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Construction and manual curated Genome Scale Metabolitic model of M. hyopneumoniae. Dynamic flux balance analysis was performed for glucose uptake
SEEK ID: https://fairdomhub.org/assays/530
Modelling Analysis
Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum anima...
Investigation: Modelling of M. pneumoniae metabolism
Study: Genome-scale, constraint-based metabolic modeling of M. hyopneumonia
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Created: 3rd May 2017 at 11:14
Last updated: 14th Jan 2019 at 16:00
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Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, WURSynBio
Institutions: Wageningen University & Research

Roles: PhD Student
Expertise: Bioinformatics, Systems Biology, Agent-based modelling, Dynamic modelling, Python, Java, R, pathogen host interaction, Molecular Biology
Tools: Copasi, libRoadrunner, Python, R, semantic web
I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model.
I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation
...
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
...
Programme: Independent Projects
Public web page: http://www.mycosynvac.eu/
Organisms: Mycoplasma pneumoniae
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
...
Snapshots: Snapshot 1, Snapshot 2, Snapshot 3
Studies: Core Model predictions, Core Model training, Core model predicting combined mutations and perturbations, Genome-scale, constraint-based metabolic modeling of M. hyopneumonia, Metabolomics measurements, Proteomics analysis, Transcriptomics of M. pneumoniae at different times of growth
Assays: 40 samples data analysis - metabolite correlation, 40 samples, OE mutants of glycolysis and pyruvate metabolism enzymes com..., All samples data, Comparison of Kcat values from the model and values from literature, Construction and training of the core model, Construction of a Genome Scale Metabolitic model of M. hyopneumoniae, Dynamic model simmulation pipeline, Metabolic control analysis (local and global), Metabolomics external metabolites measurements, Metabolomics internal metabolites, time series measurements, Proteomics assay, Transcriptomics assay of M. pneumoniae at diferent times of growth, Validation by simulating independent mutant and perturbation samples
Construction of a Genome scale constrained-based metabolic modeling of M. hyopneumonia
Person responsible: Niels Zondervan
Snapshots: No snapshots
Creator: Niels Zondervan
Submitter: Niels Zondervan
Model type: Metabolic network
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Modelling of M. pneumoniae metabolism
Studies: Genome-scale, constraint-based metabolic modeli...
Modelling analyses: Construction of a Genome Scale Metabolitic mode...
Standard Operating Procedure describing the process and software used in generating a Genome Scale Metabolic model of M. hyopneumoniae.
Used software:
Pathway tools
PathLogic
Cobrapy
the Cobra Toolbox
libSBML
Creator: Niels Zondervan
Submitter: Niels Zondervan
Investigations: Modelling of M. pneumoniae metabolism