Molecular Biologist looking for collaborator for a Metabolic Modelling Project

[Paolo Marangio]

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. 

[Francis Lee]

There's a decently active group that's dedicated to cobrapy:

https://groups.google.com/forum/#!forum/cobra-pie

They might have a larger pool of experienced users.

Otherwise I've used cobrapy a few times before, and I'm happy to chat a bit more with what you're interested in doing.

Francis

On Fri, Mar 24, 2017 at 2:30 PM, Paolo Marangio <marang...@gmail.com> 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. 

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[Ravasz]

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

[Paolo Marangio]

Hello Ravasz,

Thank you for your reply and sorry for replying to you only now. I only just saw this!

I am glad to hear you are willing to help. Can you write on here an e-mail address I can contact you on?

Cheers,

Paolo

[Paolo Marangio]

Dear Francis,

Thank you very much for your reply! Sorry for my late reply, I only just saw this!

I am already a member of the cobraby google group. Cool, can you write here an e-mail address I can contact you on?

Cheers,

Paolo

Il giorno venerdì 24 marzo 2017 18:56:00 UTC, Francis Lee ha scritto:

There's a decently active group that's dedicated to cobrapy:

https://groups.google.com/forum/#!forum/cobra-pie

They might have a larger pool of experienced users.

Otherwise I've used cobrapy a few times before, and I'm happy to chat a bit more with what you're interested in doing.

Francis

On Fri, Mar 24, 2017 at 2:30 PM, Paolo Marangio <marang...@gmail.com> 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. 

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