Difference between revisions of "Team:SCUT-ChinaA/Software"

Revision as of 14:27, 5 October 2018

Abstract

While building our model, we developed a software tool to help us find the optimal solution. After we finished, we modified the software and made it universal, which means it can be used by other researchers.

enzyme	Substrate	Turnover Number [1/s]	KM Value [mM]
ERG10	acetyl-CoA	2.1	0.33
ERG13	acetoacetyl-CoA, acetyl-CoA	4.6	acetoacetyl-CoA:0.0014, acetyl-CoA:0.05
HMG1	hydroxymethylglutaryl-CoA	0.023	0.045
ERG12	mevalonate	2.36	0.012
ERG8	phosphomevalonate	3.4	0.0042
ERG19	(R,S)-5-diphosphomevalonate	5.9	0.0091
NDPS1	isopentenyl diphosphate	0.14	0.047

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-To improve the efficiency of producing limonene, we build a model to help us design our genetic machine. We use flux balance analysis to simulate our system, with the matrix of the pathway and the  \(V_{max}\) (calculated by \(k_{cat}\) and \(E_t\) )  of each reactions. And, inspired of machine learning algorithms, we established an algorithm using gradient descent method to search for the optimal solution of \(E_t\). Finally, we got results that were close to the results on some published articles we read, and hence we decided to design our experiment based on the model. Also, while building our model, we have developed a software tool which may be helpful for those who need to optimize a pathway.
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+While building our model, we developed a software tool to help us find the optimal solution. After we finished, we modified the software and made it universal, which means it can be used by other researchers.
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-<h2 style="text-align: left">Flux Balance Analysis</h2>
-<p>
-To improve the efficiency of producing limonene, we build a model to help us design our genetic machine. We use flux balance analysis to set up a relationship of input ( substrate ) and output (the produce rate of limonene), with the matrix of the pathway and the \(V_{max}\) (calculated by \(k_{cat}\) and \(E_t\) ) of each reactions. After we get the relationship we optimize the output by finding the best solution of \(E_t\) , using Newton method.
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