Difference between revisions of "Team:UCopenhagen/Partnership"

 
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    <h1> Partnership </h1>
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<h5>Intro</h5>
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<div>Early on in our iGEM journey we discovered that Aalto-Helsinki was working on designing a biosensor for their project, just like we were. On <b> May 14th</b> we talked with Aalto-Helsinki for the first time at a coffee hour organized by us via Zoom. Initial conversations lead us to the realization that we <b>shared specific goals</b> with the Aalto team - mainly our wish was to develop comprehensive ODE <b>modelling</b> and incorporate <b>ethical considerations</b> into our project work. Our dry-lab collaboration soon proved beneficial for our teams, and this lead to a partnership throughout the <b>season</b>, and eventually extending to human practice collaborations as well. Specifically our partnership has given us:
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<br>
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<ul>
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<li> ✧ An invaluable trouble-shooting partner whom we could share our journey with. </li>
  
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<li> ✧ Great modelling feedback, raising our model sophistication to the next level. </li>
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<li> ✧ A partner on our way to improving ethical considerations for iGEM projects. </li>
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</ul>
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<br>
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The professional (and social) exchanges have not only provided us with directly useful ideas and trouble-shooting, but <b>inspired us</b> throughout our whole process to be open minded and <b>think critically</b> about our models and assumptions. It has help us understand how to communicate our project in various levels of details and convey our ideas successfully. We are extremely happy to have had the pleasure of working with Aalto-Helsinki throughout the summer and fall of 2020!</div>
  
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<div><h1>pictures?</h1></div>
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<h1>Timeline</h1>
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<h5 style="text-align:right;">Trouble-shooting Dry lab</h5>
 
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           <h2>1st meeting</h2>
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           <h3>Structural modelling</h3>
 
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               In June we decided it was time to see how the projects were going and we initiated an electronic correspondence concerning the viability of a <b>dry-lab collaboration</b>. Aalto responded positively to our proposal and we informed each other about <b>modeling prospects</b>. This led to our first meeting on <b>June 16th</b>, focused solely on dry-lab. We discussed our projects, designs, and modeling ambitions. Aalto told us about their intentions with <b>Rosetta</b> which positively influenced our own project development. They would use Rosetta to predict modifications in the <b>ligand binding site</b> of their <b>transcription factor MphR</b>, and we got inspired to use this modelling tool to determine affinity between the two parts of our truncated G-alpha. Following some more discussion, we agreed that maintaining mutual collaboration and planning more meetings made sense for both teams.
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             <h3>Reviewing initial ODE's</h3>
 
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             <div> As agreed, both teams shared their current models in July and played around with the models of the other team. In order to talk more in depth, we scheduled another meeting on <b>August 4th</b>. This was a nice, dense meeting where both parties exchanged lots of great suggestions, tips and tricks. The meeting focused mainly on how to improve included descriptions, comments and graphs, but also addressing the <b>shortcomings</b> of our current models. In particular, we addressed some oversimplification of Aalto-Helsinki's model regarding mRNA decay of MphR and the intracellular diffusion of antibiotics. They came with many recommendation on how to improve our model presentation with step-wise clarification and <b>intuitive labels</b>. </div>
 
            
 
            
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                   <h3>Final model comments</h3>
 
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During August, both teams implemented the feedback they had gotten, and another meeting was scheduled for <b>September 14th</b>. This meeting went through in a good pace as all presented models had improved greatly in quality, meaning that there were <b>less trivialities to discuss</b>. We were glad that Aalto-Helsinki discovered a <b>bug in our code</b> which we promptly fixed. We agreed the collaboration had been very beneficial for both teams so far. We agreed the next step will be <b>reviewing each other’s modeling wikis</b>. Check out both teams' final models here!
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<br> <a href="https://2020.igem.org/Team:Aalto-Helsinki/Model" >Aalto-Helsinki model</a> <br> <a href="https://2020.igem.org/Team:UCopenhagen/Model">Our model</a>
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<div><h5 id="ethics">Human Practice reflections</h5></div>
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<img src="https://static.igem.org/mediawiki/2020/8/82/T--UCopenhagen--partner-hptime.png" style="width:100%;">
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We knew early on that we wanted to troubleshoot the ethical aspects of our project with another iGEM team. We had already identified aspects of our project where ethical work would need to be done. However, in order to ensure that we did not have any major blind spots, we contacted our dry-lab partners, the Aalto iGEM team, in order to get an outside perspective. Aalto shared our interest in doing ethical work.<br><br>
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<b>Co-creating and co-hosting: The Nordic Ethics Workshop</b><br>
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After our first meeting on <b>July 16th</b>, we decided to organize a workshop focusing on ethics in iGEM. In order to make the workshop as inclusive and comprehensive as possible, <b>we decided to reach out to other iGEM teams from the Nordic countries</b>. We found out that <b>several teams in the Nordic countries were working on biosensors</b>, so it made sense to make a workshop focusing specifically on issues pertaining to the ethics revolving around GMOs in biosensors.
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The workshop was held on <b>August 25th</b> in <b>collaboration with iGEM teams from Aalto, Uppsala, Stockholm and Trondheim</b>. The guiding questions were:
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<b>How to dispose of biosensors?</b>
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<b>What are the risks of using GMOs?</b>
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        <li id="receptor">Zola H. Analysis of receptors for cytokines and growth factors in human disease. Dis Markers. 1996;12(4):225-240. doi:10.1155/1996/807021
 
