Difference between revisions of "Team:NAIT Edmonton/Logbook"

 
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<div class="cd-timeline-content">
 
<div class="cd-timeline-content">
 
<h2>Article on Synthetic Biology in Canada</h2>
 
<h2>Article on Synthetic Biology in Canada</h2>
                                 <img src="https://pbs.twimg.com/profile_images/594139192357031937/1_CXZi1v_400x400.jpg" width="300px">
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                                 <img src="https://static.igem.org/mediawiki/2015/4/4d/1_CXZi1v_400x400.jpg" width="300px">
 
<p>Submitted an article for Team iGEM Amoy China.</p>
 
<p>Submitted an article for Team iGEM Amoy China.</p>
 
<label class="btn" for="modal-010"><p class="cd-read-more">Read more</p></label>
 
<label class="btn" for="modal-010"><p class="cd-read-more">Read more</p></label>
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<h2>NAIT Photoshoot and Mini-Prep</h2>
 
<h2>NAIT Photoshoot and Mini-Prep</h2>
 
<p>We had another photo shoot with our institution! Eduardo and Joy managed to escape early,           
 
<p>We had another photo shoot with our institution! Eduardo and Joy managed to escape early,           
                                   however, because of a plasmid mini-prep.</p>
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                                   because of a plasmid mini-prep.</p>
 
<label class="btn" for="modal-017"><p class="cd-read-more">Read more</p></label>
 
<label class="btn" for="modal-017"><p class="cd-read-more">Read more</p></label>
 
<span class="cd-date">July 31</span>
 
<span class="cd-date">July 31</span>
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<h2>Digestion of Sequences</h2>
 
<h2>Digestion of Sequences</h2>
 
<p>All our sequences (23) were digested and in doing so each were cleaved at specific sites to later ligate with our plasmid, pSB1C3.</p>
 
<p>All our sequences (23) were digested and in doing so each were cleaved at specific sites to later ligate with our plasmid, pSB1C3.</p>
<label class="btn" for="modal-024"><p class="cd-read-more">Read more</p></label>
 
 
<span class="cd-date">August 26</span>
 
<span class="cd-date">August 26</span>
 
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<h2>IM[Ag]INE Shirts have Arrived!</h2>
 
<h2>IM[Ag]INE Shirts have Arrived!</h2>
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                                <center><img src="https://static.igem.org/mediawiki/2015/6/6d/NAIT_ImagineShirts.jpg" width="100%">
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                                </center><br>
 
<p>Additionally, we finished pelleting and purifying more samples of our proteins. Unfortunately, not all of them showed a concentration in the NanoDrop.</p>
 
<p>Additionally, we finished pelleting and purifying more samples of our proteins. Unfortunately, not all of them showed a concentration in the NanoDrop.</p>
 
<span class="cd-date">September 11</span>
 
<span class="cd-date">September 11</span>
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<h2>Experimental Validation</h2>
 
<h2>Experimental Validation</h2>
<p>We ran more gels to so to validate our preliminary results. However, the gels failed to run properly and we ran out of time. </p>
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<p>We ran more gels in order to validate our preliminary results. Regrettably, the gels failed to run properly and we were unable to finish in time. </p>
 
<span class="cd-date">September 14</span>
 
<span class="cd-date">September 14</span>
 
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<h2>The End of our Lab Journey</h2>
 
<h2>The End of our Lab Journey</h2>
<p>And so it ends... Today we pulled the plug on all the lab work and experiments being run. Now, it's time to focus on our Wiki, Poster and Presentation.</p>
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<p>And so it ends. Today, we pulled the plug on all remaining lab work and running experiment. Now, it's time to focus on our Wiki, Poster and Presentation.</p>
 
<span class="cd-date">September 15</span>
 
<span class="cd-date">September 15</span>
 
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<p>Had a blast browsing through our fellow iGEM team's tweets about #WikiFreeze. We're definitely scrambling. AHHH!!!!</p>
 
<p>Had a blast browsing through our fellow iGEM team's tweets about #WikiFreeze. We're definitely scrambling. AHHH!!!!</p>
 
<label class="btn" for="modal-029"><p class="cd-read-more">Read more</p></label>
 
<label class="btn" for="modal-029"><p class="cd-read-more">Read more</p></label>
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<span class="cd-date">September 18</span>
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<img src="https://static.igem.org/mediawiki/2015/2/27/NAIT_GEAR_White.png" alt="Location">
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<h2>DestiNAITion: Boston</h2>
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<center><img src="https://static.igem.org/mediawiki/2015/3/31/NAIT_DestiNAITion.jpg" width="100%">
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                                </center>
 
