Difference between revisions of "Team:TUDelft/Contributions/Main"

 
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             <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/e/e4/T--TUDelft--2018_Contributionshead.png"
 
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     <p>During the course of our iGEM project, we have developed three tools which we would like to share with the iGEM community. The first is an online tool which translates any given text in ASCII format into DNA, which we extended from a tool made by <a class="orngcrl" href="https://2014.igem.org/Team:Aberdeen_Scotland/DNA" target="_blank">iGEM Aberdeen 2014</a>. The second is a gRNA generation tool that takes into account codon substitutions by generating gRNA’s for all possible DNA sequences given an amino acid sequence. The third is a toolkit for holding a bioethics workshop, which we have developed with advice from Mr Virgil Rerimassie and the tool he co-developed: the <a class="orngcrl" href="https://live.flatland.agency/12290417/rathenau-igem/" target="_blank">iGEMers guide to the future.</a></p>
+
     <p>During the course of our iGEM project, we have developed three tools which we would like to share with the iGEM community. The first is an online tool which translates any given text in ASCII format into DNA, which we extended from a tool made by <a class="orngcrl" href="https://2014.igem.org/Team:Aberdeen_Scotland/DNA" target="_blank">iGEM Aberdeen 2014</a>. The second is a gRNA generation tool that takes into account codon substitutions by generating gRNA’s for all possible DNA sequences given an amino acid sequence. The third is a toolkit for holding a bioethics workshop, which we have developed with advice from Mr Virgil Rerimassie and the tool he co-developed: the <a class="orngcrl" href="https://live.flatland.agency/12290417/rathenau-igem/" target="_blank">iGEMers guide to the future.</a></p>
 
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<br>
 
<br>
  
−
 
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<!---->
 
 
     <h1 class="orngcrl">Barcoding Tool</h1>
 
     <h1 class="orngcrl">Barcoding Tool</h1>
 
     <p>We developed an iGEM barcoding tool by improving upon an existing iGEM DNA translation tool developed by <a class="orngcrl" href="https://2014.igem.org/Team:Aberdeen_Scotland/DNA" target="_blank">iGEM Aberdeen Scotland, 2014</a>. Our purpose for this is to enable sample multiplexing by barcoding DNA samples. This tool is very versatile however and can possibly of use to other iGEM teams. The tool can be found <a class="orngcrl" href="https://2018.igem.org/Team:TUDelft/Improve#webtool">here</a>. </p>
 
     <p>We developed an iGEM barcoding tool by improving upon an existing iGEM DNA translation tool developed by <a class="orngcrl" href="https://2014.igem.org/Team:Aberdeen_Scotland/DNA" target="_blank">iGEM Aberdeen Scotland, 2014</a>. Our purpose for this is to enable sample multiplexing by barcoding DNA samples. This tool is very versatile however and can possibly of use to other iGEM teams. The tool can be found <a class="orngcrl" href="https://2018.igem.org/Team:TUDelft/Improve#webtool">here</a>. </p>
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         We will discuss first how to set the goals of a workshop, then the general set-up, followed by the materials and people needed and finally do some suggestions on documenting the event. In each case, we will first present the general principles we followed, and then give an example based on our experience duirng the <a class="orngcrl" href="https://2018.igem.org/Team:TUDelft/EurAsianMeetup" target="_blank">iGEM EurAsian meetup </a>in a dropdown. </p>
 
         We will discuss first how to set the goals of a workshop, then the general set-up, followed by the materials and people needed and finally do some suggestions on documenting the event. In each case, we will first present the general principles we followed, and then give an example based on our experience duirng the <a class="orngcrl" href="https://2018.igem.org/Team:TUDelft/EurAsianMeetup" target="_blank">iGEM EurAsian meetup </a>in a dropdown. </p>
 
          
 
          
−
<h2 class="orngcrl">Set your goals</h2>  
+
<h2 class="orngcrl">1. Set your goals</h2>  
 
<p>Setting up the workshop starts with asking yourself some questions: </p>
 
<p>Setting up the workshop starts with asking yourself some questions: </p>
−
         <ul >
+
         <ul class="ulorngcrl">
 
