Popular apps for metabolomics and proteomics data

[Vaishali]

Hi Team,

I wanted to know the most popular apps which are used withing Cytoscape for metabolomics, proteomics and integrating different omics networks.

Since, there are many apps that is why wanted some insight on the same.

Thank you,
Vaishali

[Scooter Morris]

You may want to look at the MassSpec and Omics collections in the app
store.  They are an attempt to put together the commonly used apps for
that particular use case.  As far as metabolomics, I would suggest
taking a look at MetScape.

-- scooter

[Barry Demchak]

If there's a different collection of apps appropriate for these omics, we would entertain creating those collections, too.

Please advise.

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[vais...@strandls.com]

Thaks a ton for your help!

[vais...@strandls.com]

Hi Barry, thanks a lot - I will have a look at the app collections as suggested by Scooter and then will proceed accordingly.

[vais...@strandls.com]

Hi Barry, Scooter and Team,

I was installing the 'Mass Spec Collection' but it gave me an error: "Cannot find dependency: Mass Spec Collection requires Wikipathways 3.2.1 or later". However the latest release in the App store for Wikipathways is version 3.2.0. So how can install this collection now?

Looking forward to hear from you guys.

Best regards,
Vaishali

[Scooter Morris]

Hi Vaishali,

    Probably a mistake on my part (I forgot to update the required
version on the collection when I updated it last night). The easiest fix
is to upgrade to Cytoscape 3.6.0 (which is probably a good idea anyways).

-- scooter

[vais...@strandls.com]

Thanks for your help! Btw is it possible to do any analysis with String when I have only the Uni-Prot IDs. It was a proteomics experiment and I found 15 ID's of my interest. When I tried searching String using protein IS's it gave me no result, does it only take protein names?

[Scooter Morris]

On 12/14/2017 01:58 AM, vaishali via cytoscape-helpdesk wrote:
> Thanks for your help! Btw is it possible to do any analysis with String when I have only the Uni-Prot IDs. It was a proteomics experiment and I found 15 ID's of my interest. When I tried searching String using protein IS's it gave me no result, does it only take protein names?
>

STRING should work just fine with uniprot ID's (I use it that way all
the time).  Can you send the 15 ID's and the species name and I'll check
and see what might be going on.

-- scooter

[vais...@strandls.com]

Thanks scooter! I created a new topic to avoid confusion and you replied to me as well :)

Here you go: https://groups.google.com/forum/#!topic/cytoscape-helpdesk/kBUb1fa0cT8

[Matthias König]

Hi Vaishali,
personally I am using cy3sbml to map metabolomics and proteomics data on metabolic networks.
http://apps.cytoscape.org/apps/cy3sbml

This is more of a targeted approach where you know your pathways
(which you can encode in SBML via species, reactions and proteins as catalysts)
and than map data on the network.

Hope this helps.
Best M
Disclaimer: I am the main developer, so making advertisement here, but using it for my own workflows.

[vais...@strandls.com]

Hi Matthias,

Thanks a lot for your suggestion! I'll try out cy3smbl as well and let you know if I face any issues.

Best regards,
Vaishali