<span class="cd-date">September 18</span>
 
<span class="cd-date">September 18</span>
 
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     <center><h1>Lab Selfie!</h1></center>
 
     <center><h1>Lab Selfie!</h1></center>
     <center><img src="https://pbs.twimg.com/media/CEQ_lNuW8AECJOj.jpg:large" width="400px"></center>
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     <center><img src="https://static.igem.org/mediawiki/2015/8/88/NAIT_team_first.jpeg" width="400px"></center>
  
 
   </div>
 
   </div>
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     <p>This week, we researched on the scientific basis of color. More specifically, we looked into how the interaction between silver, protein and the polyacrylamide gel produces a certain color. We found that the size of silver nano-particles and the refraction of light is how we perceive different colors.
 
     <p>This week, we researched on the scientific basis of color. More specifically, we looked into how the interaction between silver, protein and the polyacrylamide gel produces a certain color. We found that the size of silver nano-particles and the refraction of light is how we perceive different colors.
  
We also tried to look into the electron cloud and how electron excitation produces certain wavelengths of light</p>
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We also tried to look into the electron cloud and how electron excitation produces certain wavelengths of light.</p>
  
 
   </div>
 
   </div>
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     <p>This week, we focused on perfecting our silver staining techniques. We are currently troubleshooting our gels because the stain comes out quite dark and with a lot of background staining.</p>
 
     <p>This week, we focused on perfecting our silver staining techniques. We are currently troubleshooting our gels because the stain comes out quite dark and with a lot of background staining.</p>
 
     <br>
 
     <br>
     <p>We also started reaching out to local start-ups and companies looking for sponsorship and further funding.</p>
+
     <p>We started reaching out to local start-ups and companies looking for sponsorship and further funding.</p>
 
     <br>
 
     <br>
     <p>Our team also started drafting versions of our wiki on this week. As we are not familiar with the mediaWiki interface, this task proved to be quite difficult. Our wiki did, however, go live later in the week. A lot of work is still necessary for the wiki because at this time, there was no content - just a template.</p>
+
     <p>Our team also started drafting versions of our wiki on this week. As we are not familiar with the mediaWiki interface, this task proved to be quite difficult. It did, however, go live later in the week. A lot of work is still necessary for the wiki because at this time, there was no content - just a template.</p>
 
     <br>
 
     <br>
 
     <center><img src="https://static.igem.org/mediawiki/2015/7/7d/NAIT_Wiki_Preliminary_Screenshot.jpg" height="300" width="500"></center>
 
     <center><img src="https://static.igem.org/mediawiki/2015/7/7d/NAIT_Wiki_Preliminary_Screenshot.jpg" height="300" width="500"></center>
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     <p>This week, we worked on and finalized the DNA sequences to be sent to IDT.</p>
 
     <p>This week, we worked on and finalized the DNA sequences to be sent to IDT.</p>
 
     <br>
 
     <br>
     <p><img src="http://www.bio-rad.com/webroot/web/images/lsr/products/electrophoresis/product_detail/global/lsr_silver_stain_plus_kit.jpg"> We also continued perfecting the silver staining techniques outlined by our principal investigator. Unfortunately, we are still experiencing difficulties in background clarity. We tried to switch out the vessels used during staining because we thought that residual silver was affecting our gels. However, even new pyrex containers did not make a difference in our final stained products. We are thinking now that the BioRAD Silver Stain Plus kit that was provided for us contains defective reagents.</p>
+
     <p><img src="https://static.igem.org/mediawiki/2015/a/a8/NAIT_silver_stains.jpeg"> We also continued perfecting the silver staining techniques outlined by our principal investigator. Unfortunately, we are still experiencing difficulties in background clarity. We tried to switch out the vessels used during staining because we thought that residual silver was affecting our gels. However, even new pyrex containers did not make a difference in our final stained products. We are thinking now that the BioRAD Silver Stain Plus kit that was provided for us contains defective reagents.</p>
  
 
   </div>
 
   </div>
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     <h1>Week 2 - June 8 to 12</h1>
 
     <h1>Week 2 - June 8 to 12</h1>
 
     <p>This week, we really decided to focus our efforts into perfecting our silver stain techniques. Additionally, we divided all the tasks we have to do from now until Boston and divided them according to each of our team members strengths.</p> <br>
 
     <p>This week, we really decided to focus our efforts into perfecting our silver stain techniques. Additionally, we divided all the tasks we have to do from now until Boston and divided them according to each of our team members strengths.</p> <br>
     <center><img src="https://pbs.twimg.com/media/CHMEqyEUkAAhpRg.jpg:large" width="450"></center> <br>
+
     <center><img src="https://static.igem.org/mediawiki/2015/2/23/NAIT_mentorship.jpeg" width="450"></center> <br>
 