<li>What is the goal of the workshop? </li>
 
<li>What is the goal of the workshop? </li>
 
<li>What is your starting position? </li>
 
<li>What is your starting position? </li>
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<li>What are the conditions/factors/variables to account for that will effect getting to the desired end position?</li>
 
<li>What are the conditions/factors/variables to account for that will effect getting to the desired end position?</li>
 
</ul>
 
</ul>
−
          
+
         <br>
 
<p>When answering these questions, make sure they connect to each other logically! Also make sure that the goal you are setting is realistic given your setting. If  you for example have a workshop time of one hour, it might be a bit much to ask people to come up with complete answers to questions they had not yet thought about. </p>
 
<p>When answering these questions, make sure they connect to each other logically! Also make sure that the goal you are setting is realistic given your setting. If  you for example have a workshop time of one hour, it might be a bit much to ask people to come up with complete answers to questions they had not yet thought about. </p>
−
          
+
         <br>
 
<button class="collapsible corngcrl"><span id="goalsexample"></span>Example: setting the goals of the iGEM EurAsian meetup bioethics workshop.</button>
 
<button class="collapsible corngcrl"><span id="goalsexample"></span>Example: setting the goals of the iGEM EurAsian meetup bioethics workshop.</button>
 
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<div class="content">
 
<br>
 
<br>
 
<p>
 
<p>
−
<b>Goal</b> <br>
+
<b class="orngcrl">Goal</b> <br>
 
We aimed to increase the awareness of bioethics in the participants and to trigger reflection on the bioethical questions of their own projects. <br>
 
We aimed to increase the awareness of bioethics in the participants and to trigger reflection on the bioethical questions of their own projects. <br>
−
     <b>Starting position</b> <br>
+
     <bclass="orngcrl">Starting position</b><br>
−
     Participants from iGEM teams with ages between 15-28 and very different cultural backgrounds. <br>
+
     Participants from iGEM teams with ages between 15-28 and very different cultural backgrounds. <br><br>
−
     <b>Ending position</b> <br>
+
     <b class="orngcrl">Ending position</b> <br>
 
     Each participant has started to ask bioethical questions concerning their own project. <br>
 
     Each participant has started to ask bioethical questions concerning their own project. <br>
−
     <b>Conditions/factors/variables to account for that will effect getting to the desired end position:</b> <br>
+
     <br>Conditions/factors/variables to account for that will effect getting to the desired end position: <br>
 
     </p>
 
     </p>
−
<ul>
+
<ul class="orngcrl">
 
<li>a limited time of 90 minutes</li>
 
<li>a limited time of 90 minutes</li>
−
<li>a large number of attendees (120) </li>
+
<li>a large number of attendees (120) </li><br>
 
</ul>
 
</ul>
 
</div>
 
</div>
 
        
 
        
 
          
 
          
−
   <h2 class="orngcrl">Make a set-up</h2>     
+
   <h2 class="orngcrl">2. Make a set-up</h2>     
 
         <p>When you have set your goals and determined the variables you need to take into account, you can start setting up the workshop itself. Decisions that need to be made are:</p>
 
         <p>When you have set your goals and determined the variables you need to take into account, you can start setting up the workshop itself. Decisions that need to be made are:</p>
−
           <ul >
+
           <ul class="orngcrl">
 
<li>How many topic(s) do you want to cover? </li>
 
<li>How many topic(s) do you want to cover? </li>
 
<li>What topic(s) are you going to discuss? </li>
 
<li>What topic(s) are you going to discuss? </li>
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<li>Are you going to guide the discussions and if so, how? It is important to consider this question carefully. Having a moderator per discussion group can help deepening the level of the discussion, since this person can keep asking ‘why’ questions if the discussion stays superficial. </li>
 
<li>Are you going to guide the discussions and if so, how? It is important to consider this question carefully. Having a moderator per discussion group can help deepening the level of the discussion, since this person can keep asking ‘why’ questions if the discussion stays superficial. </li>
 
<li>How long will each discussion round take?</li>
 
<li>How long will each discussion round take?</li>
−
<li>Would you like participants to prepare something beforehand?</li>
+
<li>Would you like participants to prepare something beforehand?</li><br>
 
