Re: openbabel web service (lirong wang)

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Re: openbabel web service (lirong wang)

lirong wang
Hi,
Actually , I have done several web projects based on the openbabel. Please
contact me ([hidden email]) for detail if you interested.
We just use JME as structure input or use file directly upload, use
openbabel to convert format, to generate fingerprint for similarity search.
and substructure search( though maybe not exactly right ) .
the language is PHP . platform is linux(or maybe mac, I am not sure), apache
or mysql for database.


Lirong wang
School of pharmacy
University of Pittsburgh.

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Sent: 2010年4月13日 11:37
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Subject: OpenBabel-discuss Digest, Vol 47, Issue 2

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Today's Topics:

   1. openbabel web service (Christian Meisenbichler)
   2. Re: openbabel web service (Tim Vandermeersch)
   3. Re: openbabel web service (Noel O'Boyle)
   4. Re: openbabel web service (Nina Jeliazkova)
   5. Re: openbabel web service (Rajarshi Guha)


----------------------------------------------------------------------

Message: 1
Date: Tue, 13 Apr 2010 14:02:57 +0200
From: Christian Meisenbichler <[hidden email]>
Subject: [Open Babel] openbabel web service
To: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1

Is someone interested in creating an openbabel web service?

Let me explain what I mean by that. I Just recently got convinced by
the idea of software as a service and the practical elegance of
knitting together various parts of software by http requests.
Openbabel as a converter tool would just be perfect for such a
service.

The service would accept a http post request with the file to convert
as post data.  The source and target file format is encoded in the URI
and the request returns the converted file.

As there are already python bindings, a simple python http request
handler that provides this service is something I would quite like to
implement. Question is if there is someone who would be interested to
host such a service? Maybe even as a part of the open babel project?

Motivation of course is that one sometimes wants to use openbabel
functionality but it is for some reason impossible or impractical to
install it or deal with the dependencies. In such an situation the
script or application must only be able to issue an http request. I
think thats utterly elegant.

What do you think?



------------------------------

Message: 2
Date: Tue, 13 Apr 2010 17:03:02 +0200
From: Tim Vandermeersch <[hidden email]>
Subject: Re: [Open Babel] openbabel web service
To: Christian Meisenbichler <[hidden email]>
Cc: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

On Tue, Apr 13, 2010 at 2:02 PM, Christian Meisenbichler
<[hidden email]> wrote:

> Is someone interested in creating an openbabel web service?
>
> Let me explain what I mean by that. I Just recently got convinced by
> the idea of software as a service and the practical elegance of
> knitting together various parts of software by http requests.
> Openbabel as a converter tool would just be perfect for such a
> service.
>
> The service would accept a http post request with the file to convert
> as post data. ?The source and target file format is encoded in the URI
> and the request returns the converted file.
>
> As there are already python bindings, a simple python http request
> handler that provides this service is something I would quite like to
> implement. Question is if there is someone who would be interested to
> host such a service? Maybe even as a part of the open babel project?

Technically, this isn't hard to implement. The biggest problem
probably is that dedicated hosting (or hosting that allows you to use
c++ programs) is usually expensive. However, you can easily do this on
a (linux) server at home. There are free services which will translate
a dns name to your ip. This is an easy way to play with the concept...
Depending on the usage, the home solution might not be sufficient
though.

You (or we, if there are other developers interested) can always look
for a sponsor to provide hosting later.

> Motivation of course is that one sometimes wants to use openbabel
> functionality but it is for some reason impossible or impractical to
> install it or deal with the dependencies. In such an situation the
> script or application must only be able to issue an http request. I
> think thats utterly elegant.
>
> What do you think?
>
>
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------------------------------

Message: 3
Date: Tue, 13 Apr 2010 16:27:14 +0100
From: "Noel O'Boyle" <[hidden email]>
Subject: Re: [Open Babel] openbabel web service
To: Christian Meisenbichler <[hidden email]>
Cc: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1

On 13 April 2010 13:02, Christian Meisenbichler
<[hidden email]> wrote:
> Is someone interested in creating an openbabel web service?

It sounds like you are! :-)

But seriously, it's a great idea. I've never gotten around to doing it
myself, but we really should have one plus a web site frontend. See
how Markus has set up the Chemical Identifier Resolver as a REST-based
webservice (http://cactus.nci.nih.gov/chemical/structure, and his blog
for background). In the past, it has just accepted string formats
(e.g. InChI, SMILES) but going forward it's going to accept files.

If you are planning to do this (and I would encourage you to go
ahead), we can link to it from the wiki and give it a virtual home at
openbabel.org/whatever. Where the actual home goes will depend on the
required resources - if we can get a proof of concept going that would
be the first thing (as Tim says). We can then starting thinking about
how to deploy it for mass use.

> Let me explain what I mean by that. I Just recently got convinced by
> the idea of software as a service and the practical elegance of
> knitting together various parts of software by http requests.
> Openbabel as a converter tool would just be perfect for such a
> service.

Sure - I completely agree. Google "webel cinfony" for an example of a
cheminformatics toolkit that runs only on webservices.

