Fwd: [biocurious] Metabolic Tinker

[Jonathan Reyles]

Hey Folks from Bioinformatics,

Check out the article below:
http://nar.oxfordjournals.org/content/early/2013/04/10/nar.gkt234.long

This is also the tinkering aspect:

http://osslab.ex.ac.uk/tinker.aspx

Nina, if you have Bioinformatics related ideas, feel free to shoot it to this mailing list.

Cheers,

Jon

---------- Forwarded message ----------
From: Patrik D'haeseleer <pat...@gmail.com>
Date: Thu, May 9, 2013 at 9:43 AM
Subject: Re: [biocurious] Metabolic Tinker
To: Nina DiPrimio <ndip...@gmail.com>
Cc: diybio-...@googlegroups.com

Hm - they're definitely overstating how novel this is. I believe the ability to draw metabolic paths between any two compounds has been available in GLAMM (developed at JBEI) for a while. And it is now available in BioCyc / Pathway Tools as well. The integration of thermodynamic calculations *may* be novel, although that has definitely been done before for individual pathways as well.

Meh - doesn't hurt to have yet another tool. Everybody seems to want to do metabolic engineering these days. They should make sure their website stays up though ;-)

Patrik

On Thu, May 9, 2013 at 1:37 AM, Nina DiPrimio <ndip...@gmail.com> wrote:

http://nar.oxfordjournals.org/content/early/2013/04/10/nar.gkt234.long

http://osslab.ex.ac.uk/tinker.aspx

--
Nina DiPrimio, PhD
Anderson Lab
Department of Bioengineering
UC Berkeley

Lab Phone- 510-664-4200

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Regards,
Jon
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[Patrik D'haeseleer]

And this is the one I personally use in my own research (although typically more for whole-genome pathway reconstruction and curation, than for metabolic engineering):

http://biocyc.org/
http://brg.ai.sri.com/ptools/

Patrik

On Thu, May 9, 2013 at 11:21 AM, Nina DiPrimio <ndip...@gmail.com> wrote:

this is the tool patrik mentioned:

http://140.221.84.217:7040/glamm/

[Nina DiPrimio]

Hello all-

I do want to go through these tools with you all during an IdeaLab, however I am not well versed in them and would prefer to spend some time learning and comparing before attempting to walk you through them.  

If someone has time tomorrow or Saturday to prep for that and would like to give it a shot please feel free! I would like to learn as well.

If not, I propose to discuss:

Work done by the Hecht group on de novo proteins.

http://www.ncbi.nlm.nih.gov/pubmed/21245923

http://www.ncbi.nlm.nih.gov/pubmed/23651114

Thoughts?

Sorry for the late notice- will confirm topic tomorrow.

Thanks!

Nina

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