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        <li id="organism">Gunde T, Barberis A. Yeast growth selection system for detecting activity and inhibition of dimerization-dependent receptor tyrosine kinase. Biotechniques. 2005;39(4):541-549. doi:10.2144/000112011<a href="#organism-ref" aria-label="Back to content">↩</a></li>
 
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The Nordic Ethics Workshop (NEW) was very educational. The teams took turns troubleshooting the others' projects.<br><br>
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<b>Our Takeaway from the Workshop</b><br>
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Our takeaway from the troubleshooting was mainly that our product did not come across as <b>intuitive</b> as we had hoped. The teams raised questions about the <b>placement of the patch</b>, how long one would have to wear it to get precise results, and what <b>type of sweat</b> the patch is compatible with. An <b>outsider's input</b> on the perceived uncertainties regarding our product was eye-opening. We can expect that the uncertainties voiced by other iGEM teams would also be shared by our patient group. As such, it became paramount to construct a <b>user-guide</b> for patients and to continually keep them as informed as possible.
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<b>Further Reflections with Team Aalto-Helsinki</b><br>
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We then had a second meeting on <b>August 27th</b> with Aalto-Helsinki <b>to reflect upon the workshop</b>. In this meeting, we went in-depth with some prepared comments on each other's projects. We had decided to mainly focus on the ethics regarding the possible environmental impact of Aalto-Helsinki's project, should they start to manufacture it. We created a <b>framework for estimating carbon footprint</b> and went through the estimation with calculations reflecting possible <b>assumptions</b> for their project.
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Aalto had chosen to focus on ethics regarding our product's use on humans. They had prepared questions concerning the <b>usability</b> of our product and skin-yeast interactions. This helped us improve our project presentation and collect <b>unanswered questions</b>.
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Latest revision as of 03:09, 28 October 2020

Description Design Implementation Poster
Engineering Success Modeling/Simulation Parts Overview Results Protocols Notebook Safety
Integrated Human Practices Entrepreneurship Education
Collaborations Partnership Our Contribution
Judging Form Medals
Team Members Attributions Sponsors
Intro
Early on in our iGEM journey we discovered that Aalto-Helsinki was working on designing a biosensor for their project, just like we were. On May 14th we talked with Aalto-Helsinki for the first time at a coffee hour organized by us via Zoom. Initial conversations lead us to the realization that we shared specific goals with the Aalto team - mainly our wish was to develop comprehensive ODE modelling and incorporate ethical considerations into our project work. Our dry-lab collaboration soon proved beneficial for our teams, and this lead to a partnership throughout the season, and eventually extending to human practice collaborations as well. Specifically our partnership has given us:
  • ✧ An invaluable trouble-shooting partner whom we could share our journey with.
  • ✧ Great modelling feedback, raising our model sophistication to the next level.
  • ✧ A partner on our way to improving ethical considerations for iGEM projects.

