Difference between revisions of "Team:Newcastle/Collaborations"

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We were initially contacted by Jérémy Armetta from the Evry Paris-Saclay 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.
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We were initially contacted by Jérémy Armetta from the Evry Paris-Saclay team. As our team was working on a synthetic promoter library, they were wondering if we could work together due to their plans of making a psicose synthetic promoter.
 
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<img class="result_img" src="https://static.igem.org/mediawiki/2017/2/2d/T--Newcastle--BB_Edi_Collab_email.png"/>
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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 />
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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 that way.
 
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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>.
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We suggested that, once working, we could take the biosensor created by the Evry Paris-Saclay team and implement it into our framework as a variant to the IPTG biosensor we are using as our proof of concept. By co-culturing this biosensor module to the other modules in our framework, we would be able to come up with various variants of the psicose biosensor for the Evry team.
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Revision as of 14:58, 19 October 2017

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Edinburgh OG Team

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.


Evry Paris-Saclay Team

We were initially contacted by Jérémy Armetta from the Evry Paris-Saclay team. As our team was working on a synthetic promoter library, they were wondering if we could work together due to their plans of making a psicose synthetic promoter.



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 that way.

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