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Team:Newcastle/Collaborations
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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. | 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. | ||
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Revision as of 12:52, 5 September 2013
Contents |
Collaborations
We were able to help Team Edinburgh with their modelling by supplying them with some Bacillus subtilis parameters:
| 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 |
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.
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.
