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From Ian Dunlop <ianwdun...@gmail.com>
Subject Re: Workflow Inquiry
Date Fri, 04 Mar 2016 15:21:18 GMT
Hello,

Taverna would definitely be an appropriate piece of software to use for
this analysis. Where are you getting the disease information for. Is it
from a public API? Taverna is at its best when retrieving things from web
services using the REST activity. You can also use use your own analysis
codes written in R or Java. Do you already have the code that does the
functional analysis. You probably don't need any additional plugins,
Taverna comes pre-loaded with lots of activities which can be used to fetch
and manipulate data. There are various workflows around drug discovery
available in myexperiment at http://www.myexperiment.org/groups/1125/content.
Most of these are based around the free to use Open PHACTS API
https://dev.openphacts.org/docs/2.0 which has lots of information about
drugs, diseases, targets, pathways etc. The Open PHACTS API already
contains DrugBank data and also has disease data from DisGeNet.

Cheers,

Ian


On 4 March 2016 at 15:07, Whitmire, Sarah <swhitmi2@uncc.edu> wrote:

> To whom it may concern,
>
> I'm a new user to Taverna and I'm about to create a new workflow where I
> want to input a disease and output a list of genes associated with the
> disease. From there I want to perform a functional analysis of those genes
> to find a cluster that is largely associated with disease progression. I
> want to do drug mining against this cluster of genes in a public database
> such as drugbank, DGIdb etc.
> Would Taverna be an appropriate software to use to run such query? Would I
> need to download any additional plugins?
>
> Thank you for your time and I look forward to your response.
>
> Sarah Whitmire
> UNC Charlotte Class of 2016 Levine Scholar
> Biology B.S. | Music Minor
> Professional Science Master's: Bioinformatics (2017)
> Research | Department of Kinesiology: Laboratory of Systems Physiology
> Mobile: (910) 233-5908
>
>

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