Difference between revisions of "Team:Newcastle/Collaborations"

 
(37 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
{{Newcastle5}}
+
{{Newcastle6}}
  
 
<html>
 
<html>
 +
<head>
  
 +
  <style>
 +
html, body, div, span, applet, object, iframe,
 +
h1, h2, h3, h4, h5, h6, p, blockquote, pre,
 +
a, abbr, acronym, address, big, cite, code,
 +
del, dfn, em, img, ins, kbd, q, s, samp,
 +
small, strike, strong, sub, sup, tt, var,
 +
b, u, i, center,
 +
dl, dt, dd, ol, ul, li,
 +
fieldset, form, label, legend,
 +
table, caption, tbody, tfoot, thead, tr, th, td,
 +
article, aside, canvas, details, embed,
 +
figure, figcaption, footer, header, hgroup,
 +
menu, nav, output, ruby, section, summary,
 +
time, mark, audio, video {
 +
margin: 0;
 +
padding: 0;
 +
border: 0;
 +
}
  
−
<body>
+
body{
−
<div id="wetlab" class="content-div">
+
  margin-left: 0;
−
<h2><a href="https://2017.igem.org/Team:Edinburgh_OG/Collaborations">Edinburgh OG Team</a></h2>
+
  background-color: #e8e8e8;
−
<p>
+
}
−
We were initially contacted by Anton Puzorjov from the Edinburgh Overgraduate team after meeting them at the Northern UK iGEM meet-up. As our team contained members who have been trained in modelling for synthetic biology, they were wondering if we could help them with their model as they were struggling to convert their deterministic model into a stochastic one.
+
−
<br />
+
−
<br />
+
  
 +
p{
 +
  font-family: Rubik;
 +
}
 +
hr{
 +
  background-color: #444444;
 +
}
 +
#main{
 +
  background-color: #e8e8e8;
 +
  color: #222222;
 +
  padding: 2%;
 +
  font-family: 'Rubik';
 +
}
 +
h1{
 +
  border-style: none;
 +
}
  
−
<img src="https://static.igem.org/mediawiki/2017/2/2d/T--Newcastle--BB_Edi_Collab_email.png" style="width:500px"/>
+
.navbar-nav > li{
 +
  padding-left:30px;
 +
  padding-right:30px;
 +
}
  
−
<br />
+
.dropdown-menu{
−
<br />
+
  background-color: #e8e8e8;
−
We organised a Skype call to discuss how far they had gotten and to explain the theory behind stochastic modelling. After a long talk, we understood the issues and Anton had shown us the software they were using to model with (StochPy). We were then given their code and went off to work out the issues.<br />
+
  font-family: 'Roboto', sans-serif;
−
<br />
+
  margin-top: -1px;
−
We corrected their code by fixing the reaction for infection of bacteria by phage, and converting the rate law for infection of bacteria by phage and the rate law for lysis of infected bacteria to proper stochastic rates. Their code commented with our corrections can be downloaded <a href="https://static.igem.org/mediawiki/2017/3/3b/T--Newcastle--BB_Edi_OG_model_corrections.txt">here</a>.
+
}
  
 +
.dropdown{
 +
  //background-color: black;
 +
  padding-top: 15px;
 +
  padding-bottom: 15px;
 +
}
  
−
</p>
+
.dropdown>.dropdown-menu {
−
<br />
+
  display: none;
−
<h2>Modelling Collaborations</h2>
+
}
−
<p>
+
  
−
</p>
+
.dropdown:hover>.dropdown-menu {
 +
  display: block;
 +
}
  
−
<br />
+
.dropdown-item:hover{
 +
  background-color: #a2c0eb;
 +
}
  
−
<h2>Human Practices Collaborations</h2>
+
.navbar-custom{
−
<p>
+
  min-height: 80px;
 +
  background-color: #6395de;
 +
  font-family: 'Roboto', sans-serif;
 +
  border-bottom: 1px solid #444444;
 +
}
  
