu excited in the lab.
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            </p>
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            </div>
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        </div>
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    </div>
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    <br>
 
     <h3>Lab Close-Ups</h3>
     <h3>Lab Close-Ups</h3>
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         <img src="https://static.igem.org/mediawiki/2014/d/d1/Aalto_Helsinki_Pipetting_Action.jpg" class="img-responsive"></img>
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         <img src="https://static.igem.org/mediawiki/2014/b/b8/AaltoHelsinki_labplate.jpg" class="img-responsive"></img>
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     </div>
     </div>
     <h3>Our Office</h3>
     <h3>Our Office</h3>
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     <p>
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     <div class="row">
-
      Vuori HUB &lt;3
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    </p>
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            <p>
 +
              We also needed a proper office space where we could work during the summer since not everyone was going to do lab work and our lab bench wasn’t that spacious either.
 +
            </p>
 +
            <p>
 +
              We managed to find the "Learning Hub Living Room" (Vuori Hub) in the building of Department of Materials Science and Engineering. Since it was summer, there weren't many people around to use the space and we made it our home. It was a comfortable place to work in!
 +
            </p>
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        <div class="col-md-6 img-100">
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            <img src="https://static.igem.org/mediawiki/2014/6/60/Aalto_Helsinki_Hubi2.jpg" class="img-responsive"></img>
 +
            <div class="cpright">
 +
            <p class ="kuvateksti">
 +
              Photo of Vuori Hub by <a href="http://www.dowdenphotos.com/">Stewart Dowden</a>
 +
            </p>
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    <div class="cpright">
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    <p class ="kuvateksti">
 +
      Photos of Vuori Hub.
 +
    </p>
 +
    </div>
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     <div class="link" id="Timeline"></div>
     <div class="link" id="Timeline"></div>
     <h2>Timeline</h2>
     <h2>Timeline</h2>
 +
    <h3>Thorough Documentation</h3>
 +
    <p>
 +
      Being the first team in Finland, we wanted to make sure that we documented everything we did as rigorously as possible.
 +
    </p>
 +
    <p>
 +
      We have our lab notebook in PDF files. From these you will be able to find everything that was done in the lab on a specific date.
 +
    </p>
 +
    <ul>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/6/67/AaltoHelsinki_Lab_Notebook_May-June.pdf">May-June (lab)</a></li>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/b/b2/AaltoHelsinki_Lab_Notebook_July.pdf">July (lab)</a></li>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/f/fc/AaltoHelsinki_Lab_Notebook_August.pdf">August (lab)</a></li>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/e/ee/AaltoHelsinki_Lab_Notebook_September-October.pdf">September-October (lab)</a></li>
 +
    </ul>
 +
    <br>
 +
    <p>
 +
      We borrowed a convention from the software development framework, Scrum. So, every day all the team members answered these three questions:
 +
    </p>
 +
      <ol>
 +
        <li>What did you do yesterday?</li>
 +
        <li>What will you do today?</li>
 +
        <li>What might stop you from doing what you want to do?</li>
 +
      </ol>
 +
    <p>
 +
      Each of us wrote the answers down on our online team chat tool (Flowdock). According to the answers, we then assembled a detailed description of every single working day during our official work months (from May 20th to the end of August). So if you really really want to read exactly what we did, here's 30 pages of text for you to check out:
 +
    </p>
 +
    <ul>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/d/d2/Aalto_Helsinki_WorkLogMay-June.pdf">May-June (office)</a></li>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/5/5d/Aalto_Helsinki_WorkLogJuly.pdf">July (office)</a></li>
 +
      <li><a href="https://static.igem.org/mediawiki/2014/d/d0/Aalto_Helsinki_WorkLogAugust.pdf">August (office)</a></li>
 +
    </ul>
 +
    <h3>The Actual Timeline</h3>
 +
    <p>
 +
      We gathered the highlights of our project to the timeline below so you can effortlessly skim through the story of Aalto-Helsinki Bioworks! Lab things are on the right side and everything else on the left.
 +
    </p>
 +
    <p>Timeline reference links:</p>
 +
    <ul>
 +
      <li><a href="#November">November</a></li>
 +
      <li><a href="#October">October</a></li>
 +
      <li><a href="#September">September</a></li>
 +
      <li><a href="#August">August</a></li>
 +
      <li><a href="#July">July</a></li>
 +
      <li><a href="#June">June</a></li>
 +
      <li><a href="#May">May</a></li>
 +
      <li><a href="#April">April</a></li>
 +
      <li><a href="#March">March</a></li>
 +
      <li><a href="#Beginning">The Beginning</a></li>