</ul>     
 
</ul>     
 
          
 
          
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<p>
 
<p>
 
Based on our considerations, we answered the questions in the following ways. <br><br>
 
Based on our considerations, we answered the questions in the following ways. <br><br>
−
     <b>Ambiance</b>
+
     <b class="orngcrl">Ambiance</b>
 
     We wanted to create an open discussion where there was time to progress from superficial opinions to the values that underlie them. To achieve this, it is important that:
 
     We wanted to create an open discussion where there was time to progress from superficial opinions to the values that underlie them. To achieve this, it is important that:
 
</p>
 
</p>
−
<ul >
+
<ul class="orngcrl">
 
<li>The groups are small.</li>
 
<li>The groups are small.</li>
 
<li>There is enough time per topic. </li>
 
<li>There is enough time per topic. </li>
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</ul>  
 
</ul>  
 
<p>Furthermore, we stressed that in a discussion:</p>
 
<p>Furthermore, we stressed that in a discussion:</p>
−
  <ul >
+
  <ul class="ulorngcrl">
 
<li>All views are allowed to exist and be shared.</li>
 
<li>All views are allowed to exist and be shared.</li>
 
<li>Eliminate judgments in your head.</li>
 
<li>Eliminate judgments in your head.</li>
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         <b>Preparation</b><br>
 
         <b>Preparation</b><br>
−
         We decided against asking participants to prepare something beforehand, as we wanted them to come to the discussion with an open mind.
+
         We decided against asking participants to prepare something beforehand, as we wanted them to come to the discussion with an open mind.<br><br>
 
          
 
          
 
     </p>
 
     </p>
 
       </div>
 
       </div>
 
        
 
        
−
<h2 class="orngcrl">Materials</h2>  
+
<h2 class="orngcrl">3. Materials</h2>  
−
       <p>For the workshop, you will need: <br>
+
       <p>For the workshop, you will need: <br><br>
 
       In general </p>
 
       In general </p>
−
       <ul >
+
       <ul class="ulorngcrl">
 
<li>A room with a screen,and an audio installation.</li>
 
<li>A room with a screen,and an audio installation.</li>
 
<li>A wireless microphone (so you can walk around and ask participants for their opinions). </li>
 
<li>A wireless microphone (so you can walk around and ask participants for their opinions). </li>
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<li>Tables and chairs.</li>
 
<li>Tables and chairs.</li>
 
<li>(optional) A good camera to take some pictures.</li>
 
<li>(optional) A good camera to take some pictures.</li>
−
</ul>  
+
</ul> <br> 
 
   <p>Per discussion group</p>     
 
   <p>Per discussion group</p>     
−
       <ul >
+
       <ul class="ulorngcrl">
 
<li>Big sheets of paper to draw ideas on.</li>
 
<li>Big sheets of paper to draw ideas on.</li>
 
<li>Pens/markers. </li>
 
<li>Pens/markers. </li>
 
<li>Sheets of paper with the group numbers on them to put on the tables.</li>
 
<li>Sheets of paper with the group numbers on them to put on the tables.</li>
−
</ul>  
+
</ul> <br>
 
       <p>For the moderators</p>
 
       <p>For the moderators</p>
−
               <ul >
+
               <ul class="ulorngcrl">
 
<li>A short introduction presentation or document so that they come prepared.</li>
 
<li>A short introduction presentation or document so that they come prepared.</li>
 
<li>(optional) Guiding questions or opinions that they can use if they want. </li>
 
<li>(optional) Guiding questions or opinions that they can use if they want. </li>
 
</ul>  
 
</ul>  
 
        
 
        
−
<h2 class="orngcrl">People</h2>         
+
<h2 class="orngcrl">4. People</h2>         
 
       <p>The people who help make your workshop a success:</p>
 
       <p>The people who help make your workshop a success:</p>
−
             <ul >
+
             <ul class="ulorngcrl">
 
<li>Your participants!</li>
 
<li>Your participants!</li>
 
<li>Moderators per table, who guide the discussions when needed. </li>
 
<li>Moderators per table, who guide the discussions when needed. </li>
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<li>Someone who films and/or takes pictures (ask if all participants are okay with this at the start of the workshop).</li>
 
