Subject: JUMBO and CML for compChem [ANNOUNCE]

From: Peter Murray-Rust <pm286$at$cam.ac.uk>
Date: Thu, 17 Feb 2005 17:15:38 +0000

A major release of the JUMBO system (V4.6) is now available. It contains a 
substantial kit for processing XML+CML in chemistry, including much 
computational Chemistry, Java code, XSLT stylesheets, legacy converters and 
tools. Its primary language is Java 1.4, though there are tools for 
generating C++, Python and some F90/5 from the schema.

The home page is on our Wiki at http://wwmm.ch.cam.ac.uk/moin/Jumbo4.6 and 
the initial jars will be posted during the next days. Adopters should be 
able to run Java 1.4. The working code has already been imported to the CML 
site at sourceforge (http://cml.sf.net) and can be checked out or browsed 
at http://cvs.sourceforge.net/viewcvs.py/cml/jumbo4.6/.

There is now a substantial move towards XML as an infrastructure for 
computational chemistry, especially where programs need to be chained or 
where the throughput is high. CMLComp is capable of representing the 
input/output of compChem programs and interfaces have already been 
developed for codes such as GULP, GAMESS-US, MOPAC2003, SIESTA, and others. 
We are working with groups such as CCP-1, ABINIT, FSATOM, and the Open 
chemistry community.

The distribution contains several papers describing the architecture and 
approach.  We have already built an automatic system for high-throughput 
computing and tools for automatic conversion to XML of legacy program log 
files [both of these will be reported here shortly]. We are interested in 
hearing from anyone who would benefit from having an XMLised system.

JUMBO is open source and interoperates with a number of other Open source 
efforts such as Jmol, Apache (Xindice, AXIS), Jchempaint/CDK, JOELib, 
OpenBabel, and ABINIT and we thank many collaborators

P.

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