−
</p>
+
/* change the brand and text color */
 +
.navbar-custom .navbar-brand,
 +
.navbar-custom .navbar-text {
 +
    color: #222222;
 +
}
 +
/* change the link color */
 +
.navbar-custom .navbar-nav .nav-link {
 +
    color: #222222;
 +
}
 +
/* change the color of active or hovered links */
 +
.navbar-custom .nav-item.active .nav-link,
 +
.navbar-custom .nav-item:hover .nav-link {
 +
    color: #444444;
 +
}
 +
  </style>
 +
  <link href="https://fonts.googleapis.com/css?family=Roboto" rel="stylesheet">
 +
  <link href="https://fonts.googleapis.com/css?family=Rubik" rel="stylesheet">
  
−
<br />
+
</head>
  
−
<h2>Other Collaborations</h2>
+
<body style="background-color: #e8e8e8;">
−
<p>
+
  
−
</p>
+
  <div  class="container-fluid" id="main" style="width: 100%; padding-top: 0.5%">
−
</div>
+
  <div class="container-fluid" style="max-width: 60%">
−
 
+
   
−
</body>
+
    <h1 class="text-center" style="font-family: Rubik">Collaborations</h1>
−
 
+
   
−
 
+
    <h2 style="font-family: Rubik; margin-bottom: 2%">Overview</h2>
−
 
+
   
−
 
+
    <a target="_blank" href="https://static.igem.org/mediawiki/2017/2/27/T--Newcastle--BB_collab_flyer.png">
−
 
+
    <img src="https://static.igem.org/mediawiki/2017/2/27/T--Newcastle--BB_collab_flyer.png" class="img-fluid border border-dark rounded mx-auto d-block" style="margin-right: 2%; margin-bottom: 2%; max-width: 50%;" alt="">  
−
 
+
    </a>
−
 
+
   
−
 
+
    <p>At the beginning of iGEM, we created a flyer showcasing the strengths of our team and the various ways we could help other teams. As a result of this, we were contacted by three teams: Edinburgh overgraduate team, Exeter, and Evry Paris-Saclay.</p>
−
 
+
   
−
<!--
+
    <p style="margin-top: 2%">For the Edinburgh team, we used our modelling knowledge to help fix their model. We aided the Exeter team by repeating one of their experiments, and they gathered single-cell fluorescence data for our deGFP construct using their FACS machine. Finally, Paris designed a novel psicose-regulated promoter to be used in a biosensor. We then incorporated their promoter into our framework so that many different variants of a psicose biosensor could be designed, made and tested.</p>
−
<div class="column full_size judges-will-not-evaluate">
+
   
−
<h3>★  ALERT! </h3>
+
    <hr>
−
<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
+
   
−
<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
+
    <h2 id="edi_collab" style="font-family: Rubik; margin-bottom: 2%; padding-top: 114px; margin-top: -114px;"><a href="https://2017.igem.org/Team:Edinburgh_OG/Collaborations">Edinburgh OG</a></h2>
−
</div>
+
   
−
 
+
    <p style="margin-top: 2%">We were initially contacted by Anton Puzorjov from the Edinburgh Overgraduate team after meeting them at the Northern UK iGEM meet-up. As our team contained members who have been trained in modelling for synthetic biology, they were wondering if we could help them with their model as they were struggling to convert their deterministic model into a stochastic one. </p>
−
 
+
   
−
 
+
    <img src="https://static.igem.org/mediawiki/2017/2/2d/T--Newcastle--BB_Edi_Collab_email.png" class="img-fluid border border-dark rounded mx-auto d-block" style="max-width: 80%">
−
 
+
   
−
 
+
    <p style="margin-top: 2%">We organised a Skype call to discuss how far they had gotten and to explain the theory behind stochastic modelling. After a long talk, we understood the issues and Anton had shown us the software they were using to model with (StochPy). We were then given their code and went off to work out the issues.</p>
−
<div class="clear"></div>
+
   
−
 
+
    <p style="margin-top: 2%">We corrected their code by fixing the reaction for infection of bacteria by phage, and converting the rate law for infection of bacteria by phage and the rate law for lysis of infected bacteria to proper stochastic rates. Their code commented with our corrections can be downloaded here.</p>
−
<div class="column full_size">
+
   
−
<h1>Collaborations</h1>
+
    <hr>
 +
   
 +
    <h2 id="exe_collab" style="font-family: Rubik; margin-bottom: 2%; padding-top: 114px; margin-top: -114px;"><a href="https://2017.igem.org/Team:Exeter/Collaborations">Exeter</a></h2>
  
