joelib-devel

[Joelib-devel] QSAR Project

[E.L. W. <eg...@sc...>]

=2D----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1


Good morning all,

Last friday I requested a new project, QSAR - http://www.sf.net/projects/qs=
ar,=20
which got approved. This project's goal to is guide the development of the=
=20
discussion and software development which has been discussed on the=20
cdk...@li... and joe...@li... list last wee=
k.

I would like to stress that this new SF project does not intend to reinvent=
=20
the wheel at all, but aimed at:

=2D - writing down a requirement analysis
=2D - developing a GUI that uses CDK, JChemPaint, Jmol, JOELib (alphabetical
    order) and other projects for QSAR model building

(More details are available in the thread and on the website soon.)

=46urthermore, keep in mind that though I set up this project, it is not my=
=20
intent to 'lead' the project such that my vote counts more than others.

I've set up a mailing list (has still to be approved) to which can be=20
subscribed at this page:

http://lists.sourceforge.net/lists/listinfo/qsar-devel

I've you like to join (which I hope), please send me your SF account name, =
so=20
that I can add you to the project. I would also like to repeat Peter's=20
suggestions to join the IRC chat channel (for newbies: XChat is a very good=
=20
IRC client which runs on most platforms) at #cdk on the irc.freenode.net=20
server. (Note, that when joining a channel the '#' is part of the name.)

Egon

=2D --=20
eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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Re: [Joelib-devel] QSAR Project

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

Hi Egon,

so add me as developer and if the other agree as admin.
My focus lies on extensive documentation (DocBook) and joining some code,
because my (internal) codes will go public anyway.
We can also write an open source review about QSAR ... mhh ...fine, i like
this idea.

For DocBook i would prefer SGML (jade), because i'm more familiar with
that. I know that you are using XML for Jmol. But let's discuss things in
the QSAR list in more detail.

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: [Cdk-devel] QSAR Project

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

At 09:42 19/04/2004 +0200, E.L. Willighagen wrote:
>-----BEGIN PGP SIGNED MESSAGE-----
>Hash: SHA1
>
>
>Good morning all,
>
>Last friday I requested a new project, QSAR - 
>http://www.sf.net/projects/qsar,
>which got approved. This project's goal to is guide the development of the
>discussion and software development which has been discussed on the
>cdk...@li... and joe...@li... list last week.

Well done!

please add petermr to the list

>I would like to stress that this new SF project does not intend to reinvent
>the wheel at all, but aimed at:
>
>- - writing down a requirement analysis
>- - developing a GUI that uses CDK, JChemPaint, Jmol, JOELib (alphabetical
>     order) and other projects for QSAR model building

Can I add "collecting and annotating resources - especially data and 
ontologies"

>(More details are available in the thread and on the website soon.)
>
>Furthermore, keep in mind that though I set up this project, it is not my
>intent to 'lead' the project such that my vote counts more than others.

Thanks! It is very difficult to set up projects with people you have never 
met! Henry and I did this for XML-DEV. The site (or list) owner is often 
the servant of the community, spending large amounts of time in boring work 
(editing and moving pages, mending mail lists, etc.) for which they get few 
public thanks!

>I've set up a mailing list (has still to be approved) to which can be
>subscribed at this page:
>
>http://lists.sourceforge.net/lists/listinfo/qsar-devel
>
>I've you like to join (which I hope), please send me your SF account name, so
>that I can add you to the project. I would also like to repeat Peter's
>suggestions to join the IRC chat channel (for newbies: XChat is a very good
>IRC client which runs on most platforms) at #cdk on the irc.freenode.net
>server. (Note, that when joining a channel the '#' is part of the name.)

IRC is extremely good if you have a topic which is perhaps too undefined to 
have a full mailing list discussion or casual queries. It also gives people 
a good idea of how the project is actually managed and serviced.

