joelib-devel

[Joelib-devel] Molecular Open Web Services

[Peter Murray-R. <pm...@ca...>]

[Crossposted to several OpenSource lists - please reply thoughtfully. I 
will collate significant replies]

We have been investigating Web Services as a means of distributing Open 
molecular functionality. YY has set up a range of services on our site:
http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere
I believe that web services provide a valuable approach for some of what we 
want to do. Rather than linking a library or executable into the code, a 
call is made to a WS. Thus, for example, we have set up an InChI server:
http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=generateinchi&JavaScript=enabled
where the input is supplied as CML or legacy ASCII and the output returned 
as ASCII.

Note that WS do not require graphical i/o or a human to click for the 
service - they can be called programmatically from a wide range of bindings 
(probably not FORTRAN)

WS have several advantages:
- the user doesn't have to install the code
- the user doesn't have to maintain the code
- complex architectures can be hidden behind the surface
- it leads to cleaner component design
- the developer may not have to worry about porting
- it avoids the "jar explosion and version" problem that we have when using 
other systems
- assuming the WS is open it can be cloned and installed elsewhere, thus 
adding redundancy
- several generic systems (e.g. http://taverna.sf.net) are being developed 
to support component-based approaches including WS.
- attractive when the operation is a relatively infrequent requirement
- good for teaching

There may be some disadvantages:
- the user may not always be connected or the service is not available. 
Solution: install the service on your local machine and/or create mirrors
- there may be a performance hit - is this is actually a problem?
- the application requires the state to be maintained (WS are easier for 
stateless protocols). All our protocols are  stateless.

I think WS has a lot to offer our community. For example I'd like to use 
JOELib or CDK to calculate molecular properties. It's an effort to link 
these into a single bloated app as every time some library changes the 
whole lot has to be recompiled. With WS I can calculate the properties I 
want independently of the implementation.

Are others in this community interested? What services would people like? 
Our own list includes but is not limited to:
- calculate 2D coords for connection table
- calculate 3D coords for molecule
- MM, MD, MO calculations
- calculate descriptors for molecule
- calculate properties for molecules
- legacy conversions
- search databases
- create SVG diagrams for molecules and reactions
- create PNGs

If you have a working application it's relatively easy to create a WS. YY 
has created pages:
http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage
http://wwmm.ch.cam.ac.uk/moin/WebServiceDev

P.


Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069

[Joelib-devel] Re: [QSAR-devel] Molecular Open Web Services

[Matteo F. <flo...@ya...>]

Hi  all,

> What
> services would people like? 
> Our own list includes but is not limited to:
> - calculate 2D coords for connection table
> - calculate 3D coords for molecule
> - MM, MD, MO calculations
> - calculate descriptors for molecule
> - calculate properties for molecules
> - legacy conversions
> - search databases
> - create SVG diagrams for molecules and reactions
> - create PNGs


Hi all,
as most of you know, Egon has developed a line command
for calculating descriptors with CDK. I think it could
be very easy to develop a WS, with a few minutes work
for a simple web interface. 
I see also there is a good request of "web molecular
databases". My modest opinion is that it could be
better to think at an unique WS similar to
not-chemical "web content managers".

Regards,

Matteo Floris.



> If you have a working application it's relatively
> easy to create a WS. YY 
> has created pages:
> http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage
> http://wwmm.ch.cam.ac.uk/moin/WebServiceDev
> 
> P.
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
> 
> 
> 
>
-------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT
> Products from real users.
> Discover which products truly live up to the hype.
> Start reading now. 
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Qsar-devel mailing list
> Qsa...@li...
>
https://lists.sourceforge.net/lists/listinfo/qsar-devel
>  


		
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[Joelib-devel] Re: [Cdk-devel] Re: [QSAR-devel] Molecular Open Web Services

[Christoph S. <c.s...@un...>]

Hi everybody,

I think, both things would be very beneficial for promoting=20
CDK/JOELib/Jumbo functionality to the public:

1. portal to chemoinformatics functionality and
2. a set of webservices for the tasks stated below.

My focus would be the first, but I guess, the second could just easily=20
come with the first as a spin-off.
I first thought that a nice wrapper would be a lot of work but then=20
realized that we are already sitting on all the neccessary technology.
The Apache JetSpeed portal software is exactly what is needed to display=20
chemoinformatics functionality nicely customisable in a web view. It=20
gives us all the admin stuff for free and all we need to do it wrap the=20
single functionalities in so called "portlets".
Portlets can be easily arranged to yield a full portal view using the=20
JetSpeed admin interface and, best of all, every user can create his or=20
her own arrangement and set of portals, depending on whether you want=20
visualisation, conversion of formats, structure generation or QSAR.
The principle can be inspected at http://www.nmrshiftdb.org, where, in=20
the start screen, the left, central and right part are different=20
portlets. The layout can be much more sophisticated, though.

