Re: [Jmol-developers] Re: [Joelib-help] CMLRSS and WWMM and OpenMolecules

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

> >
> > Yes. In general RSS is read-only so it would be coupled to a mailing list
> > of some sort (Henry?)
>
>I'm not that clear with the blog concept: a website of someone keeping a
>diary?, or a wiki like communal website?

Yes and yes. It's a writable website with standard HTTP tools and often 
open to all. RSS is the common way of aggregating them. I haven't looked 
recently but I expect that Slashdot would be regarded as a blog.

>Anyway, I agree that it is time to organize all chemistry open source
>initiative and come up with solutions which many projects deal with, e.g.
>atom typing and interoperability...

I think the NeSC meeting will help us a great 
deal.http://www.nesc.ac.uk/esi/events/394/


> > cdkMolecule = getCDKMolecule(cmlMolecule)
> > cdkMolecule.doSomCalculation()
> > newCmlMolecule = getCMLMolecule(cdkMolecule)
> > merge(cmlMolecule, newCMLMolecule)
> >
> > and we could do the same for JOELIB.
>
>CDK has libio to JOELib... so without the need to write anything (except the
>getJOELibMolecule() wrapper), you can already do:
>
>joelibMol = getJOELibMolecule(getCDKMolecule(cmlMolecule))
>joelibMol.doSomeCalc()
>newCMLMol = getCMLMolecule(getCDKMolecule(joelibMol))
>merge(cmlMolecule, newCMLMolecule)

Excellent. For myself it would be very useful to have these examples as 
simple standalone example programs (I have to admit I get lost looking for 
functionality in libraries, including my own!). So it's a excellent 
opportunity for volunteers to write sample programs. As an example I 
haven't used JOELib to calculate cLogp simply because I haven't had the 
time to explore it.

>BTW, Joerg, it would be very nice if you could have a CMLRSS set up that 
>takes
>all current other feeds, calculates properties and puts that only as CMLRSS
>again.

This would be fantastic. Note - at this stage I recommend that all 
aggregation should be manual. This is to avoid robots out of control which 
create denial of service, loops etc. We can move to automatic in V0.2. So 
it might work like this:

JoergW reads a list of sites.
foreach week
         foreach site
                 read new molecules (date < lastdate)
                 calculate properties
                 add to JWProperty feed
         set lastdate

At this stage I don't think Joerg should be required to merge molecules 
although you are welcome to try! This would mean the same property might be 
calculated twice. A specialist aggregator could deal with that.

I am also keen to see bitscreens being distributed. I think we could set a 
standard here


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