What I would find useful in the first few days/weeks is:
- a realistic definition of the scope. We have to be really ruthless here! 
The suggestions already made are more than we have resources to manage.
- a catalog of components
- demonstrations of what already works. I'd like to be able to run *demos* 
of CDK and/or JOELib without having to read the APIs. I find both of them 
are large and navigation is not trivial. This is true of all libraries and 
toolkits. So, for example, if there is a routine that extracts descriptors 
from a molecule it would be useful to be able to load the molecule and 
print out a list of the descriptors - maybe from a commandline in the first 
instance or from a simple test program.

Good luck

P.


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

Re: [Joelib-devel] Re: [Cdk-devel] QSAR Project

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

Hi,

> toolkits. So, for example, if there is a routine that extracts
descriptors
> from a molecule it would be useful to be able to load the molecule and
> print out a list of the descriptors - maybe from a commandline in the
first
> instance or from a simple test program.

Pretty well done !

Try JOELib with:
sh statistic.sh yourMoleculeFileWithDesc
sh descSelection.sh --help

also normalization, calculation with:
calculateDescriptors.sh and nomralize.sh

filters, e.g. hydrogen donors,  with:
sh convert.sh --help (see example given and/or tutorial)

Kind regards, Joerg


On Mon, 19 Apr 2004, Peter Murray-Rust wrote:

> At 09:42 19/04/2004 +0200, E.L. Willighagen wrote:
> >-----BEGIN PGP SIGNED MESSAGE-----
> >Hash: SHA1
> >
> >
> >Good morning all,
> >
> >Last friday I requested a new project, QSAR - 
> >http://www.sf.net/projects/qsar,
> >which got approved. This project's goal to is guide the development of the
> >discussion and software development which has been discussed on the
> >cdk...@li... and joe...@li... list last week.
> 
> Well done!
> 
> please add petermr to the list
> 
> >I would like to stress that this new SF project does not intend to reinvent
> >the wheel at all, but aimed at:
> >
> >- - writing down a requirement analysis
> >- - developing a GUI that uses CDK, JChemPaint, Jmol, JOELib (alphabetical
> >     order) and other projects for QSAR model building
> 
> Can I add "collecting and annotating resources - especially data and 
> ontologies"
> 
> >(More details are available in the thread and on the website soon.)
> >
> >Furthermore, keep in mind that though I set up this project, it is not my
> >intent to 'lead' the project such that my vote counts more than others.
> 
> Thanks! It is very difficult to set up projects with people you have never 
> met! Henry and I did this for XML-DEV. The site (or list) owner is often 
> the servant of the community, spending large amounts of time in boring work 
> (editing and moving pages, mending mail lists, etc.) for which they get few 
> public thanks!
> 
> >I've set up a mailing list (has still to be approved) to which can be
> >subscribed at this page:
> >
> >http://lists.sourceforge.net/lists/listinfo/qsar-devel
> >
> >I've you like to join (which I hope), please send me your SF account name, so
> >that I can add you to the project. I would also like to repeat Peter's
> >suggestions to join the IRC chat channel (for newbies: XChat is a very good
> >IRC client which runs on most platforms) at #cdk on the irc.freenode.net
> >server. (Note, that when joining a channel the '#' is part of the name.)
> 
> IRC is extremely good if you have a topic which is perhaps too undefined to 
> have a full mailing list discussion or casual queries. It also gives people 
> a good idea of how the project is actually managed and serviced.
> 
> What I would find useful in the first few days/weeks is:
> - a realistic definition of the scope. We have to be really ruthless here! 
> The suggestions already made are more than we have resources to manage.
> - a catalog of components
> - demonstrations of what already works. I'd like to be able to run *demos* 
> of CDK and/or JOELib without having to read the APIs. I find both of them 
> are large and navigation is not trivial. This is true of all libraries and 
> toolkits. So, for example, if there is a routine that extracts descriptors 
> from a molecule it would be useful to be able to load the molecule and 
> print out a list of the descriptors - maybe from a commandline in the first 
> instance or from a simple test program.
> 
> Good luck
> 
> P.
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
> 
> 
> 
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> 

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)