Metabolic Tinker

[Nina DiPrimio]

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

[Patrik D'haeseleer]

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

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[Nina DiPrimio]

this is the tool patrik mentioned:

http://140.221.84.217:7040/glamm/

On Thu, May 9, 2013 at 10:12 AM, Jonathan Reyles <jre...@gmail.com> wrote:

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

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Regards,
Jon
---> Jon loves the Planet Earth and is proud to display this email with Recycled Electrons. <---

[Nina DiPrimio]

Does anyone want to take a stab at walking through the metabolic engineering paper and demoing Tinker? And/or GLAMM for IdeaLab?

On Thu, May 9, 2013 at 10:12 AM, Jonathan Reyles <jre...@gmail.com> wrote:

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

--
Regards,
Jon
---> Jon loves the Planet Earth and is proud to display this email with Recycled Electrons. <---

[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

[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

Is this topic of interest?

[Nina DiPrimio]

Hello all-

I have to cancel this week's IdeaLab. I am unfortunately overloaded with work and moving this weekend. I apologize for the late notice. If you all feel like meeting, please do! Or use the time to discuss one of your projects.

The paper I suggested above http://www.ncbi.nlm.nih.gov/pubmed/21245923 is great. I find the synthetic protein space extremely intriguing. If you do not meet to discuss the paper, let me know, and I will talk about synthetic proteins at the next meeting.

Thank you.

Nina

[Jonathan Reyles]

Canceled? Well it is Richard Feynman's birthday today. But that should actually encourage us to do an IdeaLab. ;-))

[Cameron Clarke]

Maybe we can all just begin to play with GLAMM and work through it ourselves tomorrow night?

Cameron

"Don't let momentum set your course."

[Patrik D'haeseleer]

Do you guys have any specific pathways

[Patrik D'haeseleer]

Sorry - I meant to say: Do you guys have any specific pathways that you would like to explore? Or specific biochemicals for which you'd like to develop a synthetic pathways?

Patrik

[Cameron Clarke]

Here are some ideas:

Astaxanthin production

DHA/EPA Omega 3 production

Luciferin/Luciferase

Fragrances/Flavors (Oil of wintergreen, methyljasmonate/jasmonic acid)

"Don't let momentum set your course."

[Jay Hanson]

I would be interested in working on those pathways also.

-jay

[Jonathan Reyles]

Me three. When is everyone going to be there?

[Nina DiPrimio]

I think you should all still meet. Maybe look into the metabolic engineering tool or the synthetic proteins.  Just because I can't make it does not mean you can't discuss some cool science! 

[Patrik D'haeseleer]

Ok, Here's some pathways to get you started:

astaxanthin biosynthesis

Eicosapentaenoate Biosynthesis
docosahexanoate biosynthesis I
docosahexanoate biosynthesis II

volatile benzenoid biosynthesis I (ester formation)- methylsalicylate (wintergreen) and methylbenzoate

jasmonic acid biosynthesis
jasmonate O-methyltransferase

Patrik

[Patrik D'haeseleer]

I would stay away from the fatty acid biosynthesis pathways like DHA/EPA if you really want to implement any of this though. Those reactions tend to be very non-specific, many of them you won't even be able to do with purified enzyme in an aqueous environment, and you won't have the tools to distinguish the end product even if you do get it to work.

At least with astaxanthin and the fragrances you have a very easy test for the end product...

Patrik

[Cameron Clarke]

OK. Thanks Patrik! Now we actually have something to discuss.  Let's meet and hammer through some of these. Gonna be rough, but that's citizen science for ya.

Cameron

"Don't let momentum set your course."

[Patrik D'haeseleer]

There's also a nice wikipedia page with dozens of aroma compounds:

https://en.wikipedia.org/wiki/Aroma_compound

Patrik

[Roger Stager]

I have a couple questions: 

1)  how do we verify production of both the final product as well as all the intermediate steps? 

2) How do we find the existing pathways in our host organism?

From: Cameron Clarke <selur...@gmail.com>
Date: Saturday, May 11, 2013 3:31 PM
To: Patrik D'haeseleer <pat...@gmail.com>
Cc: Nina Primio <ndip...@gmail.com>, diybio-idealab <diybio-...@googlegroups.com>
Subject: Re: [biocurious] Metabolic Tinker

[Nina DiPrimio]

1. For intermediate and final prods typically people do LC (liquid chromatography) Mass Spec to identify the molec weight of the small molecule or molecules of interest. But hopefully we can start with pathways like Patrik suggested that lead to an obvious phenotypic change. 

2. Up until recently people were doing literature searches to examine host pathways (still going on). I think with BioCyc you can choose your organism and see the pathways - if they have been mapped? Patrik knows more about that than I. 

Sent from my iPhone

[Jay Hanson]

Hi Roger;

The techniques within our capabilities for product identification are probably chromatography and spectrophotometry.

This site has a database of pathways:  http://metacyc.org/

Referenced in this paper:  http://nar.oxfordjournals.org/content/40/D1/D742.long

And for some organisms that have been well studied, there are individual papers describing specific pathways.

See you this afternoon.

-jay