 +
    </ul>
</article>
</article>
<ul class="timeline">
<ul class="timeline">
 +
  <li class="month" id="November"><div class="tldate">November 2014</div></li>
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Best Wiki prize!</h4>
 +
        <p><small class="text-muted">3.11.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>
 +
          Amazing!! This wiki won the prize for the best undergraduate wiki! We're so happy to bring a prize to home as the first-ever Finnish team. Good job everybody and big thanks to the people who have been helping us getting there!
 +
        </p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/thumb/1/10/Aaltohelsinki_prize.jpg/800px-Aaltohelsinki_prize.jpg" class="img-responsive">
 +
    </div>
 +
  </li>
 +
  <li class="month" id="October"><div class="tldate">October 2014</div></li>
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Giant Jamboree in Boston</h4>
 +
        <p><small class="text-muted">30.10.-3.11.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Flights from Helsinki to Boston on 27th October. A full week in Boston. Presenting our project in front of thousands of people.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Bootcamp Weekend</h4>
 +
        <p><small class="text-muted">25.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Perfecting everything and admiring our work. All is well and we can just relax before the Jamboree.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Presentation at HYBER Workshop</h4>
 +
        <p><small class="text-muted">24.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>A presentation for HYBER Workshop in Långvik; great practice for the Giant Jamboree!</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Furiously Finishing the Wiki</h4>
 +
        <p><small class="text-muted">8.10.-17.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Even though we had started developing the wiki early, the freeze deadline somehow snuck up on us. So little time, so many things to do. And finishing the wiki wasn't even the only thing we had to do before going to Boston!</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Lab Freeze</h4>
 +
        <p><small class="text-muted">14.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Unfortunately, due to time running out we had to freeze the lab work and we couldn't quite finish our wet lab project. Still, after almost five months of continuous work in the lab, we can be proud of what we've achieved and learned during this project!</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Our New Biobricks Were Sequenced</h4>
 +
        <p><small class="text-muted">9.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <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! We were really happy about this since we did have some doubts about making parts with PCR on our own.</p>
 +
      </div>
 +
    </div>
 +
    <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Team Hoodies Arrived</h4>
 +
        <p><small class="text-muted">  8.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Getting ready for the Giant Jamboree!</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/a/ad/Aalto_Helsinki_Hoodie.jpg" class="img-responsive center-block" id="tlsmallimg">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Our Biobricks Started Their Journey to Boston</h4>
 +
        <p><small class="text-muted">6.10.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Finally our own Biobricks were ready to be sent to iGEM HQ. We put them in a box and wished them a safe journey.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/b/b3/AaltoHelsinki_shipment.JPG" class="img-responsive">
 +
    </div>
 +
  </li>
-
   <li class="month"><div class="tldate">October 2014</div></li>
+
   <li class="month" id="September"><div class="tldate">September 2014</div></li>
   <li class="entry">
   <li class="entry">
     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>Jamboree Bootcamp at Mikkeli Summer Cottage</h4>
+
         <h4>Interview for the National Radio</h4>
-
         <p><small class="text-muted"> 25.10.2014</small></p>
+
         <p><small class="text-muted">10.9.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>Out of nowhere we were invited to be interviewed for the national radio YLE! We talked about our project and showed the interviewer our lab.
 +
        </p>
       </div>
       </div>
     </div>
     </div>
   </li>
   </li>
-
   <li class="month"><div class="tldate">September 2014</div></li>
+
   <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Problems in the Lab (Again)</h4>
 +
        <p><small class="text-muted">1.9.-30.9.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We had a lot of problems with one specific ligation. Every time we tried, only one of the inserts seemed to ligate with the backbone and moreover the PCR and restriction digestion results on the gel looked bizarre.</p>
 +
        <p>For the longest time we pondered what could be wrong with our protocols or parts but then with the help of a professor we figured out that the problem might be that we had repetitive sequences in both inserts. Apparently <em>E. coli</em> doesn't like having two similar sequences in the same plasmid and it splices the other one out.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
 