The professional (and social) exchanges have not only provided us with directly useful ideas and trouble-shooting, but inspired us throughout our whole process to be open minded and think critically about our models and assumptions. It has help us understand how to communicate our project in various levels of details and convey our ideas successfully. We are extremely happy to have had the pleasure of working with Aalto-Helsinki throughout the summer and fall of 2020!
Trouble-shooting Dry lab

Structural modelling

In June we decided it was time to see how the projects were going and we initiated an electronic correspondence concerning the viability of a dry-lab collaboration. Aalto responded positively to our proposal and we informed each other about modeling prospects. This led to our first meeting on June 16th, focused solely on dry-lab. We discussed our projects, designs, and modeling ambitions. Aalto told us about their intentions with Rosetta which positively influenced our own project development. They would use Rosetta to predict modifications in the ligand binding site of their transcription factor MphR, and we got inspired to use this modelling tool to determine affinity between the two parts of our truncated G-alpha. Following some more discussion, we agreed that maintaining mutual collaboration and planning more meetings made sense for both teams.

Reviewing initial ODE's

As agreed, both teams shared their current models in July and played around with the models of the other team. In order to talk more in depth, we scheduled another meeting on August 4th. This was a nice, dense meeting where both parties exchanged lots of great suggestions, tips and tricks. The meeting focused mainly on how to improve included descriptions, comments and graphs, but also addressing the shortcomings of our current models. In particular, we addressed some oversimplification of Aalto-Helsinki's model regarding mRNA decay of MphR and the intracellular diffusion of antibiotics. They came with many recommendation on how to improve our model presentation with step-wise clarification and intuitive labels.

Final model comments

During August, both teams implemented the feedback they had gotten, and another meeting was scheduled for September 14th. This meeting went through in a good pace as all presented models had improved greatly in quality, meaning that there were less trivialities to discuss. We were glad that Aalto-Helsinki discovered a bug in our code which we promptly fixed. We agreed the collaboration had been very beneficial for both teams so far. We agreed the next step will be reviewing each other’s modeling wikis. Check out both teams' final models here!
Aalto-Helsinki model
Our model




Human Practice reflections
We knew early on that we wanted to troubleshoot the ethical aspects of our project with another iGEM team. We had already identified aspects of our project where ethical work would need to be done. However, in order to ensure that we did not have any major blind spots, we contacted our dry-lab partners, the Aalto iGEM team, in order to get an outside perspective. Aalto shared our interest in doing ethical work.

Co-creating and co-hosting: The Nordic Ethics Workshop
After our first meeting on July 16th, we decided to organize a workshop focusing on ethics in iGEM. In order to make the workshop as inclusive and comprehensive as possible, we decided to reach out to other iGEM teams from the Nordic countries. We found out that several teams in the Nordic countries were working on biosensors, so it made sense to make a workshop focusing specifically on issues pertaining to the ethics revolving around GMOs in biosensors. The workshop was held on August 25th in collaboration with iGEM teams from Aalto, Uppsala, Stockholm and Trondheim. The guiding questions were:
How to dispose of biosensors?
What are the risks of using GMOs?
How do we formulate guidelines for end-users using our biosensors?
Who will benefit and who might be opposed to the projects?
How do we ensure sustainable production of the biosensors?
How do we tackle the public perception of GMO?
The Nordic Ethics Workshop (NEW) was very educational. The teams took turns troubleshooting the others' projects.

Our Takeaway from the Workshop
Our takeaway from the troubleshooting was mainly that our product did not come across as intuitive as we had hoped. The teams raised questions about the placement of the patch, how long one would have to wear it to get precise results, and what type of sweat the patch is compatible with. An outsider's input on the perceived uncertainties regarding our product was eye-opening. We can expect that the uncertainties voiced by other iGEM teams would also be shared by our patient group. As such, it became paramount to construct a user-guide for patients and to continually keep them as informed as possible.

Further Reflections with Team Aalto-Helsinki
We then had a second meeting on August 27th with Aalto-Helsinki to reflect upon the workshop. In this meeting, we went in-depth with some prepared comments on each other's projects. We had decided to mainly focus on the ethics regarding the possible environmental impact of Aalto-Helsinki's project, should they start to manufacture it. We created a framework for estimating carbon footprint and went through the estimation with calculations reflecting possible assumptions for their project. Aalto had chosen to focus on ethics regarding our product's use on humans. They had prepared questions concerning the usability of our product and skin-yeast interactions. This helped us improve our project presentation and collect unanswered questions.

About us

Comprising this team are nine ambitious students from various walks of life, who have come together to produce CIDosis - a non-invasive device that can help people with chronic inflammatory diseases visualize their level of inflammation.

Helpful Links

The Team
Promotional Video
Poster
Medals

Address

University of Copenhagen
Thorvaldsensvej 40, Frederiksberg C
Denmark

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