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SOP for generating a Genome Scale Metabolic model of M. hyopneumoniae

SOP for generating a Genome Scale Metabolic model of M. hyopneumoniae
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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

Format: Word document

Size: 65.4 KB

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Creative Commons Attribution 4.0

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Views: 153 Downloads: 0

Created: 3rd May 2017 at 11:35

Last updated: 14th Jan 2019 at 16:00

Last used: 18th Apr 2019 at 11:26

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Niels Zondervan

Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, WURSynBio

Institutions: Wageningen University & Research

https://orcid.org/0000-0001-7049-5334

Roles: PhD Student

Expertise: Molecular Biology, Dynamic modelling, Python, Java, R, pathogen host interaction, Bioinformatics, Systems Biology, Agent-based modelling

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
...

MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine

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

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