Team:Newcastle/Collaborations

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Collaborations

Edinburgh University

We were able to supply Team Edinburgh with some Bacillus subtilis parameters to aid their projects modelling:

Definition Value Source
Cell division rate, growth rate 30-73mins http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Genome equivalents of DNA per cell 1.6 - 3.3 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Replication time of chromosome, "C period" 50-58 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Delay before cell division, "D period" 21-34 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Number of replicating forks 2 -
Number of replicating origins 0.43-1.7 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Cell volume 0.85±0.38 μm^3 http://www.ncbi.nlm.nih.gov/pubmed/21395229
Minimal replication time of chromosome 55min http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Numbe of rrn operons per chomosome 10 operons http://www.ncbi.nlm.nih.gov/pubmed/12644506

Leeds University


On Friday the 12th of July our team was at UCL for the iGEM U.K. meet up. We delivered a workshop about Mathematical modelling, including teaching the basics of using the rule-based modelling language BioNetGen. We also supplied attendees with all the software needed to produce BioNetGen models on a handy USB. This workshop introduced the Leeds iGEM team to BioNetGen, who went on to use BioNetGen to model the Cpx pathway in their project.

These are the slides from our modelling presentation:

A downloadable version can be found here.

This is the handout from our modelling workshop:

A downloadable version can be found here.


Manchester University

We have helped the Manchester team with their 'introduction to modelling', giving ideas on how this could be achieved and producing a tutorial video giving a brief introduction to modelling using BioNetGen.

Newcastle University The Centre for Bacterial Cell Biology Newcastle Biomedicine The School of Computing Science The School of Computing Science