cicc web services and issues

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CICC Web services and Issues Jungkee (Jake) Kim Community Grids Laboratory

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CICC Web services and Issues. Jungkee (Jake) Kim Community Grids Laboratory. CICC Web Services I. BCI Clustering Provides Bernard Chemical Information (BCI) clustering packages A module of the workflow for HTS data organization and flagging Status: - PowerPoint PPT Presentation

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Page 1: CICC Web services and Issues

CICC Web services and Issues

Jungkee (Jake) Kim

Community Grids Laboratory

Page 2: CICC Web services and Issues

CICC Web Services I• BCI Clustering

– Provides Bernard Chemical Information (BCI) clustering packages– A module of the workflow for HTS data organization and flagging– Status:

• Added URL output support to the previous solid prototype (Multi-user durable)

• Taverna Beanshell Scripting for data format adjusting (e.g. Filtering out the head part listing column names)

– To do: Evaluating the URI(URL) based workflow design• ToxTree

– Estimates toxic hazard by applying a decision tree approach– A module of the workflow for HTS data organization and flagging– Status: A test prototype producing the level of toxicity in a brief or

verbose explanation against a SMILE structure– To do:

• Refining the Web service for cluster input and external property support• The Taverna Beanshell scripting for data merging not used in some modules

Page 3: CICC Web services and Issues

CICC Web Services II• Workflow for HTS data organization and flagging

– Demonstrates how screening data can be flagged and organized for human analysis

– Status: Individual modules except the visualization are in prototype– To do:

• Defining at least XML schema or DTD for the workflow data (at most the Ontology)

• Redefining current workflow model to reflect the new feature of Taverna 1.4 supporting complex data structures and the provenance plugin

• Other Planed Web Services– Open Source Chemistry Analysis Routines (OSCAR)

• Extracts chemical information from text and produces an XML instance highlighting the chemical information

• A module of the PMR workflow• Status: OSCAR3 is available and works fine as a Java application• To do: Studying XML instances for extracting chemical names

Page 4: CICC Web services and Issues

BCI Clustering URL Service Methods

Service Method Description Input URLOutput

makebitsURLGenerate

Generate fingerprints from a SMILES structure

SMIstring Fingerprint and program output

divkmURLGenerate

Cluster fingerprints with Divkmeans

SCNstring DKM data and program output

smile2dkmURL Makebits + divkm SMIstring All SMI, DKM and std. outputs

optclusURLGenerate

Generate the best levels in a hierarchy

SMIstring

DKMstring

Best data and program output

rnnclusURLGenerate

Extract individual cluster partitions

SMIstring

DKMstring

New partition and std. output

smile2ClusterPartitionedURL

Generate a new SMILES structure w/ extra col.

SMIstring All intermediate data and output

Page 5: CICC Web services and Issues

Workflow for smile2ClusterPartitionedURL

Page 6: CICC Web services and Issues

Workflow for Toxic Hazard in Verbose

Page 7: CICC Web services and Issues

Diagram of Workflow2Input/Output

Web Services

Beanshell Scripting