[DIYbio] Re: Molecular Biologist looking for collaborator for a Metabolic Modelling Project

Hi there,

I'm another molecular biologist / bioinformatician also in Edinburgh. I know little about modelling per se, but I'm teaching python to biologists and I'm an avid DIYbio person, so I am certain we can come up with something if you need help. If you want to meet up just let me know, I'm at King's Buildings.

Cheers,
Mate


On Friday, 24 March 2017 18:35:14 UTC, Paolo Marangio wrote:

I am a Molecular Biology Resarch Assistant based in Edinburgh and I recently came across an interesting paper where they used modelling for coming up with deletion strategies that allow increased production of cis-aconitic acid in E. coli (you can read all about it here: https://www.ncbi.nlm.nih.gov/pubmed/27269589). SInce I found this approach particularly powerful, I decided to do some modelling out of interest. I am planning on using the python package Cobrapy for this (http://opencobra.github.io/cobrapy/) as I don't know how to use MATLAB. After I will have identified some deletion strategies, I could test them directly as I have access to a lab. I was therefore wondering if there is anybody on here who has experience with this package or constraint-based modelling in general and would like to collaborate in this small project.