     <p> We also changed the look of our wiki this week. We opted for a more centralized design. Our new logo went live this week as well (we had to change it due to branding issues with our institution). We took inspiration from the separated protein bands in SDS-PAGE and we are quite happy with how it turned out. </p><br>
 
     <p> We also changed the look of our wiki this week. We opted for a more centralized design. Our new logo went live this week as well (we had to change it due to branding issues with our institution). We took inspiration from the separated protein bands in SDS-PAGE and we are quite happy with how it turned out. </p><br>
 
     <p> On June 11th, we were joined by Ms. Linda Hoang and Blaze from our institution in a professional photo shoot for NAIT's <b>techlife magazine</b>. The majority of us had never been in a photoshoot before so it was quite the experience. Our mentors, Marcelo and Matt&eacute;a laughed at us at every step of the way. They also joined the shoot at the end. </p><br>
 
     <p> On June 11th, we were joined by Ms. Linda Hoang and Blaze from our institution in a professional photo shoot for NAIT's <b>techlife magazine</b>. The majority of us had never been in a photoshoot before so it was quite the experience. Our mentors, Marcelo and Matt&eacute;a laughed at us at every step of the way. They also joined the shoot at the end. </p><br>
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     <center><h1>Thank You, Office of Research and Innovation</h1></center>
 
     <center><h1>Thank You, Office of Research and Innovation</h1></center>
     <center><img src="https://pbs.twimg.com/media/B1TzI0rIAAA1t1w.jpg" width="400px"></center><br>
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     <center><img src="https://static.igem.org/mediawiki/2015/e/e3/NAIT_nexen.jpeg" width="400px"></center><br>
 
     <p>We are so lucky to have the support of such amazing people at NAIT. Eduardo did a phenomenal job presenting our ideas to the Office of Research and Innovation which made them very excited for the future of our project. They gave excellent critique about our presentation and we definitely plan to consider their comments for our iGEM presentation in September. After today, we decided to schedule two more meetings before we leave for Boston! We are successfully spreading our excitement about this project!</p>
 
     <p>We are so lucky to have the support of such amazing people at NAIT. Eduardo did a phenomenal job presenting our ideas to the Office of Research and Innovation which made them very excited for the future of our project. They gave excellent critique about our presentation and we definitely plan to consider their comments for our iGEM presentation in September. After today, we decided to schedule two more meetings before we leave for Boston! We are successfully spreading our excitement about this project!</p>
 
<br>
 
<br>
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     <center><h1>Who Are We? Team ARGENTUM!</h1></center>
 
     <center><h1>Who Are We? Team ARGENTUM!</h1></center>
 
     <center><img src="https://static.igem.org/mediawiki/2015/c/c7/NAIT_IGEM_Separated.png" width="250px"></center>
 
     <center><img src="https://static.igem.org/mediawiki/2015/c/c7/NAIT_IGEM_Separated.png" width="250px"></center>
     <p>Today, we met with NAIT's Branding department to try and come up with a new identity for our team. Previously, we had derived our team logo from the original iGEM logo. Sana and Derek at the Branding and Marketing office gave great advice on how we can make our team stand out. Although our original logo was nice and nicely embodied our project, it did not give our team its own personal identity.  </p><br>
+
     <p>Today, we met with NAIT's Branding department to try and come up with a new identity for our team. Previously, we had derived our team logo from the original iGEM logo. Sana and Derek at the Branding and Marketing office gave great advice on how we can make our team stand out. Although our original logo was nice and embodied out project well, it did not give our team its own personal identity.  </p><br>
 
     <p>We settled on a new team name: ARGENTUM. The Latin word for silver, our project is mainly about the reaction between silver staining reagents and proteins. We had already used Argentum as our project name so the transition from project name to team name was easy. Woo hoo!</p>
 
     <p>We settled on a new team name: ARGENTUM. The Latin word for silver, our project is mainly about the reaction between silver staining reagents and proteins. We had already used Argentum as our project name so the transition from project name to team name was easy. Woo hoo!</p>
  