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Juggling Between Lab and School</h4>
 +
        <p><small class="text-muted">8.9.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>At this point everyone already had courses going but luckily the lab is right upstairs from the lecture halls so we could still continue working almost full time in the lab. We just needed to time everything perfectly so we could go listen to the lectures while we had incubations or PCRs running.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
 
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Presentation at VTT Technical Research Centre of Finland</h4>
 +
        <p><small class="text-muted">5.9.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We held a presentation about our project at VTT. It was the first time we presented ourselves to a real scientific audience and we got some really good feedback from the researchers.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
 
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Pitch Night</h4>
 +
        <p><small class="text-muted">4.9.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Pitch Night was part of the Thinkfest arranged by the University of Helsinki in celebration of the university's 375th anniversary. Oskari gave an inspiring speech about following your dreams and introduced our project to the audience which mostly consisted of middle-aged people.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
 
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Aalto Party</h4>
 +
        <p><small class="text-muted">2.9.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>To kick off the academic year, Aalto University hosts a party every year during the first week of school. Despite the name, it's not really a party but more of an exhibition to show all the cool stuff the university has to offer. We were there to represent our team and to tell people about iGEM and our project.</p>
 +
      </div>
 +
    </div>
 +
  </li>
-
   <li class="month"><div class="tldate">August 2014</div></li>
+
   <li class="month" id="August"><div class="tldate">August 2014</div></li>
   <li class="entry timeline-inverted">
   <li class="entry timeline-inverted">
     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>Testing the DNA Constructs</h4>
+
         <h4>Another Round of Testing</h4>
-
         <p><small class="text-muted"> 28.8.2014</small></p>
+
         <p><small class="text-muted">28.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>Testing the first DNA constructs.</p>
+
         <p>We had another round of testing with a part of our prototype and the LED rig. The results seemed really promising!</p>
       </div>
       </div>
     </div>
     </div>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>We planned to go to a room escape thing but when all the suitable times were booked, Minttu took us bowling instead.</p>
       </div>
       </div>
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>The LED Rig Is Ready!</h4>
 +
        <p><small class="text-muted">22.8.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>It’s like our bacteria got their own personalized disco!</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/0/09/AaltoHelsinki_readyLEDrig.jpg" class="img-responsive">
 +
    </div>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>A Microscope That Can Almost Make You a Cup of Coffee</h4>
 +
        <p><small class="text-muted">21.8.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We got to try a super cool programmable microscope. 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>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/3/3f/AaltoHelsinki_supermicroscope.jpg" class="img-responsive center-block" id="tlsmallimg">
     </div>
     </div>
   </li>
   </li>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>The Night of the Arts in Helsinki and More Pinball</h4>
         <h4>The Night of the Arts in Helsinki and More Pinball</h4>
-
         <p><small class="text-muted"> 21.8.2014, 22.8.2014</small></p>
+
         <p><small class="text-muted">21.8.2014, 22.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p> We went to visit the observatory 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>
-
         <p> The next day we go back to playing pinball and Crash Team Racing because it was so much fun last week.</p>
+
         <p> The next day we went back to playing pinball and Crash Team Racing because it was so much fun last week.</p>
 +
        <img src="https://static.igem.org/mediawiki/2014/b/b1/Aalto_Helsinki_Pinball.jpg" class="img-responsive">
       </div>
       </div>
     </div>
     </div>
Line 248: Line 529:
     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>Testing Starts!</h4>
+
         <h4>Testing Started!</h4>
-
         <p><small class="text-muted"> 19.8.2014</small></p>
+
         <p><small class="text-muted">19.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We build the first part of the prototype and start testing!</p>
+
         <p>We built the first part of the prototype and started testing!</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>Our Synthetized Genes Arrive!</h4>
+
         <h4>Our Synthesized Genes Arrived!</h4>
-
         <p><small class="text-muted"> 18.8.2014</small></p>
+
         <p><small class="text-muted">18.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>After a long while, our genes finally arrived. Now we could take them and other parts we had assembled and put the whole ingenious genetically engineered machine together.</p>
       </div>
       </div>
     </div>
     </div>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Meeting at Heureka Science Center!</h4>
         <h4>Meeting at Heureka Science Center!</h4>
-
         <p><small class="text-muted"> 18.8.2014</small></p>
+
         <p><small class="text-muted">18.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>We met the event manager and event organizer of Heureka and came up with an idea of a synthetic biology weekend workshop we could organize in the spring.</p>
-
         <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>
+
         <p>They were very excited about us and everything we had to show and tell.</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.</p>
       </div>
       </div>
     </div>
     </div>
Line 289: Line 570:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Pinball Night</h4>
         <h4>Pinball Night</h4>
-
         <p><small class="text-muted"> 14.8.2014</small></p>
+
         <p><small class="text-muted">14.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>Lassi takes us to play pinball. It's surprisingly fun. We play a ton of Crash Team Racing too.</p>
+
         <p>Lassi took us to play pinball. It was surprisingly fun. We played a ton of Crash Team Racing too.</p>
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/2/24/Aalto_Helsinki_CTR.jpg" class="img-responsive center-block" id="tlsmallimg">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Early Version of the LED Rig</h4>
 +
        <p><small class="text-muted">14.8.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Pietu had been busy making the LED rig inspired by Tabor Lab. This is what the early version looked like. The LED rig would be the tool to control our light sensitive bacteria.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/7/73/AaltoHelsinki_earlyLEDrig.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>HYBER Takes Interest In Us!</h4>
+
         <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>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>We met with The Academy of Finland's Center of Excellence HYBER 2014-2019. They wanted to support us and invited us to talk in workshop that would be arranged just before the Giant Jamboree.</p>
-
         <p>In the evening Oskari takes us to play laser tag! He is way better at it than anyone else.</p>
+
         <p>In the evening Oskari took us to play laser tag! He was way better at it than anyone else.</p>
 +
      </div>
 +
    </div>
 +
  </li>
 +
 
