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Posted to dev@ctakes.apache.org by Andrew McMurry <an...@invitae.com> on 2013/12/21 02:01:38 UTC
cTAKES Virtual Machine update
"Eating your own dog food"
I've bundled a NLP appliance containing UMLS and cTAKES and I'm migrating services to the AWS cloud.
Throughout this process I have extensively documented the steps and I made a VM target for Ubuntu 13.04.
I would have used the iDASH appliance but it is no longer maintained and was way out of date.
From conversations and experiences witth iDASH and NCBO bioportal I strongly support a VM option for cTAKES downloads.
Suggestions
#[ 1 ] Public demo server (instance of VM)
For new users, this is the "hook" that motivates them to get involved BEFORE licensing and install.
http://bioportal.bioontology.org/annotator
#[ 2 ] Downloading the public demo server is power !
http://nlp-ecosystem.ucsd.edu/
http://bioportal.bioontology.org/virtual_appliance
#[ 3 ] Example code for each cTAKES component is game changing
cTAKES has an impressive set of components, but no way to try them out.
http://ctakes.apache.org/components.html
Whereas you can play with the components of Bioportal, for example
http://data.bioontology.org/documentation
I'm sharing these experiences and suggestions because I truly do believe they are crucial and likely more important than any level of new-features that can be added.
Hoping this message finds you well.
I will soon circulate a copy of a VM to play around with and get feedback.
Thoughts?
--AndyMC
Re: cTAKES Virtual Machine update
Posted by Joshua Weiner <jo...@gmail.com>.
Hey guys,
I know this is probably a dumb question but I can't for the life of me
figure it out. I finally got a UMLS username and password, but I don't
think I am updating the BAT files correctly... here is what I did: note my
username is joshuaweiner2 and my password (for this example) is mypasswordd
(see below).... I now can't get the CVD to run. my error is:
Error: Could not find or load main class org.apache.uima.tools.cvd.CVD
Thank you for your help...
:okHome
cd %CTAKES_HOME%
java -Dctakes.umlsuser=joshuawiener2 -Dctakes.umlspw=<mypasswordd -cp
"%CTAKES_HOME%/lib/*;%CTAKES_HOME%/desc/;%CTAKES_HOME%/resources/"
-Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xms512M
-Xmx1024M org.apache.uima.tools.cvd.CVD
:end
On Mon, Dec 23, 2013 at 11:44 AM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> I can ping ASF infra to see if they offer any vm's for Demo's etc. will
> revert back to see what I find out.
>
> Sent from my iPhone
>
> > On Dec 23, 2013, at 10:17 AM, "Masanz, James J." <Ma...@mayo.edu>
> wrote:
> >
> > Hi Andy,
> >
> > It's great to see such enthusiasm!
> >
> > I like all the ideas. I don't know how we ensure our image doesn't end
> up out of date, but I think it's worth doing -- and given the size of our
> community, I hope it will be able to be kept up to date.
> >
> > I'm not sure where we would host the public demo server, and since
> keeping the image itself up to date would be needed in order to keep the
> live public/demo server up to date, my thoughts are to start with 2 and 3
> and decide about #1 later.
> >
> > -- James
> >
> >
> > -----Original Message-----
> > From: dev-return-2339-Masanz.James=mayo.edu@ctakes.apache.org [mailto:
> dev-return-2339-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of
> Andrew McMurry
> > Sent: Friday, December 20, 2013 7:02 PM
> > To: dev@ctakes.apache.org
> > Subject: cTAKES Virtual Machine update
> >
> > "Eating your own dog food"
> >
> > I've bundled a NLP appliance containing UMLS and cTAKES and I'm
> migrating services to the AWS cloud.
> > Throughout this process I have extensively documented the steps and I
> made a VM target for Ubuntu 13.04.
> >
> > I would have used the iDASH appliance but it is no longer maintained and
> was way out of date.
> > From conversations and experiences witth iDASH and NCBO bioportal I
> strongly support a VM option for cTAKES downloads.
> >
> > Suggestions
> >
> > #[ 1 ] Public demo server (instance of VM)
> > For new users, this is the "hook" that motivates them to get involved
> BEFORE licensing and install.
> > http://bioportal.bioontology.org/annotator
> >
> > #[ 2 ] Downloading the public demo server is power !
> > http://nlp-ecosystem.ucsd.edu/
> > http://bioportal.bioontology.org/virtual_appliance
> >
> > #[ 3 ] Example code for each cTAKES component is game changing
> >
> > cTAKES has an impressive set of components, but no way to try them out.
> > http://ctakes.apache.org/components.html
> >
> > Whereas you can play with the components of Bioportal, for example
> > http://data.bioontology.org/documentation
> >
> > I'm sharing these experiences and suggestions because I truly do believe
> they are crucial and likely more important than any level of new-features
> that can be added.
