SOP for generating a Genome Scale Metabolic model of M. hyopneumoniae Version 1
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
SEEK ID: https://fairdomhub.org/sops/288?version=1
Filename:
SOP Construction of Genome Scale Metabolic model M. hyopneumoniae.docx
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Created: 3rd May 2017 at 11:35
Last updated: 14th Jan 2019 at 16:00
Last used: 21st Feb 2019 at 13:37
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https://orcid.org/0000-0001-7049-5334I 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
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Programme: Independent Projects
Public web page: http://www.mycosynvac.eu/
Construction of a Genome scale constrained-based metabolic modeling of M. hyopneumonia
Person responsible: Niels Zondervan
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Construction and manual curated Genome Scale Metabolitic model of M. hyopneumoniae. Dynamic flux balance analysis was performed for glucose uptake
Contributor: Niels Zondervan
Biological problem addressed: Model Analysis Type
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