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>MIT Media Lab People Came to Visit Us</h4>
 +
        <p><small class="text-muted">7.8.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>Marko Ahtisaari and Madeleine Abromowitz from MIT Media Lab came to visit our office and lab. We discussed about a possible pop-up media lab in Helsinki and threw some ideas in the air. We were also invited to go visit the actual MIT Media Lab in Boston when we go there for the Giant Jamboree.</p>
       </div>
       </div>
     </div>
     </div>
Line 314: Line 621:
     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>The First Sequencing Results Arrive!</h4>
+
         <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>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>We got our first sequencing results that were in confusing .ab1-files. Then it turned out that Geneious program makes analysing them incredibly easy. Most of the sequences looked good, some not so much.</p>
       </div>
       </div>
     </div>
     </div>
Line 327: Line 634:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Friday Sushi Lunch</h4>
         <h4>Friday Sushi Lunch</h4>
-
         <p><small class="text-muted"> 1.8.2014</small></p>
+
         <p><small class="text-muted">1.8.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <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>
+
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/0/00/AaltoHelsinki_sushi.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
-
   <li class="month"><div class="tldate">July 2014</div></li>
+
   <li class="month" id="July"><div class="tldate">July 2014</div></li>
   <li class="entry">
   <li class="entry">
Line 343: Line 649:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Building the Synthesizable Sequences</h4>
         <h4>Building the Synthesizable Sequences</h4>
-
         <p><small class="text-muted"> 31.7.2014</small></p>
+
         <p><small class="text-muted">31.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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 assembled the sequences we wanted to synthesize. They included the lambda repressor <em>O</em><sub>R</sub> sites that we designed. We found out that the synthesizing costs the same for 0-1000 nucleotides, so we included a few surrounding BioBricks to save on lab time. (The <em>O</em><sub>R</sub> sites are fairly small.)</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 First Ligations Are Sent to Be Sequenced</h4>
+
         <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>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We have a number of ligations ready for assembling and it turns out there's a sequencing place like 5 kilometers away.</p>
+
         <p>We had a number of ligations ready for assembling and it turned out there was a sequencing lab about 5 kilometers away.</p>
-
         <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>
       </div>
       </div>
     </div>
     </div>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Meeting with Tania</h4>
         <h4>Meeting with Tania</h4>
-
         <p><small class="text-muted"> 22.7.2014</small></p>
+
         <p><small class="text-muted">22.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p> We met Tania, an ex-iGEMer from the <a href="https://2012.igem.org/Team:Amsterdam/team/members">2012 Amsterdam team.</a> It was a great meeting and we finally got some validation that we're doing some things right.</p>
 +
        <p>In the evening Martina took us geocaching! It is amazing what can be hidden completely in plain sight.</p>
 +
      </div>
 +
    </div>
 +
  </li>
-
         <p>In the evening Martina takes us geocaching! It is amazing what can be hidden in completely plain sight.</p>
+
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>New Primers</h4>
 +
         <p><small class="text-muted">22.7.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>The new primers designed by Lassi arrived and we tested them in amplifying the backbones with PCR. The primers bind to the RFP insert instead of the prefix and suffix which have a palindromic site and can cause troubles. In the end we didn't use PCR amplification of the backbones since we opted for multiplying the whole plasmids in bacteria and gel purifying them instead. However, we did submit the primers to the Registry and you can find them here <a href="http://parts.igem.org/Part:BBa_K1443003">BBa_K1443003</a> and <a href="http://parts.igem.org/Part:BBa_K1443004">BBa_K1443004</a>.</p>
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/2/2f/AaltoHelsinki_primers.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Demo Day</h4>
         <h4>Demo Day</h4>
-
         <p><small class="text-muted"> 15.7.2014</small></p>
+
         <p><small class="text-muted">15.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We present our idea to hundreds of people and hold a booth for 6 hours.</p>
+
         <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">
+
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/0/06/Aalto_Helsinki_Demoday.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>A Movie Night with the Team</h4>
         <h4>A Movie Night with the Team</h4>
-
         <p><small class="text-muted"> 14.7.2014</small></p>
+
         <p><small class="text-muted">14.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>In the evening Mikko took us to watch the movies <i>The Skin I Live In</i>, <i>Scott Pilgrim vs. The World</i> and <i>The Grand Budapest Hotel</i>.</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 Gene Circuit Is Finished</h4>
+
         <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>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We have the lambda repressor figured out and integrated into our system. We start planning for the parts to be synthesized.</p>
+
         <p>We finished the gene circuit and now we could start designing the parts that would be synthesized.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/a/a5/Aalto_Helsinki_loop.png" class="img-responsive">
 +
    </div>
 +
  </li>
-
        <img src="https://static.igem.org/mediawiki/2014/2/2d/Aalto_Helsinki_Genecircus.jpg" class="img-responsive">
+
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>Working Hard in the Lab</h4>
 +
        <p><small class="text-muted">13.7.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>We were working hard in the lab during July and got many new ligations done. At this point the lab had started to feel like a home already.</p>
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/a/aa/AaltoHelsinki_labbenchtop.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Summer of Startups Tallinn Trip!</h4>
         <h4>Summer of Startups Tallinn Trip!</h4>
-
         <p><small class="text-muted"> 10-11.7.2014</small></p>
+
         <p><small class="text-muted">10-11.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <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>
       </div>
       <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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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Extensive Research on the Lambda Repressor</h4>
         <h4>Extensive Research on the Lambda Repressor</h4>
-
         <p><small class="text-muted"> 8.7.2014</small></p>
+
         <p><small class="text-muted">8.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <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>
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/f/f6/Aalto_Helsinki_Dark_Science.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>The "Fun Master" System Begins</h4>
+
         <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>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>We decided we should do something (not iGEM-related) fun every week as a group. Each 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>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/b/b4/Aalto_Helsinki_Friday_Juice.jpg" class="img-responsive center-block" id="tlsmallimg">
 +
    </div>
 +
  </li>
-
        <img src="https://static.igem.org/mediawiki/2014/b/b4/Aalto_Helsinki_Friday_Juice.jpg" class="img-responsive">
+
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>A N00b in the Lab</h4>
 +
        <p><small class="text-muted">3.7.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>As Niklas had never been in a lab before and he was eager to see what we do there, we took him in for the day and showed him all the cool stuff. He even got to try some pipetting (with water only, although it didn't seem to lessen his enthusiasm)!</p>
       </div>
       </div>
     </div>
     </div>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>The First Team Member Chimera</h4>
         <h4>The First Team Member Chimera</h4>
-
         <p><small class="text-muted"> 2.7.2014</small></p>
+
         <p><small class="text-muted">2.7.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>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.</p>
+
         <p>Because chimera is a term both in gene technology 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.</p>
         <p>To read more about the chimeras, head to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#chimeras">"chimeras" section on the Outreach page</a>.</p>
         <p>To read more about the chimeras, head to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#chimeras">"chimeras" section on the Outreach page</a>.</p>
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       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <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>
+
         <p>We got the idea of explaining synthetic biology as turning bacteria into superheroes from a meeting with Micki Honkavaara. We started working on a new pitch based on that.</p>
-
         <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>
+
         <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>
       </div>
       </div>
     </div>
     </div>
   </li>
   </li>
-
   <li class="month"><div class="tldate">June 2014</div></li>
+
   <li class="month" id="June"><div class="tldate">June 2014</div></li>
   <li class="entry">
   <li class="entry">
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>BioBrick Seeker on the iGEM Help and Community Pages</h4>
         <h4>BioBrick Seeker on the iGEM Help and Community Pages</h4>
-
         <p><small class="text-muted"> 25.6.2014</small></p>
+
         <p><small class="text-muted">25.6.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>Our BioBrick Seeker has been mentioned on the official help page for a while. We only noticed it now.</p>
+
         <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>
-
 
-
      <p><img src="https://static.igem.org/mediawiki/2014/a/a7/Aalto_Helsinki_kasi_vectored_light.png" class="img-responsive"></img></p>
 
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/a/a7/Aalto_Helsinki_kasi_vectored_light.png" class="img-responsive center-block" id="tlsmallimg"></img>
     </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>The First BioBrick Ligation Combo Works</h4>
+
         <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>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
         <p>We even checked it with a gel.</p>
         <p>We even checked it with a gel.</p>
-
        <p>KUVA??</p>
 