<li>Someone who films and/or takes pictures (ask if all participants are okay with this at the start of the workshop).</li>
 
</ul>     
 
</ul>     
−
   <h2 class="orngcrl">Documentation</h2>       
+
   <h2 class="orngcrl">5. Documentation</h2>       
 
       <p>Please think of the way you want to document your workshop beforehand, if at all. Keep in mind that you ask for permission and that your documentation does not interfere with the workshop ambiance. A good way to document is to ask people for quotes.</p>
 
       <p>Please think of the way you want to document your workshop beforehand, if at all. Keep in mind that you ask for permission and that your documentation does not interfere with the workshop ambiance. A good way to document is to ask people for quotes.</p>
 
        
 
        
−
   <h2 class="orngcrl">Recommendations</h2>           
+
   <h2 class="orngcrl">6. Recommendations</h2>           
 
       <p>From our own experience, we would like to give some recommendations on parts that did not go according to plan.</p><br>
 
       <p>From our own experience, we would like to give some recommendations on parts that did not go according to plan.</p><br>
−
                   <ul >
+
                   <ul class="ulorngcrl">
 
<li>Different from our plan was that we had bigger groups of 15 to 20 people, because we did not have enough moderators to enable smaller groups. The discussions were still interesting, but this did mean that some of the depth we had hoped for was lost. Feedback from our moderators was that 20 minutes was not enough time to have everyone in the group participate fully. So if in any way possible, make the groups small.</li>
 
<li>Different from our plan was that we had bigger groups of 15 to 20 people, because we did not have enough moderators to enable smaller groups. The discussions were still interesting, but this did mean that some of the depth we had hoped for was lost. Feedback from our moderators was that 20 minutes was not enough time to have everyone in the group participate fully. So if in any way possible, make the groups small.</li>
 
<li>As expected, the discussions on gene drives were more broad than the ones on bioluminescent trees. Choosing the introduction material is very important. If you have a shy, bigger group more guided material is good. For people to really think of their own views and values, less guided starting material is better. </li>
 
<li>As expected, the discussions on gene drives were more broad than the ones on bioluminescent trees. Choosing the introduction material is very important. If you have a shy, bigger group more guided material is good. For people to really think of their own views and values, less guided starting material is better. </li>
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</ul>  
 
</ul>  
 
       <div id="references"></div>
 
       <div id="references"></div>
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     <h2 class="orngcrl">References</h2>           
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     <h1 class="orngcrl">References</h1>           
 
     <ol class="orngcrl">
 
     <ol class="orngcrl">
 
         <li><a class="orngcrl" href="https://www.youtube.com/watch?v=75iP50LEHrU" target="_blank">Empinado, H. (2015, December 11). What is a Gene Drive? - STAT on YouTube. Retrieved October 17, 2018, from https://www.youtube.com/watch?v=75iP50LEHrU</a></li>
 
         <li><a class="orngcrl" href="https://www.youtube.com/watch?v=75iP50LEHrU" target="_blank">Empinado, H. (2015, December 11). What is a Gene Drive? - STAT on YouTube. Retrieved October 17, 2018, from https://www.youtube.com/watch?v=75iP50LEHrU</a></li>
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Latest revision as of 02:12, 18 October 2018

Contributions Image

During the course of our iGEM project, we have developed three tools which we would like to share with the iGEM community. The first is an online tool which translates any given text in ASCII format into DNA, which we extended from a tool made by iGEM Aberdeen 2014. The second is a gRNA generation tool that takes into account codon substitutions by generating gRNA’s for all possible DNA sequences given an amino acid sequence. The third is a toolkit for holding a bioethics workshop, which we have developed with advice from Mr Virgil Rerimassie and the tool he co-developed: the iGEMers guide to the future.