> The service would accept a http post request with the file to convert
> as post data. ?The source and target file format is encoded in the URI
> and the request returns the converted file.

> As there are already python bindings, a simple python http request
> handler that provides this service is something I would quite like to
> implement. Question is if there is someone who would be interested to
> host such a service? Maybe even as a part of the open babel project?

> Motivation of course is that one sometimes wants to use openbabel
> functionality but it is for some reason impossible or impractical to
> install it or deal with the dependencies. In such an situation the
> script or application must only be able to issue an http request. I
> think thats utterly elegant.
>
> What do you think?

Bring it on. But do think about the API at least as much as the
technical aspects.

>
----------------------------------------------------------------------------
--

> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>



------------------------------

Message: 4
Date: Tue, 13 Apr 2010 18:35:22 +0300
From: Nina Jeliazkova <[hidden email]>
Subject: Re: [Open Babel] openbabel web service
To: "Noel O'Boyle" <[hidden email]>
Cc: [hidden email]
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Noel O'Boyle wrote:

> On 13 April 2010 13:02, Christian Meisenbichler
> <[hidden email]> wrote:
>  
>> Is someone interested in creating an openbabel web service?
>>    
>
> It sounds like you are! :-)
>
> But seriously, it's a great idea. I've never gotten around to doing it
> myself, but we really should have one plus a web site frontend. See
> how Markus has set up the Chemical Identifier Resolver as a REST-based
> webservice (http://cactus.nci.nih.gov/chemical/structure, and his blog
> for background). In the past, it has just accepted string formats
> (e.g. InChI, SMILES) but going forward it's going to accept files.
>
> If you are planning to do this (and I would encourage you to go
> ahead), we can link to it from the wiki and give it a virtual home at
> openbabel.org/whatever. Where the actual home goes will depend on the
> required resources - if we can get a proof of concept going that would
> be the first thing (as Tim says). We can then starting thinking about
> how to deploy it for mass use.
>
>  
>> Let me explain what I mean by that. I Just recently got convinced by
>> the idea of software as a service and the practical elegance of
>> knitting together various parts of software by http requests.
>> Openbabel as a converter tool would just be perfect for such a
>> service.
>>    
>
> Sure - I completely agree. Google "webel cinfony" for an example of a
> cheminformatics toolkit that runs only on webservices.
>
>  
>> The service would accept a http post request with the file to convert
>> as post data.  The source and target file format is encoded in the URI
>> and the request returns the converted file.
>>    
>
>  
>> As there are already python bindings, a simple python http request
>> handler that provides this service is something I would quite like to
>> implement. Question is if there is someone who would be interested to
>> host such a service? Maybe even as a part of the open babel project?
>>    
>
>  
>> Motivation of course is that one sometimes wants to use openbabel
>> functionality but it is for some reason impossible or impractical to
>> install it or deal with the dependencies. In such an situation the
>> script or application must only be able to issue an http request. I
>> think thats utterly elegant.
>>
>> What do you think?
>>    
>
> Bring it on. But do think about the API at least as much as the
> technical aspects.
>  

Regarding the REST API - we are trying to do something similar (although
not only format conversions, but various predictions ) in OpenTox
project http://opentox.org/.   The developer's  list is open to everybody.

Best regards,
Nina Jeliazkova

>  
>>
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>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>    
>
>
----------------------------------------------------------------------------
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> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>  

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------------------------------

Message: 5
Date: Tue, 13 Apr 2010 11:36:49 -0400
From: Rajarshi Guha <[hidden email]>
Subject: Re: [Open Babel] openbabel web service
To: Christian Meisenbichler <[hidden email]>
Cc: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1

At one point IU and Cambridge both had services based on OpenBabel. I
think the IU services are still up. They were originally written as
SOAP services (blech!) but may have been updated to REST interfaces

http://www.chembiogrid.org/projects/proj_ws_all.html

On Tue, Apr 13, 2010 at 8:02 AM, Christian Meisenbichler
<[hidden email]> wrote:

> Is someone interested in creating an openbabel web service?
>
> Let me explain what I mean by that. I Just recently got convinced by
> the idea of software as a service and the practical elegance of
> knitting together various parts of software by http requests.
> Openbabel as a converter tool would just be perfect for such a
> service.
>
> The service would accept a http post request with the file to convert
> as post data. ?The source and target file format is encoded in the URI
> and the request returns the converted file.
>
> As there are already python bindings, a simple python http request
> handler that provides this service is something I would quite like to
> implement. Question is if there is someone who would be interested to
> host such a service? Maybe even as a part of the open babel project?
>
> Motivation of course is that one sometimes wants to use openbabel
> functionality but it is for some reason impossible or impractical to
> install it or deal with the dependencies. In such an situation the
> script or application must only be able to issue an http request. I
> think thats utterly elegant.
>
> What do you think?
>
>
----------------------------------------------------------------------------
--

> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>



--
Rajarshi Guha
NIH Chemical Genomics Center



------------------------------

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Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev

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