       </div>
       </div>
 +
        <img src="https://static.igem.org/mediawiki/2014/c/cd/AaltoHelsinki_ligationgel.jpg" class="img-responsive center-block" id="tlsmallimg">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>We Had Visitors in the Lab</h4>
 +
        <p><small class="text-muted">23.6.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>The Summer of Startups people came to visit our lab and see what we’re actually doing.</p>
 +
      </div>
 +
        <img src="https://static.igem.org/mediawiki/2014/0/0a/AaltoHelsinki_SoSLab.JPG" class="img-responsive">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <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. It 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 center-block" id="tlsmallimg">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry timeline-inverted">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>First Colony PCR: No Successful 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 center-block" id="tlsmallimg">
 +
    </div>
 +
  </li>
 +
 +
  <li class="entry">
 +
    <div class="timeline-panel">
 +
      <div class="tl-heading">
 +
        <h4>BioBrick Seeker Spreading</h4>
 +
        <p><small class="text-muted">10.6.2014</small></p>
 +
      </div>
 +
      <div class="tl-body">
 +
        <p>BioBrick Seeker received attention on Twitter. People really seemed to like the tool.</p>
 +
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/9/93/AaltoHelsinki_seekertweet.png" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
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       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Writing Sponsorship Applications</h4>
         <h4>Writing Sponsorship Applications</h4>
-
         <p><small class="text-muted"> 10.6.2014</small></p>
+
         <p><small class="text-muted">9.6.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>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>
+
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/7/73/Aalto_Helsinki_Team.jpg" class="img-responsive"></img>
     </div>
     </div>
   </li>
   </li>
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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 didn'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>
     </div>
   </li>
   </li>
-
   <li class="entry">
+
   <li class="entry timeline-inverted">
     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>BioBrick Seeker spreading</h4>
+
         <h4>The Ligation Calculator</h4>
-
         <p><small class="text-muted"> 2.6.2014</small></p>
+
         <p><small class="text-muted">5.6.2014</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 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>
+
      </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/4/4d/AaltoHelsinki_ligationcalculator.png" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
-
   <li class="month"><div class="tldate">May 2014</div></li>
+
   <li class="month" id="May"><div class="tldate">May 2014</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>Precipitation of the Cell Membranes</h4>
         <h4>Precipitation of the Cell Membranes</h4>
-
         <p><small class="text-muted"> 30.5.2014</small></p>
+
         <p><small class="text-muted">30.5.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>This process would be repeated about 50 times during the summer, but this was the first. Video link: <a href="http://www.youtube.com/watch?v=TI_EuzNIaPg">http://www.youtube.com/watch?v=TI_EuzNIaPg</a>.</p>
+
         <p>This process would be repeated about 50 times during the summer, but this was the first.<a href="http://www.youtube.com/watch?v=TI_EuzNIaPg"><img src="https://static.igem.org/mediawiki/2014/f/f5/Aalto_Helsinki_Cell_Membrane_Video.png" class="img-responsive"></a>.</p>
       </div>
       </div>
     </div>
     </div>
   </li>
   </li>
-
 
   <li class="entry">
   <li class="entry">
Line 574: Line 981:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>The First Version of BioBrick Seeker</h4>
         <h4>The First Version of BioBrick Seeker</h4>
-
         <p><small class="text-muted"> 30.5.2014</small></p>
+
         <p><small class="text-muted">30.5.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>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.</p>
+
         <p>It started from the mild inconvenience of searching for BioBricks from four different excel sheets in the lab. At this point, the Registry pages didn't yet have the updated info about part availability either. With the tool we could search through this year's distribution effortlessly. Because it was so useful for us, we decided to share it to others, too.</p>
       </div>
       </div>
     </div>
     </div>
 +
  </li>
   <li class="entry timeline-inverted">
   <li class="entry timeline-inverted">
Line 585: Line 993:
       <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">
+
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/3/30/Aalto_Helsinki_First_Transformation.jpg" class="img-responsive">
 +
    </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>
Line 598: Line 1,019:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Website Is Done</h4>
         <h4>Website Is 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://2014.aaltohelsinki.com/">http://2014.aaltohelsinki.com/</a>. Check it out!</p>
       </div>
       </div>
     </div>
     </div>
Line 609: Line 1,030:
     <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>
       <div class="tl-body">
       <div class="tl-body">
         <p>...by making plates. Not that mind-blowing, but very important.</p>
         <p>...by making plates. Not that mind-blowing, but very important.</p>
-
 
-
        <p><img src="https://static.igem.org/mediawiki/2014/f/f9/Aalto_Helsinki_Making_Plates.jpg" class="img-responsive"></a></p>
 