Barcoding Tool

We developed an iGEM barcoding tool by improving upon an existing iGEM DNA translation tool developed by iGEM Aberdeen Scotland, 2014. Our purpose for this is to enable sample multiplexing by barcoding DNA samples. This tool is very versatile however and can possibly of use to other iGEM teams. The tool can be found here.


gRNA generation tool

We developed a gRNA generation tool that is able to generate all possible gRNA’s at a given position, including all possibilities for codon substitutions. It does this by searching for an overlap between regions that the user is interested in, positions where a PAM sequences are found and regions with very little possible codon substitutions. Our purpose for this is to exclude codon substitution as a way to circumvent our detection method. It can also be useful for any other application that deals with high amounts of synonymous mutations in the gene they want to find. A more detailed explanation of the functioning of the tool can be found here and the code here.



Guide to organizing a bioethics workshop


The best way to teach people is by involving them actively in discussions and workshops. We did this during the iGEM Eurasian meetup by discussing bioethics with the attendees. We designed this workshop with the active involvement of bioethicist Virgil Rerimassie and the tool he co-developed: the iGEMers guide to the future, frame reflection tool. We would like to share how to develop a workshop like this with the iGEM community, so that teams of the future can use this guide to further develop awareness of bioethics. Are you interested in the experiences of the workshop we organized? Please visit our education and public outreach page.
We will discuss first how to set the goals of a workshop, then the general set-up, followed by the materials and people needed and finally do some suggestions on documenting the event. In each case, we will first present the general principles we followed, and then give an example based on our experience duirng the iGEM EurAsian meetup in a dropdown.

1. Set your goals

Setting up the workshop starts with asking yourself some questions:

  • What is the goal of the workshop?
  • What is your starting position?
  • What is the end position you want to reach?
  • What are the conditions/factors/variables to account for that will effect getting to the desired end position?

When answering these questions, make sure they connect to each other logically! Also make sure that the goal you are setting is realistic given your setting. If you for example have a workshop time of one hour, it might be a bit much to ask people to come up with complete answers to questions they had not yet thought about.



Goal
We aimed to increase the awareness of bioethics in the participants and to trigger reflection on the bioethical questions of their own projects.
Starting position
Participants from iGEM teams with ages between 15-28 and very different cultural backgrounds.

Ending position
Each participant has started to ask bioethical questions concerning their own project.

Conditions/factors/variables to account for that will effect getting to the desired end position:

  • a limited time of 90 minutes
  • a large number of attendees (120)

2. Make a set-up

When you have set your goals and determined the variables you need to take into account, you can start setting up the workshop itself. Decisions that need to be made are:

  • How many topic(s) do you want to cover?
  • What topic(s) are you going to discuss?
  • How are you going to introduce the topic(s)?
  • Do you want a plenary discussion, discussion in smaller groups, or a mixture?
  • Are you going to guide the discussions and if so, how? It is important to consider this question carefully. Having a moderator per discussion group can help deepening the level of the discussion, since this person can keep asking ‘why’ questions if the discussion stays superficial.
  • How long will each discussion round take?
  • Would you like participants to prepare something beforehand?


Based on our considerations, we answered the questions in the following ways.

Ambiance We wanted to create an open discussion where there was time to progress from superficial opinions to the values that underlie them. To achieve this, it is important that:

  • The groups are small.
  • There is enough time per topic.
  • The groups are guided by an impartial person who keeps asking: “why?”, so that participants are forced to explain what underlies their initial statement.

Furthermore, we stressed that in a discussion:

  • All views are allowed to exist and be shared.
  • Eliminate judgments in your head.
  • Sharing more is better, improvise, ‘cheat the rules’ (for creativity).
  • All ideas created here are from the whole group, ownership cannot be claimed.

Topics
We decided to cover two topics in rounds of 30 minutes, and to leave the final half an hour open for participants to reflect on their own projects. We covered the two topics Bioluminesent trees and gene drives, because they were both topics that iGEM teams had worked on in the past (Cambridge 2010, Minnesota 2016) and that could have implications that were not limited to a single country or continent.

Topic introduction
We introduced both topics with short movies. The first movie on bioluminescent trees (van Ekelen, 2013) presented a future scenario where bio luminescent trees have been planted in parks, and reflects on the implications this could have. This movie presented a possible opinion, which made starting the discussion a bit easier. The second movie on gene drives (Empinado, 2015), was far less opinionated, which allowed the discussion to move into more diverse directions. After the short movies we asked the bioethics experts present to give a short reflection on what they saw and what questions they would start to ask. We then let the groups start their own discussions.

