Transcript Community Grids Lab CICC Activities Geoffrey Fox, Marlon Pierce Indiana University CGL Contributions to CICC • Build Web/Grid services for connecting – Data sources – Applications.

Community Grids Lab CICC
Activities
Geoffrey Fox, Marlon Pierce
Indiana University
CGL Contributions to CICC
• Build Web/Grid services for connecting
– Data sources
– Applications (simulation, data mining, data assimilation, imaging,
etc).
– Computing resources
– Information services.
• Third party tool evaluation
– Workflow (Taverna)
– Grid tools: Globus and Condor (for interacting with TeraGrid)
• Building standards-based Web portal environments.
– OGCE grid portal project
– JSR 168 Java standards.
– This activity will begin in earnest over the summer.
BCI Clustering Service Methods
Service Method
Description
Input
Output
makebitsGenerate
Generate fingerprints
SMIstring
from a SMILES structure
Fingerprint
string
divkmGenerate
Cluster fingerprints with
Divkmeans
SCNstring Clustered
Hierarchy
smile2dkm
Makebits + divkm
SMIstring
optclusGenerate
Generate the best levels DKMstring Best partition
in a hierarchy
cluster level
rnnclusGenerate
Extract individual cluster
partitions
Clustered
Hierarchy
DKMstring Indiv. cluster
partitions
smile2ClusterPartiti Generate a new SMILES SMIstring
oned
structure w/ extra col.
New SMILES
structure
Local Web Service Methods for
WWMM of PMR’s Group
Services
Descriptions
Input
Output
InChIGoogle Search an InChI
inchiBasic
structure through Google type
Search result in
HTML format
InChIServer
Generate InChI
version
format
An InChI
structure
OBServer
Transform a chemical
format to another using
Open Babel
format
inputData
outputData
options
Converted
chemical
structure string
CMLRSSSer Generate CMLRSS feed
ver
from CML data
mol, title
Converted
description CMLRSS feed
link, source of CML data
More Services
VOTables
and related
services.
General purpose service for manipulating tabular
data. Comes with third party tools for parsing,
manipulating, displaying data. Includes import
tools. Using this as an intermediary for data
exchange between data bases.
Draw2d
Uses CDK tools to create 2d images from SDF
formatted data.
Common
Substructure
Another CDK service that can be used to calculate
the common substructure between two molecules.
Other CDK
Services
See
http://www.chembiogrid.org/wiki/index.php/Web_Se
rvices_Infrastructure. Based on Dr. Rajarshi
Guha’s services.
ToxTree Service
• An open Java source application by Nina Jeliazkova
• Estimates toxic hazard by applying a decision tree
approach.
• Encodes the Cramer scheme
(Cramer G. M., R. A. Ford, R. L. Hall, Estimation of
Toxic Hazard - A Decision Tree Approach, J. Cosmet.
Toxicol., Vol.16, pp. 255-276, Pergamon Press, 1978)
• Could be applied to datasets from various compatible
file types.
• We are converting this GUI application to a textbased web service
OSCAR3 Service
• An under-development open Java source application
by Peter Murray-Rust group at Cambridge, UK. (Not
published yet)
• Extracts chemical information from either a
paragraph of experimental data, or a full paper (e.g.
melting points, Rf, infra-red and NMR data, and mass
spectral information)
• Produces an XML instance highlighting the chemical
information with an Extensible Stylesheet Language
(XSL) file
• We are attaching SOAP input/output engine for a web
service
Other Areas of Lab Expertise
• Distributed messaging systems for web services and
other applications.
– NaradaBrokering.org
– Apache Axis contributions
• Audio/Video Collaboration
– Globalmmcs.org
• Web Services for Geographical Information Systems
– www.crisisgrid.org
• Web services for information, metadata, and
management
– HPSearch.org
– Opengrids.org