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/f/f9/Aalto_Helsinki_Making_Plates.jpg" class="img-responsive">
     </div>
     </div>
   </li>
   </li>
Line 624: Line 1,044:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>A Tour in the Lab</h4>
         <h4>A Tour in the Lab</h4>
-
         <p><small class="text-muted"> 19.5.2014</small></p>
+
         <p><small class="text-muted">19.5.2014</small></p>
       </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. 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>
Line 635: Line 1,055:
     <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 the Distribution Kit 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 center-block" id="tlsmallimg">
     </div>
     </div>
   </li>
   </li>
-
   <li class="month"><div class="tldate">April 2014</div></li>
+
   <li class="month" id="April"><div class="tldate">April 2014</div></li>
   <li class="entry">
   <li class="entry">
Line 651: Line 1,071:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Getting Ready for the Summer of Startups</h4>
         <h4>Getting Ready for the Summer of Startups</h4>
-
         <p><small class="text-muted"></i>22.4.2014, 25.4.2014, 28.4.2014</small></p>
+
         <p><small class="text-muted">22.4.2014, 25.4.2014, 28.4.2014</small></p>
       </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 in the end.</p>
         <p>They accepted us in the program.</p>
         <p>They accepted us in the program.</p>
       </div>
       </div>
Line 664: Line 1,084:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Expert Meeting at Aalto University</h4>
         <h4>Expert Meeting at Aalto University</h4>
-
         <p><small class="text-muted"></i>10.4.2014</small></p>
+
         <p><small class="text-muted">10.4.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
Line 676: Line 1,096:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Meeting with Markus at Helsinki Think Company</h4>
         <h4>Meeting with Markus at Helsinki Think Company</h4>
-
         <p><small class="text-muted"></i>10.4.2014</small></p>
+
         <p><small class="text-muted">10.4.2014</small></p>
       </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>
   </li>
   </li>
-
   <li class="month"><div class="tldate">March 2014</div></li>
+
   <li class="month" id="March"><div class="tldate">March 2014</div></li>
   <li class="entry">
   <li class="entry">
Line 690: Line 1,110:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Making an Introduction Video</h4>
         <h4>Making an Introduction Video</h4>
-
         <p><small class="text-muted"></i>30.3.2014</small></p>
+
         <p><small class="text-muted">30.3.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>We made an introduction video of us so we could apply to Summer of Startups. It turned out pretty good! Video link: <a href="http://www.youtube.com/watch?v=LJX21WthZQg">http://www.youtube.com/watch?v=LJX21WthZQg</a>.</p>
+
         <p>We made an introduction video of us so we could apply to the Summer of Startups incubator program. It turned out pretty good! Video link: <a href="http://www.youtube.com/watch?v=LJX21WthZQg">http://www.youtube.com/watch?v=LJX21WthZQg</a>.</p>
       </div>
       </div>
     </div>
     </div>
Line 702: Line 1,122:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Hackathon</h4>
         <h4>Hackathon</h4>
-
         <p><small class="text-muted"></i>23.3.2014</small></p>
+
         <p><small class="text-muted">23.3.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
Line 713: Line 1,133:
     <div class="timeline-panel">
     <div class="timeline-panel">
       <div class="tl-heading">
       <div class="tl-heading">
-
         <h4>Coming up with Ideas</h4>
+
         <h4>Coming Up With Ideas</h4>
-
         <p><small class="text-muted"></i>18.3.2014, 25.3.2014</small></p>
+
         <p><small class="text-muted">18.3.2014, 25.3.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
         <p>Some brainstorming. Wild ideas. Rating the ideas. Then an unbelievably cool post-it gradient of all the ideas.</p>
         <p>Some brainstorming. Wild ideas. Rating the ideas. Then an unbelievably cool post-it gradient of all the ideas.</p>
-
        <img src="https://static.igem.org/mediawiki/2014/5/5e/Aalto_Helsinki_Ideagradientti.jpg" class="img-responsive">
 
       </div>
       </div>
 +
      <img src="https://static.igem.org/mediawiki/2014/5/5e/Aalto_Helsinki_Ideagradientti.jpg" class="img-responsive center-block" id="tlsmallimg">
     </div>
     </div>
   </li>
   </li>
Line 727: Line 1,147:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>The First Meeting</h4>
         <h4>The First Meeting</h4>
-
         <p><small class="text-muted"></i>14.3.2014</small></p>
+
         <p><small class="text-muted">14.3.2014</small></p>
       </div>
       </div>
       <div class="tl-body">
       <div class="tl-body">
-
         <p>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.</p>
+
         <p>The first team meeting was held on a Friday afternoon. Some of us met each other for the first time ever, some had already met before. We talked about the project and got to know each other.</p>
       </div>
       </div>
     </div>
     </div>
Line 739: Line 1,159:
       <div class="tl-heading">
       <div class="tl-heading">
         <h4>Picking the Team</h4>
         <h4>Picking the Team</h4>
-
         <p><small class="text-muted"></i>5.3.2014 - 12.3.2014</small></p>
+
         <p><small class="text-muted">5.3.2014 - 12.3.2014</small></p>
       </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 held 19 more interviews during the week. Nine people were chosen to be in the final team.</p>
       </div>
       </div>
     </div>
     </div>
   </li>
   </li>
-
   <li class="month"><div class="tldate">The Beginning</div></li>
+
   <li class="month" id="Beginning"><div class="tldate">The Beginning</div></li>
   <li class="entry">
   <li class="entry">
       <div class="timeline-panel">
       <div class="timeline-panel">
         <div class="tl-heading">
         <div class="tl-heading">
-
           <h4>Meetings with Aalto University and University of Helsinki</h4>
+
           <h4>Meetings with Aalto University and the University of Helsinki</h4>
-
           <p><small class="text-muted"></i>31.1.2014, 5.2.2014</small></p>
+
           <p><small class="text-muted">31.1.2014, 5.2.2014</small></p>
         </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>
Line 764: Line 1,184:
     <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">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>
Line 793: Line 1,213:
     Do not put href attribute, it will be replaced with a link to the image.
     Do not put href attribute, it will be replaced with a link to the image.
     Moreover, inner html of the anchor tag will be "figure x" where x is the
     Moreover, inner html of the anchor tag will be "figure x" where x is the
-
     correct figure number.
+
     correct figure number. If span or anchor has "." as the inner html, the
 +
    caption will be capitalized.
     */
     */
     var images = $('img[ref]');
     var images = $('img[ref]');
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                 } else {
                 } else {
                     e2.innerHTML = "figure " + (index+1);
                     e2.innerHTML = "figure " + (index+1);
 +
                }
 +
            });
 +
        }
 +
    );
 +
 +
    // Table reference script
 +
    /*
 +
    USAGE:
 +
    tag table with a tab that is connected to the table, such as:
 +
    <table ref="intensities" />
 +
    When you insert a reference in text, put a tag with a ref attribute:
 +
    <a tab="intensities"></a>
 +
    Do not put href attribute, it will be replaced with a link to the image.
 +
    Moreover, inner html of the anchor tag will be "table x" where x is the
 +
    correct table number. If span or anchor has "." as the inner html, the
 +
    caption will be capitalized.
 +
    */
 +
    var tables = $('table[tab], img[tab]');
 +
    $.each(tables, function(index, e){
 +
            var tableName = e.getAttribute("tab");
 +
            if (!e.id){
 +
                e.setAttribute("id","table"+(index+1));
 +
            }
 +
            $.each($('a[tab="'+tableName+'"]'), function(j, e2){
 +
                e2.setAttribute("href","#"+e.id);
 +
                if (e2.innerHTML == "."){
 +
                    e2.innerHTML = "Table " + (index+1);
 +
                } else {
 +
                    e2.innerHTML = "table " + (index+1);
 +
                }
 +
            });
 +
            $.each($('span[tab="'+tableName+'"]'), function(j, e2){
 +
                e2.setAttribute("href","#"+e.id);
 +
                if (e2.innerHTML == "."){
 +
                    e2.innerHTML = "Table " + (index+1);
 +
                } else {
 +
                    e2.innerHTML = "table " + (index+1);
                 }
                 }
             });
             });