 
<p>
 
<p>
−
Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.
+
The collaboration between our team and the Exeter iGEM team was two-fold. As one of our reporter modules for the Sensynova multicellular biosensor framework, we standardised and characterised a variant of Green Fluorescent Protein (GFP) not submitted to the registry before; deGFP. The Exeter team collected single cell data for <i>E. coli</i> cells expressing deGFP. To see more about this data, check out our <a href="https://2017.igem.org/Team:Newcastle/Results">results page</a>.<br />
−
</p>
+
  
−
<h3>Silver Medal Criterion #2</h3>
+
<img src="https://static.igem.org/mediawiki/2017/c/cc/T--Newcastle--BB_deGFP_FACS.png" class="img-fluid border border-dark rounded mx-auto d-block" style="max-width: 80%"/>
−
<p>
+
−
Complete this page if you intend to compete for the silver medal criterion #2 on collaboration. Please see the <a href="https://2017.igem.org/Judging/Medals">2017 Medals Page</a> for more information.  
+
−
</p>
+
  
−
<div class="column half_size">
 
  
−
<h4> Which other teams can we work with? </h4>
+
<br />
−
<p>
+
The Exeter iGEM team have been working on a filtration system for water from mines using modified bacteria. A feature of their system will be to use UV to kill any bacteria in the system after use. To assist the team, we performed an experiment to independently determine the effectiveness of UV as a method to sterilise their system. We grew up Top10 <i>E. coli</i> cells and subjected them to UV for 0, 1,2.5, 5, or 10 mins, before plating out the culture. The cultures were static incubated overnight and the number of colonies on the plate were counted. This data was then sent to Exeter for further analysis.
−
You can work with any other team in the competition, including software, hardware, high school and other tracks. You can also work with non-iGEM research groups, but they do not count towards the iGEM team collaboration silver medal criterion.
+
 
</p>
 
</p>
  
−
<p>
+
<img src="https://static.igem.org/mediawiki/2017/b/b2/T--Newcastle--BB_Exeter_collab.png" class="img-fluid border border-dark rounded mx-auto d-block" style="max-width: 80%"/>
−
In order to meet the silver medal criteria on helping another team, you must complete this page and detail the nature of your collaboration with another iGEM team.
+
−
</p>
+
  
−
</div>
+
   
 +
    <hr>
 +
   
 +
    <h2 id="eps_collab" style="font-family: Rubik; margin-bottom: 2%; padding-top: 114px; margin-top: -114px;"><a href="https://2017.igem.org/Team:Evry_Paris-Saclay/Collaborations">Evry Paris-Saclay</a></h2>
 +
   
 +
    <p style="margin-top: 2%">We were initially contacted by Jérémy Armetta from the Evry Paris-Saclay team as our team was working on a synthetic promoter library and they were wondering if we could work together as they aimed to make a psicose synthetic promoter in order to create a biosensor. </p>
 +
   
 +
    <img src="https://static.igem.org/mediawiki/2017/a/a3/T--Newcastle--Lais--Colab--Paris--Email.png" class="img-fluid border border-dark rounded mx-auto d-block" style="max-width: 80%">
 +
   
 +
    <p style="margin-top: 2%">We organised a Skype call to discuss how our projects intertwined. After a little chat, it was clear that we were taking different approaches to achieving our synthetic promoters and therefore could not help each other in such a manner. </p>
 +
   
 +
    <p style="margin-top: 2%">We suggested that, once working, we could take the biosensor created by the Evry Paris-Saclay team and implement it to our framework as a variant to the IPTG biosensor currently used as our proof of concept. By co-culturing this biosensor module to the framework's other modules, we would be able to come up with various variants of the psicose biosensor for the Evry team. </p>
 +
   
 +
    <p style="margin-top: 2%">However, due to synthesis issues causing delays and therefore time constraints, we have been able to implement the psicose biosensor into our framework but lacked the time to co-culture this part with the Sensynova platform's multiple modules in order for the creation of variants. </p>
 +
   