> >
> > Hoping this message finds you well.
> > I will soon circulate a copy of a VM to play around with and get
> feedback.
> >
> > Thoughts?
> >
> > --AndyMC
> >
>
--
Joshua S. Weiner
joshuaweiner2@gmail.com
201.638.0047
Re: cTAKES Virtual Machine update
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I can ping ASF infra to see if they offer any vm's for Demo's etc. will revert back to see what I find out.
Sent from my iPhone
> On Dec 23, 2013, at 10:17 AM, "Masanz, James J." <Ma...@mayo.edu> wrote:
>
> Hi Andy,
>
> It's great to see such enthusiasm!
>
> I like all the ideas. I don't know how we ensure our image doesn't end up out of date, but I think it's worth doing -- and given the size of our community, I hope it will be able to be kept up to date.
>
> I'm not sure where we would host the public demo server, and since keeping the image itself up to date would be needed in order to keep the live public/demo server up to date, my thoughts are to start with 2 and 3 and decide about #1 later.
>
> -- James
>
>
> -----Original Message-----
> From: dev-return-2339-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2339-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Andrew McMurry
> Sent: Friday, December 20, 2013 7:02 PM
> To: dev@ctakes.apache.org
> Subject: cTAKES Virtual Machine update
>
> "Eating your own dog food"
>
> I've bundled a NLP appliance containing UMLS and cTAKES and I'm migrating services to the AWS cloud.
> Throughout this process I have extensively documented the steps and I made a VM target for Ubuntu 13.04.
>
> I would have used the iDASH appliance but it is no longer maintained and was way out of date.
> From conversations and experiences witth iDASH and NCBO bioportal I strongly support a VM option for cTAKES downloads.
>
> Suggestions
>
> #[ 1 ] Public demo server (instance of VM)
> For new users, this is the "hook" that motivates them to get involved BEFORE licensing and install.
> http://bioportal.bioontology.org/annotator
>
> #[ 2 ] Downloading the public demo server is power !
> http://nlp-ecosystem.ucsd.edu/
> http://bioportal.bioontology.org/virtual_appliance
>
> #[ 3 ] Example code for each cTAKES component is game changing
>
> cTAKES has an impressive set of components, but no way to try them out.
> http://ctakes.apache.org/components.html
>
> Whereas you can play with the components of Bioportal, for example
> http://data.bioontology.org/documentation
>
> I'm sharing these experiences and suggestions because I truly do believe they are crucial and likely more important than any level of new-features that can be added.
>
> Hoping this message finds you well.
> I will soon circulate a copy of a VM to play around with and get feedback.
>
> Thoughts?
>
> --AndyMC
>
RE: cTAKES Virtual Machine update
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Hi Andy,
It's great to see such enthusiasm!
I like all the ideas. I don't know how we ensure our image doesn't end up out of date, but I think it's worth doing -- and given the size of our community, I hope it will be able to be kept up to date.
I'm not sure where we would host the public demo server, and since keeping the image itself up to date would be needed in order to keep the live public/demo server up to date, my thoughts are to start with 2 and 3 and decide about #1 later.
-- James
-----Original Message-----
From: dev-return-2339-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2339-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Andrew McMurry
Sent: Friday, December 20, 2013 7:02 PM
To: dev@ctakes.apache.org
Subject: cTAKES Virtual Machine update
"Eating your own dog food"
I've bundled a NLP appliance containing UMLS and cTAKES and I'm migrating services to the AWS cloud.
Throughout this process I have extensively documented the steps and I made a VM target for Ubuntu 13.04.
I would have used the iDASH appliance but it is no longer maintained and was way out of date.
>From conversations and experiences witth iDASH and NCBO bioportal I strongly support a VM option for cTAKES downloads.
Suggestions
#[ 1 ] Public demo server (instance of VM)
For new users, this is the "hook" that motivates them to get involved BEFORE licensing and install.
http://bioportal.bioontology.org/annotator
#[ 2 ] Downloading the public demo server is power !
http://nlp-ecosystem.ucsd.edu/
http://bioportal.bioontology.org/virtual_appliance
#[ 3 ] Example code for each cTAKES component is game changing
cTAKES has an impressive set of components, but no way to try them out.
http://ctakes.apache.org/components.html
Whereas you can play with the components of Bioportal, for example
http://data.bioontology.org/documentation
I'm sharing these experiences and suggestions because I truly do believe they are crucial and likely more important than any level of new-features that can be added.
Hoping this message finds you well.
I will soon circulate a copy of a VM to play around with and get feedback.
Thoughts?
--AndyMC