We might just start with setting up a basic interface, called=20
www.cdkweb.org, or so, and start with a structure input portlet, which=20
can load structures either from file or as SMILES, a central viewer=20
portlet and a portlet to the right which displays some information (ring=20
set, or so) about each molecule.

Cheers,

Chris

--=20
Dr. habil. Christoph Steinbeck (c.s...@un...)
Head of the Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..


Matteo Floris wrote:
>>What
>>services would people like?=20
>>Our own list includes but is not limited to:
>>- calculate 2D coords for connection table
>>- calculate 3D coords for molecule
>>- MM, MD, MO calculations
>>- calculate descriptors for molecule
>>- calculate properties for molecules
>>- legacy conversions
>>- search databases
>>- create SVG diagrams for molecules and reactions
>>- create PNGs
>=20
>=20
>=20
> Hi all,
> as most of you know, Egon has developed a line command
> for calculating descriptors with CDK. I think it could
> be very easy to develop a WS, with a few minutes work
> for a simple web interface.=20
> I see also there is a good request of "web molecular
> databases". My modest opinion is that it could be
> better to think at an unique WS similar to
> not-chemical "web content managers".

[Joelib-devel] Re: [QSAR-devel] Molecular Open Web Services

[Peter Murray-R. <pm...@ca...>]

At 16:12 15/12/2004 +0100, E.L. Willighagen wrote:
>-----BEGIN PGP SIGNED MESSAGE-----
>Hash: SHA1
>
>On Monday 13 December 2004 13:36, Matteo Floris wrote:
> > > What services would people like?
> > > Our own list includes but is not limited to:
> > > - calculate 2D coords for connection table
> > > - calculate 3D coords for molecule
> > > - MM, MD, MO calculations
> > > - calculate descriptors for molecule
> > > - calculate properties for molecules
> > > - legacy conversions
> > > - search databases
> > > - create SVG diagrams for molecules and reactions
> > > - create PNGs
>
>Peter, the system you describe, is that using SOAP?

I shall let YY answer definitively, but I am sure it does.

>  So that it could integrate
>with SciTegic's PipeLine Pilot, which can use SOAP services as nodes in the
>pipeline?

I you have PLP and want to integrate, then fine. I have worked with PLP and 
it is a good product. However I do not know its data architecture but I 
strongly suspect it is not compatible with what we are developing here.

>At the CIC Workshop I met Asutosh Yagnik of SciTegic and talked with him a 
>bit
>on their software, and talked about integrating CDK functionality with
>PipeLine pilot... And it was reasonably straightforward to integrate SOAP
>services...

My concern is primarily about the data objects, particularly the XML 
serialisation. If PLP does not support them then it may not be easy to do it.

What I am suggesting here is that we look at systems like Taverna (or 
Kepler). We have built a very successful workflow with Taverna that works 
well. There is quite a large development team and they are very responsive. 
They already have Jmol as a viewer. They have a model where (say) other 
renderers such as JCP could be integrated. The system can run as 
standalone, web services grid-enabled, etc.

The first task is for us to agree on the object we pass. These are safest 
if they are serialized (e.g. in CML) but it appears that for non-persistent 
objects Java will work (works fine for me). It could be that octet has a 
role here.

YY is currently setting up pages where you can develop your own simple WS 
aggregation. A typical example is
"find the molecular mass for a SMILES".*

We can do this in two steps:
- convert SMILES to CML (OB)
- calculate MWt (JUMBO: MoleculeTool.getMolecularMass());

The idea will be to create (very simple) workflow on-the-fly. It is likely 
that we shall be able to save these as Taverna XML objects

P.

* - I expect that some systems may be able to do this directly, but this is 
just an example. Moreover it could be that other components could be 
substituted for each step


>Egon
>
>- --
>e.w...@sc...
>PhD-student on Molecular Representation in Chemometrics
>Radboud University Nijmegen
>http://www.cac.science.ru.nl/people/egonw/
>GPG: 1024D/D6336BA6
>-----BEGIN PGP SIGNATURE-----
>Version: GnuPG v1.0.7 (SunOS)
>
>iD8DBQFBwFRbd9R8I9Yza6YRApFvAKCcOzK+9n5xiT2cPCAtvB9WqrEzZQCfYI73
>D1dZx7wtYnfNiMfRltni0us=
>=XDrF
>-----END PGP SIGNATURE-----

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069

[Joelib-devel] Re: [QSAR-devel] Molecular Open Web Services

[Joerg K. W. <we...@in...>]

Hi all,

>>I think WS has a lot to offer our community. For example I'd like to use 
>>JOELib or CDK to calculate molecular properties. It's an effort to link 
>>these into a single bloated app as every time some library changes the 
>>whole lot has to be recompiled. With WS I can calculate the properties I 
>>want independently of the implementation.