Latest revision as of 16:12, 30 November 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.

Scroll down to read more
There and Back Again
Safety
Timeline

Photo © Tanja Maria

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

In March, we had 9 students who were excited about a new field of science that was hardly known in Finland. No experience, some studies, but a lot of excitement.

In October, we had developed a genetically engineered machine from scratch, made a mathematical model and a simulation based on it, ran our own research lab for five months, designed web applications to make research easier, built a pitch explaining synthetic biology to the general public, figured out a new way to do business and built a massive wiki documenting all of this. How did that happen? Check it out here.

Our priorities during the summer were:

  1. Have Fun
  2. Learn New Things
  3. Work Hard
  4. Make Something New

We worked at least 8 hours a day from the middle of May until the end of August in Aalto University's science campus in Otaniemi. There was a huge learning hub/living room in the building adjacent to our lab, so we made it our HQ during the summer. Then we kept on working as much as possible in the autumn while continuing our studies. Some managed to pull off the same hours as before while still keeping up with their studies!

It's a dangerous business, Frodo, going out your door. You step onto the road, and if you don't keep your feet, there's no knowing where you might be swept off to. J.R.R. Tolkien, The Lord of the Rings

Safety

General Safety Matters

All of our team members who worked in the lab have had 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 lab bench and we got to use all the instruments and equipment in the department. We also did some measurements in the labs of the VTT Technical Research Centre of Finland.

Oskari, Martina and Minttu excited in the lab.



Photos © Stewart Dowden

Lab Close-Ups

Our Office

We also needed a proper office space where we could work during the summer since not everyone was going to do lab work and our lab bench wasn’t that spacious either.

We managed to find the "Learning Hub Living Room" (Vuori Hub) in the building of Department of Materials Science and Engineering. Since it was summer, there weren't many people around to use the space and we made it our home. It was a comfortable place to work in!

Photo of Vuori Hub by Stewart Dowden

Photos of Vuori Hub.

Timeline

Thorough Documentation

Being the first team in Finland, we wanted to make sure that we documented everything we did as rigorously as possible.

We have our lab notebook in PDF files. From these you will be able to find everything that was done in the lab on a specific date.


We borrowed a convention from the software development framework, Scrum. So, every day all the team members answered these three questions:

  1. What did you do yesterday?
  2. What will you do today?
  3. What might stop you from doing what you want to do?

Each of us wrote the answers down on our online team chat tool (Flowdock). According to the answers, we then assembled a detailed description of every single working day during our official work months (from May 20th to the end of August). So if you really really want to read exactly what we did, here's 30 pages of text for you to check out:

The Actual Timeline

We gathered the highlights of our project to the timeline below so you can effortlessly skim through the story of Aalto-Helsinki Bioworks! Lab things are on the right side and everything else on the left.

Timeline reference links:

  • November 2014

  • Best Wiki prize!

    3.11.2014

    Amazing!! This wiki won the prize for the best undergraduate wiki! We're so happy to bring a prize to home as the first-ever Finnish team. Good job everybody and big thanks to the people who have been helping us getting there!

  • October 2014

  • Giant Jamboree in Boston

    30.10.-3.11.2014

    Flights from Helsinki to Boston on 27th October. A full week in Boston. Presenting our project in front of thousands of people.

  • Bootcamp Weekend

    25.10.2014

    Perfecting everything and admiring our work. All is well and we can just relax before the Jamboree.

  • Presentation at HYBER Workshop

    24.10.2014

    A presentation for HYBER Workshop in Långvik; great practice for the Giant Jamboree!

  • Furiously Finishing the Wiki

    8.10.-17.10.2014

    Even though we had started developing the wiki early, the freeze deadline somehow snuck up on us. So little time, so many things to do. And finishing the wiki wasn't even the only thing we had to do before going to Boston!

  • Lab Freeze

    14.10.2014

    Unfortunately, due to time running out we had to freeze the lab work and we couldn't quite finish our wet lab project. Still, after almost five months of continuous work in the lab, we can be proud of what we've achieved and learned during this project!

  • 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! We were really happy about this since we did have some doubts about making parts with PCR on our own.

  • Team Hoodies Arrived

    8.10.2014

    Getting ready for the Giant Jamboree!