 +
    <p style="margin-top: 2%">Further details of the psicose biosensor implementation into the Sensynova platform can be found on our <a href="https://2017.igem.org/Team:Newcastle/Results">results</a> page, under "Detector Modules".</p>
 +
   
 +
  </div>
 +
  </div>
  
−
 
+
</body>
−
 
+
−
<div class="column half_size">
+
−
<p>
+
−
Here are some suggestions for projects you could work on with other teams:
+
−
</p>
+
−
 
+
−
<ul>
+
−
<li> Improve the function of another team's BioBrick Part or Device</li>
+
−
<li> Characterize another team's part </li>
+
−
<li> Debug a construct </li>
+
−
<li> Model or simulating another team's system </li>
+
−
<li> Test another team's software</li>
+
−
<li> Help build and test another team's hardware project</li>
+
−
<li> Mentor a high-school team</li>
+
−
</ul>
+
−
</div>
+
−
 
+
−
-->
+
 
</html>
 
</html>
 +
{{Newcastle_footer}}

Latest revision as of 19:25, 1 November 2017

spacefill

Collaborations

Overview

At the beginning of iGEM, we created a flyer showcasing the strengths of our team and the various ways we could help other teams. As a result of this, we were contacted by three teams: Edinburgh overgraduate team, Exeter, and Evry Paris-Saclay.

For the Edinburgh team, we used our modelling knowledge to help fix their model. We aided the Exeter team by repeating one of their experiments, and they gathered single-cell fluorescence data for our deGFP construct using their FACS machine. Finally, Paris designed a novel psicose-regulated promoter to be used in a biosensor. We then incorporated their promoter into our framework so that many different variants of a psicose biosensor could be designed, made and tested.

Edinburgh OG

We were initially contacted by Anton Puzorjov from the Edinburgh Overgraduate team after meeting them at the Northern UK iGEM meet-up. As our team contained members who have been trained in modelling for synthetic biology, they were wondering if we could help them with their model as they were struggling to convert their deterministic model into a stochastic one.

We organised a Skype call to discuss how far they had gotten and to explain the theory behind stochastic modelling. After a long talk, we understood the issues and Anton had shown us the software they were using to model with (StochPy). We were then given their code and went off to work out the issues.

We corrected their code by fixing the reaction for infection of bacteria by phage, and converting the rate law for infection of bacteria by phage and the rate law for lysis of infected bacteria to proper stochastic rates. Their code commented with our corrections can be downloaded here.

Exeter

The collaboration between our team and the Exeter iGEM team was two-fold. As one of our reporter modules for the Sensynova multicellular biosensor framework, we standardised and characterised a variant of Green Fluorescent Protein (GFP) not submitted to the registry before; deGFP. The Exeter team collected single cell data for E. coli cells expressing deGFP. To see more about this data, check out our results page.

The Exeter iGEM team have been working on a filtration system for water from mines using modified bacteria. A feature of their system will be to use UV to kill any bacteria in the system after use. To assist the team, we performed an experiment to independently determine the effectiveness of UV as a method to sterilise their system. We grew up Top10 E. coli cells and subjected them to UV for 0, 1,2.5, 5, or 10 mins, before plating out the culture. The cultures were static incubated overnight and the number of colonies on the plate were counted. This data was then sent to Exeter for further analysis.

Evry Paris-Saclay

We were initially contacted by Jérémy Armetta from the Evry Paris-Saclay team as our team was working on a synthetic promoter library and they were wondering if we could work together as they aimed to make a psicose synthetic promoter in order to create a biosensor.

We organised a Skype call to discuss how our projects intertwined. After a little chat, it was clear that we were taking different approaches to achieving our synthetic promoters and therefore could not help each other in such a manner.

We suggested that, once working, we could take the biosensor created by the Evry Paris-Saclay team and implement it to our framework as a variant to the IPTG biosensor currently used as our proof of concept. By co-culturing this biosensor module to the framework's other modules, we would be able to come up with various variants of the psicose biosensor for the Evry team.

However, due to synthesis issues causing delays and therefore time constraints, we have been able to implement the psicose biosensor into our framework but lacked the time to co-culture this part with the Sensynova platform's multiple modules in order for the creation of variants.

Further details of the psicose biosensor implementation into the Sensynova platform can be found on our results page, under "Detector Modules".