1. i've no experience with web services, can i execute those services 
you mentioned, because i got only XML code.
I would be very interested for some help here.

2. i would prefer a neutral web-link, like
sf.qsar.net/service
or
...
the name should be as general as possible and not mainly connected one 
specific library.

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)

[Joelib-devel] Re: [QSAR-devel] Molecular Open Web Services

[Stefan K. <ste...@un...>]

Hi everybody,
I just wanted to mention that NMRShiftDB offers certain web services, lik=
e=20
searches etc. These are mainly used by the stand-alone client, similar to=
=20
RPC, but can be used by every client. They are actually restricted to acc=
ess=20
from Java programs, since some input is cdk objects, but this could be=20
changed. We do also currently not have WSDL descriptions, since I did not=
=20
find a good description/example of it. But I would try to do this, so we=20
could do something like a chemoinformatics web services directory.
Generally speaking I got the impression that the interoperability of web=20
servies has its limitions. Apart from the obvious problem with data types=
, I=20
would not bet on being able to use any service with any client indepently=
 of=20
langage, server etc. used.
Stefan Kuhn

Am Sunday 12 December 2004 17:17 schrieb Peter Murray-Rust:
> [Crossposted to several OpenSource lists - please reply thoughtfully. I
> will collate significant replies]
>
> We have been investigating Web Services as a means of distributing Open
> molecular functionality. YY has set up a range of services on our site:
> http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere
> I believe that web services provide a valuable approach for some of wha=
t we
> want to do. Rather than linking a library or executable into the code, =
a
> call is made to a WS. Thus, for example, we have set up an InChI server=
:
> http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=3Dgenerateinchi&Java=
Script
>=3Denabled where the input is supplied as CML or legacy ASCII and the ou=
tput
> returned as ASCII.
>
> Note that WS do not require graphical i/o or a human to click for the
> service - they can be called programmatically from a wide range of bind=
ings
> (probably not FORTRAN)
>
> WS have several advantages:
> - the user doesn't have to install the code
> - the user doesn't have to maintain the code
> - complex architectures can be hidden behind the surface
> - it leads to cleaner component design
> - the developer may not have to worry about porting
> - it avoids the "jar explosion and version" problem that we have when u=
sing
> other systems
> - assuming the WS is open it can be cloned and installed elsewhere, thu=
s
> adding redundancy
> - several generic systems (e.g. http://taverna.sf.net) are being develo=
ped
> to support component-based approaches including WS.
> - attractive when the operation is a relatively infrequent requirement
> - good for teaching
>
> There may be some disadvantages:
> - the user may not always be connected or the service is not available.
> Solution: install the service on your local machine and/or create mirro=
rs
> - there may be a performance hit - is this is actually a problem?
> - the application requires the state to be maintained (WS are easier fo=
r
> stateless protocols). All our protocols are  stateless.
>
> I think WS has a lot to offer our community. For example I'd like to us=
e
> JOELib or CDK to calculate molecular properties. It's an effort to link
> these into a single bloated app as every time some library changes the
> whole lot has to be recompiled. With WS I can calculate the properties =
I
> want independently of the implementation.
>
> Are others in this community interested? What services would people lik=
e?
> Our own list includes but is not limited to:
> - calculate 2D coords for connection table
> - calculate 3D coords for molecule
> - MM, MD, MO calculations
> - calculate descriptors for molecule
> - calculate properties for molecules
> - legacy conversions
> - search databases
> - create SVG diagrams for molecules and reactions
> - create PNGs
>
> If you have a working application it's relatively easy to create a WS. =
YY
> has created pages:
> http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage
> http://wwmm.ch.cam.ac.uk/moin/WebServiceDev
>
> P.
>
>
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Qsar-devel mailing list
> Qsa...@li...
> https://lists.sourceforge.net/lists/listinfo/qsar-devel

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Joelib-devel] Re: [QSAR-devel] Molecular Open Web Services

[Peter Murray-R. <pm...@ca...>]

At 13:13 15/12/2004 +0100, Stefan Kuhn wrote:
>Hi everybody,

I have answered this on the QSAR list - a brief additional comment

>I just wanted to mention that NMRShiftDB offers certain web services, like
>searches etc. These are mainly used by the stand-alone client, similar to
>RPC, but can be used by every client. They are actually restricted to=
 access
>from Java programs, since some input is cdk objects, but this could be
>changed. We do also currently not have WSDL descriptions, since I did not
>find a good description/example of it. But I would try to do this, so we
>could do something like a chemoinformatics web services directory.
>Generally speaking I got the impression that the interoperability of web
>servies has its limitions. Apart from the obvious problem with data types,=
 I
>would not bet on being able to use any service with any client indepently=
 of
>langage, server etc. used.

