Validation by simulating independent mutant and perturbation samples

Projects that do not fall under current programmes.

The MycoSynVac project AIMS at using cutting-edge synthetic biology methodologies to engineer Mycoplasma pneumoniae as a universal chassis for vaccination. Designing a universal Mycoplasma chassis that can be deployed as single- or multi-vaccine in a range of animal hosts. Annually, infections caused by Mycoplasma species in poultry, cows, and pigs result in multimillion Euro losses in the USA and Europe. There is no effective vaccination against many Mycoplasmas that infect pets, humans and farm ...

1. To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae
2. To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization
3. To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2) aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a serum-free growth medium and; 4) assess, at genome scale, the metabolic ...

Validation of the core model of glycolysis, pyruvate metabolism and ATPase reaction using OE, KO mutant samples and perturbation samples

Comparison of model SS metabolite concentrations with measured values using 1000x sampling from the Gausian distribution of the measured values based on multiple replicates per measured conditions. Graphs showing the distribution of measured and simulated metabolite concentration for 95 mutand (KO, OE), perturbation and time series measurements. Model simulations performed using 24h proteomics with modification of enzyme parameters for KO and OE mutants.

Contains a Jupyter notebook file that uses libroadrunner and tellurium to run all simmulations and analysis based on the 40 independent samples. The Readme.txt file contains information on how to recreate the complete modelling environment used for all simmulations and analysis using Anaconda.

Contains relative mutant (OE, KO) perturbation and time series samples metabolite concentrations and enzyme fold change of targeted enzymes used for model validation. Measured are the relative fold change, Mean and SD of log2 fold change values are based on multiple measurements per sample (minimum of three). Contains input data for Automated Model simulations pipeline to load and update the models metabolite concentrations and enzyme parameters to simulate all sample using a custom python script ...

Symmetric mean absolute percentage error per sample graph for the 40 independent samples

Contains relative metabolite concentrations for 40 samples based on technical triplicates. Medium and SD values were calculated and used for 1000 sampled simmulations (sampling from the measurement distribution per metabolite) per sample. Also contains annotion to link metabolite concentrations and protein fold change measurements for OE and KO mutants to the model as well as external glucose, acetate and lactate concentrations. A SBtab like format was used to easily load the MEAN and SD metabolite ...

Dynamic model of glycolysis, pyruvate metabolism and NoxE. The model is parameterized by selecting the best out of 100 parameter set using Copasi's Genetic algorithm with 1000 itterations and 500 simmulatanious models.