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    <center><h1>Office of Research and Innovation - Presentation 2</h1>
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<img src="https://static.igem.org/mediawiki/2015/1/1b/NAIT_Pres2.jpg" width="100%"></center>
 +
    <p>In this presentation we went through the run down of SDS PAGE and the bio brick backbone used to create our proteins. We also went deeper in the process on how to produce the colour and specific amino acid configurations we engineered. The point for this presentation is to practice our presentation skills and also get feedback on our progress. The Office of Research and Innovation gave us excellent suggestions for improving our final PowerPoint for iGEM.</p>
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    <center><h1>Transforming our Bacteria</h1>
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<img src="https://static.igem.org/mediawiki/2015/d/d6/NAIT_Tplate1.jpeg" width="100%"></center><br>
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    <p>From ligation, all novel sequence plates had growth which means some of those colonies may contain our custom DNA!!! </p>
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    <center><h1>First Day of School!</h1>
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<img src="https://static.igem.org/mediawiki/2015/a/ad/NAIT_Stuff.jpeg" width="100%"></center><br>
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    <p>Darn. We no longer have the entire institution to ourselves...</p>
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    <center><h1>Preliminary Results!</h1>
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<img src="https://static.igem.org/mediawiki/2015/7/7d/NAIT_PrelimResultsSelfie.jpg" width="100%"></center><br>
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    <p>We can see the light!!!!</p>
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    <center><h1>AHHHH!!! The HOME STRETCH</h1>
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<img src="https://static.igem.org/mediawiki/2015/5/58/NAIT_WikiFREEEEEZE.jpg" width="100%"></center><br>
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    <p>It's a mad rush here at NAIT's HP Centre. OH MY GODDDDD.</p>
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Latest revision as of 03:11, 19 September 2015

Team NAIT 2015

Log Book
Picture

First Day in Lab!

Our team got the overview of our work space for the summer. We were geared and ready to start the iGEM adventure!

May 4
Movie

Research into Silver Staining

Before beginning a project, it is of great importance to fully understand what it is you are planning to research. Our team focused on understanding the basics and chemistry of silver staining completely.

May 4 to 8
Picture

Formation of Color in Silver Staining

What was the scientific basis of color formation post silver staining?

May 11 to 15
Location

Spruce Grove High School Lab

Students taking Biology 30 at SGHS came to NAIT today and we were lucky enough to be able to T.A for them.

May 21
Location

Alberta Innovates and geekStarter

Team NAIT went on a road trip to the University of Calgary!

May 24
Location

Research Continued...

Getting our wiki set up and looking for sponsorships.

May 25 to 29
Location

Getting Our Timeline Set Up

Time is ticking! We are already into the second month of the summer!

June 1 to 5
Location

techLife and NAIT Photoshoot


We had a photoshoot with NAIT's techLife magazine. Thank you to Ms. Linda Hoang and Blaise for your patience!

June 11
Location

Ongoing Research and Practice

Perfecting our silver stain techniques!

June 12
Location

Sequences Ordered!

First four sequences of our own design ordered from IDT!

June 16
Location

Met the President!

No, not Obama. We met NAIT's President! Dr. Glenn Felthan and NAIT's VP External and CDO, Mr. George Andrews were most accommodating.

June 18
Location

Article on Synthetic Biology in Canada

Submitted an article for Team iGEM Amoy China.

June 20
Location

Plasmid and Sequence Digestion

A plasmid double digestion was performed along with digestion of four of our sequences. The sequences used were Arginine, Lysine, Glutamic Acid and Cysteine samples.

June 22
Location

Sequences Arrived!

June 24
Location

Research, Presentations and Practice

"If we knew what it was we were doing, it would not be called research, would it?" - Albert Einstein

June 22 to 25
Location

Presentation to the Office of Research and Innovation

Today, we were lucky enough to have ORnI hear, assess and critique our preliminary presentation for iGEM. We are so happy to know that we have the full support of so many amazing individuals at the Office of Research and Innovation and at NAIT.

June 26
Location

Happy Canada Day!

July 1
Location

Pumping out those Sequences

This week, our team really focused on creating a variety of sequences for testing. Equipped with the knowledge from our literature searches in prior weeks, we crafted each sequence carefully and diligently. As a team, we created and ordered over 25 this week!

June 29 to July 3
Location

And so the cloning begins...

Dr. Marcet helped us get started with cloning! But first, we had to test our enzymes to see if they will properly linearize our plasmid!

July 6
Location

Expressing our Custom Sequences in our E. coli

Got our sequences inserted (hopefully) and now we want to grow our bacteria!

July 10
Location

Team BBQ!

We had an awesome Sunday barbecue! The sun was shining bright, we had cold drinks and great company - A perfect day.

July 12
Location

Maya Monday

Slowly cranking out those animations! Stay tuned!

July 13
Location

Experiment and Protocols Flowchart

Drafted and published the first version of our experimental protocols and design! You can view it here.

