qs_sinsystem_s.meliloti
Science Score: 57.0%
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Low similarity (7.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Leth13
- Language: MATLAB
- Default Branch: main
- Size: 93.8 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Quorum-sensing simulation of the Sin system of Sinorhizobium meliloti
This project contains three algorythms to simulate on Matlab the quorum sensing Sin system in Sinorhizobium meliloti.
Model
There are a total of 23 reactions characterizing the model.
The transcription and translation reactions were simplified in one reaction with one rate, beta.
Reaction Rates
The reaction rates are in the parameters.txt file. They were extracted from the data of Bettenworth et al. or, when information was lacking, assumed identical to the simulation of the LuxR/LuxI quorum sensing system of Vibrio fisheri in Buceta et al.. If new literature comes out about the actual rates of the S. meliloti species, it's advised to update them.
Deterministic simulations
The deterministic simulation is based on a set of ODES resolved by the ODEset solver of Matlab.
It needs all 15 reactions rates and the starting number of all metabolite/genes, except DNAexpr, which is an internal variable.
myode_full.m is the wild-type model of the Sin QS system.
myode_expr.m simulates a mutant lacking the expr gene by setting the internal variable DNAexpr = 0.
Stochastic simulation
SSA_QS.m contains a single-cell gillespie style simulation of the Sin QS system.
It needs all 15 reactions rates and the starting number of all metabolite/genes. The internal variable V, extracted from Xiongfeng et al., accounts for the statistical effect of the volume of the cell on reactions of one order or more.
function [SINIplot, SINRplot, EXPRstarplot, EXPRplot, timeplot, meantime] = SSA_QS(y, parameters, numberofcells, numberofreactions)
Mutants can be simulated by changing the values of the reactions rates or the genes.
Confronting simulations
See the file exampleconfrontingsimulations.m.
Frequency of SinI expression
We used the peakfinder function to calculate the frequency of pulses of expression of SinI.
See examplestatanalysis_pulses.m.
Credit
Owner
- Login: Leth13
- Kind: user
- Repositories: 1
- Profile: https://github.com/Leth13
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Marini" given-names: "Sara" orcid: "https://orcid.org/0009-0006-4112-0449" title: "QS_Sinsystem_S.meliloti" version: 1.0.0 date-released: 2023-12-10 url: "https://github.com/Leth13/QS_Sinsystem_S.meliloti"