  • Our Biobricks Started Their Journey to Boston

    6.10.2014

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

  • September 2014

  • Interview for the National Radio

    10.9.2014

    Out of nowhere we were invited to be interviewed for the national radio YLE! We talked about our project and showed the interviewer our lab.

  • Problems in the Lab (Again)

    1.9.-30.9.2014

    We had a lot of problems with one specific ligation. Every time we tried, only one of the inserts seemed to ligate with the backbone and moreover the PCR and restriction digestion results on the gel looked bizarre.

    For the longest time we pondered what could be wrong with our protocols or parts but then with the help of a professor we figured out that the problem might be that we had repetitive sequences in both inserts. Apparently E. coli doesn't like having two similar sequences in the same plasmid and it splices the other one out.

  • Juggling Between Lab and School

    8.9.2014

    At this point everyone already had courses going but luckily the lab is right upstairs from the lecture halls so we could still continue working almost full time in the lab. We just needed to time everything perfectly so we could go listen to the lectures while we had incubations or PCRs running.

  • Presentation at VTT Technical Research Centre of Finland

    5.9.2014

    We held a presentation about our project at VTT. It was the first time we presented ourselves to a real scientific audience and we got some really good feedback from the researchers.

  • Pitch Night

    4.9.2014

    Pitch Night was part of the Thinkfest arranged by the University of Helsinki in celebration of the university's 375th anniversary. Oskari gave an inspiring speech about following your dreams and introduced our project to the audience which mostly consisted of middle-aged people.

  • Aalto Party

    2.9.2014

    To kick off the academic year, Aalto University hosts a party every year during the first week of school. Despite the name, it's not really a party but more of an exhibition to show all the cool stuff the university has to offer. We were there to represent our team and to tell people about iGEM and our project.

  • August 2014

  • Another Round of Testing

    28.8.2014

    We had another round of testing with a part of our prototype and the LED rig. The results seemed really promising!

  • Bowling

    26.8.2014

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

  • The LED Rig Is Ready!

    22.8.2014

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

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

    21.8.2014

    We got to try a super cool programmable microscope. 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 observatory 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 Synthesized 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 ingenious 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 an idea of a synthetic biology weekend workshop we could organize in the spring.

    They were very excited about us and everything we had to show and tell.

    We hope to inspire young people to study synthetic biology in the future and let the older people know it exists.

  • 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 LED Rig

    14.8.2014

    Pietu had been busy making the LED rig inspired by Tabor Lab. This is what the early version looked like. The LED rig 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 to support us and invited us to talk in workshop that would be arranged just before the Giant Jamboree.

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

  • MIT Media Lab People Came to Visit Us

    7.8.2014

    Marko Ahtisaari and Madeleine Abromowitz from MIT Media Lab came to visit our office and lab. We discussed about a possible pop-up media lab in Helsinki and threw some ideas in the air. We were also invited to go visit the actual MIT Media Lab in Boston when we go there for the Giant Jamboree.

  • 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 program 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.

  • July 2014

  • Building the Synthesizable Sequences

    31.7.2014

    We assembled the sequences we wanted to synthesize. They included the lambda repressor OR sites that we designed. We found out that the synthesizing costs the same for 0-1000 nucleotides, so we included 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 about 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 met Tania, an ex-iGEMer from the 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 completely in plain sight.

  • New Primers

    22.7.2014

    The new primers designed by Lassi arrived and we tested them in amplifying the backbones with PCR. The primers bind to the RFP insert instead of the prefix and suffix which have a palindromic site and can cause troubles. In the end we didn't use PCR amplification of the backbones since we opted for multiplying the whole plasmids in bacteria and gel purifying them instead. However, we did submit the primers to the Registry and you can find them here BBa_K1443003 and BBa_K1443004.

  • 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 movies The Skin I Live In, Scott Pilgrim vs. The World and The Grand Budapest Hotel.

  • The Gene Circuit Was Finished

    14.7.2014

    We finished the gene circuit and now we could start designing the parts that would be synthesized.

  • Working Hard in the Lab

    13.7.2014

    We were working hard in the lab during July and got many new ligations done. At this point the lab had started to feel like a home already.

  • 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 we should do something (not iGEM-related) fun every week as a group. Each 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.

  • A N00b in the Lab

    3.7.2014

    As Niklas had never been in a lab before and he was eager to see what we do there, we took him in for the day and showed him all the cool stuff. He even got to try some pipetting (with water only, although it didn't seem to lessen his enthusiasm)!

  • The First Team Member Chimera

    2.7.2014

    Because chimera is a term both in gene technology 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 Is Born

    1.7.2014, 2.7.2014

    We got the idea of explaining synthetic biology as turning bacteria into superheroes from a meeting with Micki Honkavaara. 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. It seemed like 55 °C would be the answer to our problems.

  • First Colony PCR: No Successful 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.

  • BioBrick Seeker Spreading

    10.6.2014

    BioBrick Seeker received attention on Twitter. People really seemed to like the tool.

  • Writing Sponsorship Applications

    9.6.2014

    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 didn'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.

  • 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..

  • The First Version of BioBrick Seeker

    30.5.2014

    It started from the mild inconvenience of searching for BioBricks from four different excel sheets in the lab. At this point, the Registry pages didn't yet have the updated info about part availability either. With the tool 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 Is Done

    23.5.2014

    This time it did actually look cool! The actual website might still be available on http://2014.aaltohelsinki.com/. 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. 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 the Distribution Kit 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 in 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 the Summer of Startups incubator program. 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 already met before. 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 held 19 more interviews during the week. Nine people were chosen to be in the final team.

  • The Beginning

  • Meetings with Aalto University and the 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.

Retrieved from "http://2014.igem.org/Team:Aalto-Helsinki/Journal"