On Thu, Jan 5, 2012 at 6:38 PM, Andrew Lang <[email protected]> wrote:
> Thanks Guys.
>
>
>
> I don't have the mad skills of most people on this list, so I'll be
> exploring all your suggestions over the next semester. The advice is
> invaluable.
>
One of the great things about F/OSS and the Blue Obelisk approaches is that
no-one has to be an expert in everything.We share our skills. Many
subgroups use skype, twitter, FriendFeed, Etherpads etc as ways to
collaborate in almost real time.
Ignorance is not a crime!
>
> Thanks,
>
> Andrew Lang
> Professor of Mathematics
> GC1E08
> Oral Roberts University
> Tulsa, OK
> 74171
>
> | professor of
> mathematics<http://webapps.oru.edu/facultyplace/view_profile.php?user_id=74>|
> blog <http://snsf.blogspot.com> |
> flickr<http://www.flickr.com/photos/hirosheridan/>|
> youtube <http://youtube.com/user/hirosheridan> |
> friendfeed<http://friendfeed.com/hirosheridan>|
>
>
> > Date: Sun, 4 Dec 2011 00:24:08 +0200
> > Subject: Re: [BlueObelisk-discuss] How to distribute models
> > From: [email protected]
> > To: [email protected]
> > CC: [email protected]
>
> >
> > Hi Andrew and others,
> >
> > > There are plenty of ways I now know to create CDK descriptors and build
> > > models but I'm looking for the best way to distribute them as a desktop
> > > application.
> > >
> >
> > First of all, are you looking for an ODOSOS-spirited solution for
> > distributing models or a ready to use desktop application? If you're
> > more into the former (and don't mind some Java programming) then
> > perhaps I may suggest you to take a look at the QsarDB project
> > (http://qsardb.googlecode.com), which is a proposal for the electronic
> > organization and archiving of QSAR/QSPR model information.
> >
> > Basically, QsarDB enables you to encapsulate a QSAR model (and all of
> > its supporting information) into a single so-called QDB file. QDB
> > files are easy to distribute and archive. When handled in a proper
> > run-time environment they readily lend themselves to programmatic
> > execution, such as making a prediction.
> >
> > > My dream program would be one where you would input a SMILES (GUI), it
> would
> > > generate the CDK descriptors and then report back (user selected)
> predicted
> > > properties based upon Open models (linear, random forest, etc) with the
> > > ability to download and add new models (like you can add new
> functionality
> > > with R). A command line option that does batches would be important
> too.
> > >
> > > Does this program exist?
> > >
> >
> > Recently I did some research about QSAR model data formats and
> > couldn't find anything major except Bioclipse's QSAR-ML data format
> > (http://pele.farmbio.uu.se/qsar-ml/). Unfortunately, QSAR-ML appears
> > to be limited to the representation of raw datasets (ie. chemical
> > structures, property and descriptor values) and doesn't cover the rest
> > of a typical QSAR modelling workflow.
> >
> > QsarDB handles statistical models in the PMML data format. While
> > Rajarshi suggested to use the Weka toolkit for loading and storing
> > PMML models, our group decided to develop a new light-weight Java PMML
> > library called JPMML (http://jpmml.googlecode.com) for this purpose.
> > At the moment JPMML can do linear regression, decision tree and neural
> > network models.
> >
> > Given the QsarDB, JPMML and CDK libraries, it should be pretty
> > straightforward to write a command-line application that does exactly
> > what you describe. The application would take the input SMILES and the
> > list of executable QDB files as its arguments. The calculation of CDK
> > descriptors can be performed locally or they can be fetched from a
> > remote REST service. As a bonus, it will be possible to quantify the
> > goodness of every prediction.
> >
> > Please let me know if you're interested in exploring the possiblities
> > of QsarDB in more detail.
> >
> >
> > Best regards,
> > VR
>
>
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--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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