All,

I am forwarding this message to OpenTox developers list since it is very
similar to what OpenTox project (http://www.opentox.org)  is about.

Perhaps we can collaborate with reusing/extending existing OpenTox REST
services with similar functionality and sharing experience with development
of  web services based on RDF .

Best regards,
Nina

On 23 October 2010 19:51, Peter Murray-Rust <pm286 at cam.ac.uk> wrote:

> [Copied to BlueObelisk list and Quixote - be careful with reply addresses].
>
> A group of us who met at Zaragosa for the ZCAM meeting have just spent a
> month creating an infrastructure for computational chemistry. Details (wiki,
> Etherpads and mailing lists) can be found on the wiki:
> http://quixote.wikispot.org/Front_Page.  Some of us were able to meet in
> Cambridge on Thursday and as a result have come up with a prototype which is
> able to:
> * automatically download compchem legacy files from any HTTP server
> exposing a directory.
> * convert these to CMLComp
> * convert these to RDF
> * upload to a different HTTP server using REST
>
> All code is Open Source, all data is Open Data. (Not all the compchem codes
> are Open, but that is a secondary consideration, although I will personally
> support Open codes such as NWChem and QuantumEspresso).
>
> This has been possible because of the many years of work put in by Blue
> Obelisk members and I regard this as a Blue Obelisk project. It is largely
> an integration project, carried out by a number of people in different
> locations and based on several BlueOb projects:
> * Avogadro (for display, and hopefully soon for control) - C++
> * JUMBOConverters and other JUMBO libraries - Java
> * Lensfield2 (Sam Adams) - a make-like build system for automating
> conversion
> * RESTfull upload/download (mainly Sam)
> * CML2RDF and TripleStore (Weerapong)
> * CDK for 2-D coordinates
>
> very shortly we would expect to integrate OpenBabel in for chemistry
> (sub)structure search
>
> We would be very interested in:
> * new collaborators. The main basis is Java, but we also need people who
> loike integration things, writing docs and tutorials, etc.
> * examples of log files. It would be particularly useful to have a wider
> variety of content, both chemical and methodological.
> * help with dictionaries either on a code-specific basis (GAMESS, NWChem,
> etc.) or general (i.e. applying to all compchem)
> * help with parsers for files (log files, punch/dump/arc files, input
> files). Note that we intend to parse the whole log file to help work out
> what the calculation was. This is rather like doing puzzles - sometimes
> tedious, sometimes fun. The JUMBO technology allows us to split up the
> process so different people can work n different bits (e.g. nmr,
> frequencies, orbitals, etc.)
> * people who understand firewalls, proxies, etc. (This is where most of the
> problems have arisen)
>
> This project is now indicative of one direction the Blue Obelisk is going.
> There are a sufficient number of high-quality components that  can be
> assembled rapidly and we can build a variety of systems that are
> distributable. By making the data and code Open there are several areas we
> can make rapid progress in.
>
> I think it could also be valuable to create a catalogue of Blue Obelisk
> products and services so that we help people navigate to the right places.
> Indeed a map of Blue Obelisk land could be useful.
>
> I am also thinking it could be useful to have a regular skype, or Etherpad
> or IRC meeting for the Blue Obelisk.
>
> P.
>
> --
> 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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