This need not be a problem.

Web services does not necessarily need a human-operated client emitting=20
photons. They can be called from a program. So it would be perfectly=20
possible to create a WS  chain with contributions like
- read journal TOC (JUMBO)
- substructure search of known data (OB)
- extract supplemental 3D data and spectra (JUMBO)
- calculate NMR spectrum GAMESS
- calculate NMR spectrum (NMRShiftDB)
- calculate descriptors (CDK, JOELib)

etc. - this is just an example to show that different groups contribute=20
different services

If the data are agreed types and all serialized in agreed format then it's=
=20
trivial to call them from programs. That is what we are all working on...

If there are objects (e.g. spectra) we need agreed representations=20
(CMLSpect, JCAMP) and GUIs for humans. But we need this anyway.

P.

>Stefan Kuhn
>
>Am Sunday 12 December 2004 17:17 schrieb Peter Murray-Rust:
> > [Crossposted to several OpenSource lists - please reply thoughtfully. I
> > will collate significant replies]
> >
> > We have been investigating Web Services as a means of distributing Open
> > molecular functionality. YY has set up a range of services on our site:
> > http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere
> > I believe that web services provide a valuable approach for some of what=
 we
> > want to do. Rather than linking a library or executable into the code, a
> > call is made to a WS. Thus, for example, we have set up an InChI server:
> >=
 http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=3Dgenerateinchi&JavaScri=
pt
> >=3Denabled where the input is supplied as CML or legacy ASCII and the=
 output
> > returned as ASCII.
> >
> > Note that WS do not require graphical i/o or a human to click for the
> > service - they can be called programmatically from a wide range of=
 bindings
> > (probably not FORTRAN)
> >
> > WS have several advantages:
> > - the user doesn't have to install the code
> > - the user doesn't have to maintain the code
> > - complex architectures can be hidden behind the surface
> > - it leads to cleaner component design
> > - the developer may not have to worry about porting
> > - it avoids the "jar explosion and version" problem that we have when=
 using
> > other systems
> > - assuming the WS is open it can be cloned and installed elsewhere, thus
> > adding redundancy
> > - several generic systems (e.g. http://taverna.sf.net) are being=
 developed
> > to support component-based approaches including WS.
> > - attractive when the operation is a relatively infrequent requirement
> > - good for teaching
> >
> > There may be some disadvantages:
> > - the user may not always be connected or the service is not available.
> > Solution: install the service on your local machine and/or create=
 mirrors
> > - there may be a performance hit - is this is actually a problem?
> > - the application requires the state to be maintained (WS are easier for
> > stateless protocols). All our protocols are  stateless.
> >
> > I think WS has a lot to offer our community. For example I'd like to use
> > JOELib or CDK to calculate molecular properties. It's an effort to link
> > these into a single bloated app as every time some library changes the
> > whole lot has to be recompiled. With WS I can calculate the properties I
> > want independently of the implementation.
> >
> > Are others in this community interested? What services would people=
 like?
> > Our own list includes but is not limited to:
> > - calculate 2D coords for connection table
> > - calculate 3D coords for molecule
> > - MM, MD, MO calculations
> > - calculate descriptors for molecule
> > - calculate properties for molecules
> > - legacy conversions
> > - search databases
> > - create SVG diagrams for molecules and reactions
> > - create PNGs
> >
> > If you have a working application it's relatively easy to create a WS.=
 YY
> > has created pages:
> > http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage
> > http://wwmm.ch.cam.ac.uk/moin/WebServiceDev
> >
> > P.
> >
> >
> > Peter Murray-Rust
> > Unilever Centre for Molecular Informatics
> > Chemistry Department, Cambridge University
> > Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> > Tel: +44-1223-763069
> >
> >
> >
> > -------------------------------------------------------
> > SF email is sponsored by - The IT Product Guide
> > Read honest & candid reviews on hundreds of IT Products from real users.
> > Discover which products truly live up to the hype. Start reading now.
> > http://productguide.itmanagersjournal.com/
> > _______________________________________________
> > Qsar-devel mailing list
> > Qsa...@li...
> > https://lists.sourceforge.net/lists/listinfo/qsar-devel
>
>--
>Stefan Kuhn M. A.
>Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
>Z=FClpicher Str. 47, 50674 Cologne
>Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
>My public PGP key is available at http://pgp.mit.edu

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069