Difference between revisions of "Team:UNOTT/Model"
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| − | <p>When developing <i> Key. coli</i>, we found it was important to mathematically model possible situations | + | <p>When developing <i> Key. coli</i>, we found it was important to mathematically model possible situations in order to investigate the effects of different situations that we might encounter throughout different stages of development as well as during implementation. |
| − | Software was developed to compare the fluorescence levels with the mother colony to check if there was a high enough degree of similarity. | + | Software was developed to compare the fluorescence levels of the key colony with the mother colony to check if there was a high enough degree of similarity. |
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| − | This information was used by the wet lab to assist them by informing them in what to expect. This was done through the use of programming to create visual graphs | + | This information was used by the wet lab to assist them by informing them in what to expect. This was done through the use of programming to create visual graphs and simulations, as well as development of tools to allow for comparison between fluorescence levels without needing to actually create more synthetic organisms. Another advantage is that this is far quicker than creating these results in the lab. </h5> |
<a href="https://github.com/BurgundyIsAPublicEnemy/iGEMNotts2017/blob/master/Tellurium%20-%20Python%20Models%20for%20IGEM%20NOTTS%202017">The source code for these models can be accessed from our GitHub page</a> | <a href="https://github.com/BurgundyIsAPublicEnemy/iGEMNotts2017/blob/master/Tellurium%20-%20Python%20Models%20for%20IGEM%20NOTTS%202017">The source code for these models can be accessed from our GitHub page</a> | ||
| − | The models | + | The models were not perfect at first: refinement from lab results helped to optimize and correct the models.</h5> |
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| − | <li> To assist the processes within the | + | <li> To assist the processes within the wet lab by informing them and allowing for simulations. This would be especially useful when predicting the required fluorescence </li> |
<li> Test our biological systems with conditions that might not be possible to replicate in a lab environment. This allows us to future proof our methods as well as identify any vulnerabilities </li> | <li> Test our biological systems with conditions that might not be possible to replicate in a lab environment. This allows us to future proof our methods as well as identify any vulnerabilities </li> | ||
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| − | <p>In order to achieve these aims, | + | <p>In order to achieve these aims, we created a simulation for measuring fluorescence intensity when given parameters such as protein concentrations and wavelengths of lasers. </li> |
<p><a href="https://2017.igem.org/Team:UNOTT/Modelling">Find out more about our modeling</a> | <p><a href="https://2017.igem.org/Team:UNOTT/Modelling">Find out more about our modeling</a> | ||
| − | <p><a href="https://github.com/BurgundyIsAPublicEnemy/iGEMNotts2017/blob/master/LuciferA.c">This simulation can be downloaded from our GitHub page</a> | + | <p><a href="https://github.com/BurgundyIsAPublicEnemy/iGEMNotts2017/blob/master/LuciferA.c">This simulation can be downloaded from our GitHub page.</a> |
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<li> To check between fluorescence levels during implementation of Key.Coli between the mother colony and the Key.Coli capsules. </li> | <li> To check between fluorescence levels during implementation of Key.Coli between the mother colony and the Key.Coli capsules. </li> | ||
| − | <li> Develop an internal development environment to | + | <li> Develop an internal development environment to help next year's iGEM team quickly develop models as well as software.</li> |
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| − | <p>In order to achieve these aims, | + | <p>In order to achieve these aims, we created an image comparing software as well as an internal development environment where members can easily add their own code as well as access other code made by others and other files. |
<p> <a href="https://2017.igem.org/Team:UNOTT/CultureModelling">Find out more about our software </a> | <p> <a href="https://2017.igem.org/Team:UNOTT/CultureModelling">Find out more about our software </a> | ||
<p> <a href="https://github.com/BurgundyIsAPublicEnemy/iGEMNotts2017/blob/master/LuciferA.c">This environment can be downloaded from our GitHub page</a> | <p> <a href="https://github.com/BurgundyIsAPublicEnemy/iGEMNotts2017/blob/master/LuciferA.c">This environment can be downloaded from our GitHub page</a> | ||
Revision as of 09:48, 6 October 2017
Overview
When developing Key. coli, we found it was important to mathematically model possible situations in order to investigate the effects of different situations that we might encounter throughout different stages of development as well as during implementation. Software was developed to compare the fluorescence levels of the key colony with the mother colony to check if there was a high enough degree of similarity. This information was used by the wet lab to assist them by informing them in what to expect. This was done through the use of programming to create visual graphs and simulations, as well as development of tools to allow for comparison between fluorescence levels without needing to actually create more synthetic organisms. Another advantage is that this is far quicker than creating these results in the lab. The source code for these models can be accessed from our GitHub page The models were not perfect at first: refinement from lab results helped to optimize and correct the models.