July 16
Location

Officially Registered!

SO EXCITED!!!!!!!!!

July 20
Location

AITF and geekStarter Workshop

NAIT is off for the 6 hour drive to visit a workshop hosted by our co-Albertan team, Team Lethbridge!

July 24 to 26
Picture

Team Re-Branding

Today, we stepped away from our original iGEM inspired logo and tried to come up with a new team identity so that we could stand out from the crowd and our team would leave a lasting impression in iGEM.

July 30
Picture

NAIT Photoshoot and Mini-Prep

We had another photo shoot with our institution! Eduardo and Joy managed to escape early, because of a plasmid mini-prep.

July 31
Picture

Let's Work Together!

Our team is new to iGEM so we are helping out others as best we can. We've completed many surveys and given feedback to many teams!

August 6
Picture

Title and Abstract.. Submitted!

Today was the due date for the final abstract and title for iGEM's brochures and websites.

August 7
Picture

Officially Argentum!

Received our new logo concepts from our friend and design advisor, Derek Lue. We changed the layout of our Wiki to what you see now!

August 10
Picture

Abbie's Back!

Abbie’s last day working her full-time summer student position as a lab tech for Keyera AEF. Time to get into the lab and work on the project!

August 14
Picture

Go, Team NAIT, GO!

We're getting an overwhelming amount of support from NAIT. We're even getting golf shirts to wear in Boston!

August 17
Picture

Argentum ... Re- IM[Ag]INE 'd

Turns out, we cannot use Argentum as our team name. There is a local company that has trademarked that brand and we do not want to get into any trouble.

August 19
Picture

Watch our Intro Video!

We have a new respect for anyone who has to be in front of the camera as their career.. This less-than-two-minutes video took us a few hours to shoot and edit.

Watch it! August 20
Picture

iGEM Banner

Final banner design finished and ready for sending to iGEM HQ. We cannot wait to see our banner hanging at the Hynes Convention Centre.


August 21
Picture

Collaboration with our New Application Track

As you know, we're a first-time team. We reached out to our Track mates and asked them to help us out.

August 26-28
Picture

Digestion of Sequences

All our sequences (23) were digested and in doing so each were cleaved at specific sites to later ligate with our plasmid, pSB1C3.

August 26
Picture

IDT Interview

We got interviewed by one of our primary sponsors, IDT!

Read more August 27
Picture

Digestion of Plasmids + rSAP

We digested our pSB1C3 plasmids to cleave each at specific restriction sites to be able to insert our sequences of interest.

August 28
Picture

Presentation.. Round Two!

We presented to NAIT's Office of Research and Innovation again to give them a rundown on our current progress for our project.

August 28
Picture

Sequence and Plasmid Ligation

Ligation was conducted on our sequences of interest to join and bind with our plasmid pSB1C3 (T7+RBS) backbone.

August 29
Picture

Transformation!

From ligation, all novel sequences were transformed and plated. We counted a total of 302 colonies from this experiment. (THEY ARE ALIVE!!!!)

August 31 to September 2
Picture

Colony PCR

Four 96 well plates and many agarose gels later... We obtained the colonies that showed to have taken up our sequences!

September 2
Picture

Grew Our Colonies

To ensure our colonies would produce adequate protein when induced, we prepared them for harvest during their log phase of growth.

September 5
Location

IPTG Induction of Proteins

We're starting to see the light at the end of the tunnel! We induced our proteins with IPTG when they had an absorbance of approximately 0.8.

September 8
Location

Back to School for NAIT students!

Noooooooooo

september 8
Location

Ni NTA Kit Purification!

Received our Ni-NTA kit from the University of Alberta.

September 10
Location

IM[Ag]INE Shirts have Arrived!


Additionally, we finished pelleting and purifying more samples of our proteins. Unfortunately, not all of them showed a concentration in the NanoDrop.

September 11
Location

Preliminary Results

After four months of work, we completed the last step of our experimental design - SDS PAGE and Silver Staining of our synthetic proteins.

September 13
Location

Experimental Validation

We ran more gels in order to validate our preliminary results. Regrettably, the gels failed to run properly and we were unable to finish in time.

September 14
Location

The End of our Lab Journey

And so it ends. Today, we pulled the plug on all remaining lab work and running experiment. Now, it's time to focus on our Wiki, Poster and Presentation.

September 15
Location

Wiki FREEZE!!!!!

Had a blast browsing through our fellow iGEM team's tweets about #WikiFreeze. We're definitely scrambling. AHHH!!!!

September 18
Location

DestiNAITion: Boston

September 18