Groups
We decided on groups of five or six participants with a moderator each, so that there would be enough time to let everyone speak and also to ask each other questions. We hoped this would enable the discussion gets to the value level. We also wanted to expose our participants to as many different opinions as possible. This is why we decided to form new groups per discussion round, and why we decided on a short plenary discussion of 5 minutes after each round. In this plenary part, we asked groups to shortly present what they had discussed and allowed the groups to react to each other.

Guidance
We asked supervisors present at the meetup to moderate each table. They would be impartial moderators that would ensure everyone had the opportunity to speak and that would ask “Why?” questions if the discussion was superficial. Per topic, we also prepared questions that our moderators could ask to steer the discussion away from dead ends and opinionated sources that could trigger a fresh discussion topic. The moderators were free to use these if they thought they needed them. We introduced the workshop to them in a short presentation the day before so that they had time to prepare.

Time per round
We decided on 30 minutes per round, of which 5 were to introduce the topic, 20 to discuss in groups and 5 minutes to discuss plenary.

Preparation
We decided against asking participants to prepare something beforehand, as we wanted them to come to the discussion with an open mind.

3. Materials

For the workshop, you will need:

In general

  • A room with a screen,and an audio installation.
  • A wireless microphone (so you can walk around and ask participants for their opinions).
  • A presentation with your introduction slides and (optionally) movies on it.
  • Tables and chairs.
  • (optional) A good camera to take some pictures.

Per discussion group

  • Big sheets of paper to draw ideas on.
  • Pens/markers.
  • Sheets of paper with the group numbers on them to put on the tables.

For the moderators

  • A short introduction presentation or document so that they come prepared.
  • (optional) Guiding questions or opinions that they can use if they want.

4. People

The people who help make your workshop a success:

  • Your participants!
  • Moderators per table, who guide the discussions when needed.
  • A presenter who introduces each topic and keeps track of time (can two or several as well).
  • Someone who films and/or takes pictures (ask if all participants are okay with this at the start of the workshop).

5. Documentation

Please think of the way you want to document your workshop beforehand, if at all. Keep in mind that you ask for permission and that your documentation does not interfere with the workshop ambiance. A good way to document is to ask people for quotes.

6. Recommendations

From our own experience, we would like to give some recommendations on parts that did not go according to plan.


  • Different from our plan was that we had bigger groups of 15 to 20 people, because we did not have enough moderators to enable smaller groups. The discussions were still interesting, but this did mean that some of the depth we had hoped for was lost. Feedback from our moderators was that 20 minutes was not enough time to have everyone in the group participate fully. So if in any way possible, make the groups small.
  • As expected, the discussions on gene drives were more broad than the ones on bioluminescent trees. Choosing the introduction material is very important. If you have a shy, bigger group more guided material is good. For people to really think of their own views and values, less guided starting material is better.
  • If you want to assign participants to (several) tables, you need some sort of system to do this. We decided to hand out sheets of paper with two numbers on it (a group number for the first and second round). You can also assign people by counting or let them choose themselves.

References

  1. Empinado, H. (2015, December 11). What is a Gene Drive? - STAT on YouTube. Retrieved October 17, 2018, from https://www.youtube.com/watch?v=75iP50LEHrU
  2. iGEM team Cambridge 2010 (2010). Team:Cambridge/Tools/Lighting - 2010.igem.org. Retrieved October 17, 2018, from https://2010.igem.org/Team:Cambridge/Tools/Lighting
  3. iGEM team Minnesota 2016 (2016). Team:Minnesota - 2016.igem.org. Retrieved October 17, 2018, from https://2016.igem.org/Team:Minnesota
  4. Stemerding, d., Rerimassie, V., Betten, W., van der Meij, M., Kupper, F., Sonck, M., Delgado, A., Robay, Z., Ashour, K. (2017). Interactive iGem Rathenau - Flatland Agency. Retrieved October 17, 2018, from https://live.flatland.agency/12290417/rathenau-igem/
  5. Van Eekelen, S. (2013, December 23). Rathenau Instituut - Bioluminescent Streetlamps on Vimeo. Retrieved October 17, 2018, from https://vimeo.com/82544956