Mailing-List: contact users-help@taverna.incubator.apache.org; run by ezmlm
Precedence: bulk
Reply-To: users@taverna.incubator.apache.org
MIME-Version: 1.0
In-Reply-To: 
 <CAPAhP8qgP3yfr=FBBLiPvMFwckJB0p=Keg3TxRU3qyuSkc0Oyg@mail.gmail.com>
References: 
 <CAPAhP8poGz9PMHrOOnXE1ys8CN7mtHg_n2yExcLpD8OS1PnmSQ@mail.gmail.com>
	<CAPAhP8qgP3yfr=FBBLiPvMFwckJB0p=Keg3TxRU3qyuSkc0Oyg@mail.gmail.com>
Date: Fri, 4 Mar 2016 15:21:18 +0000
Message-ID: 
 <CAEngrgmC=ttOKd8ZjoJ+8PgXyUPoJLXhuq_8BJ6mqs7By12Vuw@mail.gmail.com>
Subject: Re: Workflow Inquiry
From: Ian Dunlop <ianwdunlop@gmail.com>
To: users@taverna.incubator.apache.org
Cc: "Shah, Nirav R" <Nirav.R.Shah@carolinashealthcare.org>
Content-Type: multipart/alternative; boundary=001a1149c6c0b4601a052d3aaae4

--001a1149c6c0b4601a052d3aaae4
Content-Type: text/plain; charset=UTF-8

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
>
>

--001a1149c6c0b4601a052d3aaae4
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr">Hello,<div><br></div><div>Taverna would definitely be an a=
ppropriate piece of software to use for this analysis. Where are you gettin=
g the disease information for. Is it from a public API? Taverna is at its b=
est when retrieving things from web services using the REST activity. You c=
an also use use your own analysis codes written in R or Java. Do you alread=
y have the code that does the functional analysis. You probably don&#39;t n=
eed any additional plugins, Taverna comes pre-loaded with lots of activitie=
s which can be used to fetch and manipulate data. There are various workflo=
ws around drug discovery available in myexperiment at <a href=3D"http://www=
.myexperiment.org/groups/1125/content">http://www.myexperiment.org/groups/1=
125/content</a>. Most of these are based around the free to use Open PHACTS=
 API=C2=A0<a href=3D"https://dev.openphacts.org/docs/2.0">https://dev.openp=
hacts.org/docs/2.0</a> 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.</div><div>=C2=A0</div><div>Cheers,=
</div><div><br></div><div>Ian</div><div><br></div></div><div class=3D"gmail=
_extra"><br><div class=3D"gmail_quote">On 4 March 2016 at 15:07, Whitmire, =
Sarah <span dir=3D"ltr">&lt;<a href=3D"mailto:swhitmi2@uncc.edu" target=3D"=
_blank">swhitmi2@uncc.edu</a>&gt;</span> wrote:<br><blockquote class=3D"gma=
il_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-lef=
t:1ex"><div dir=3D"ltr">To whom it may concern,<br><div class=3D"gmail_quot=
e"><div dir=3D"ltr"><br><div>I&#39;m a new user to Taverna and I&#39;m abou=
t to create a new workflow where I want to input a disease and output a lis=
t of genes associated with the disease. From there I want to perform a func=
tional 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. <br></div><div>Wou=
ld Taverna be an appropriate software to use to run such query? Would I nee=
d to download any additional plugins?<br><br></div><div>Thank you for your =
time and I look forward to your response.<span class=3D"HOEnZb"><font color=
=3D"#888888"><span><font color=3D"#888888"><br></font></span></font></span>=
</div><span class=3D"HOEnZb"><font color=3D"#888888"><span><font color=3D"#=
888888"><div><br clear=3D"all"><div><div><div dir=3D"ltr"><div><div dir=3D"=
ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div style=3D"color=
:rgb(0,0,0);margin:0px"><div style=3D"font-size:small;margin:0px"><div styl=
e=3D"margin:0px"><font face=3D"arial, helvetica, sans-serif" size=3D"2">Sar=
ah Whitmire<br></font></div><div style=3D"margin:0px"><font face=3D"arial, =
helvetica, sans-serif" size=3D"2">UNC Charlotte Class of 2016 Levine Schola=
r=C2=A0</font></div><div style=3D"margin:0px"><font face=3D"arial, helvetic=
a, sans-serif" size=3D"2">Biology B.S.=C2=A0|=C2=A0Music Minor</font></div>=
<div style=3D"margin:0px"><font face=3D"arial, helvetica, sans-serif" size=
=3D"2">Professional Science Master&#39;s: Bioinformatics (2017)</font></div=
><div style=3D"margin:0px"><font face=3D"arial, helvetica, sans-serif" size=
=3D"2">Research | Department of Kinesiology: Laboratory of Systems Physiolo=
gy=C2=A0<br></font></div><div style=3D"margin:0px"><font face=3D"arial, hel=
vetica, sans-serif" size=3D"2">Mobile:=C2=A0<a href=3D"tel:%28910%29%C2%A02=
33-5908" value=3D"+19102335908" target=3D"_blank">(910)=C2=A0233-5908</a></=
font></div></div></div></div></div></div></div></div></div></div></div>
</div></font></span></font></span></div>
</div><br></div>
</blockquote></div><br></div>

--001a1149c6c0b4601a052d3aaae4--