# Presentation: 066986

## caWorkbench-caARRAY integration

- Manjunath Kustagi
- PI: Andrea Califano
- Columbia University
- Joint Centers for Systems Biology

## caWorkbench..?

**Integrated genomics analysis application**
- Support for gene expression and sequence data.
- Seamless access to remote data sources.
- Seamless access to remote computational services.
- Integration with biological annotation sources.
- Data management and visualization components.
- Analysis components.
**Development platform**
- Open source, Java-based.
- Component architecture, facilitating customization

## caWorkbench Lineage

- caWorkbench 1.0 (NCICB sponsored)
**caWorkbench 2.0** (AMDeC/Columbia sponsored)
- caWorkbench 3.0 (caBIG sponsored) - source released.
- A platform for caGRID enablement
- A platform for module interoperability (CDE)

## caWorkbench Plugin Model

**Plug&Play Client**
**Application**

**Data-Grid**
**Enabled**
**Databases**

**Computational-Grid**
**Enabled**
**Algorithms**

## caWorkbench Architecture

**caWorkbench Backbone (Ontology Anchored, Grid-Enabled)**

- Adapter Layer

- Adapter Layer

**caWorkbench**

## caWorkbench Modules

- Microarray Analysis
- Normalization (Plugin)
- Filtering (Plugin)
- Analysis (Plugin)
- Biclustering (Plugin)
- Microarray Visualization
- Color Mosaic
- Dendrograms
- SOM
- Expression Profiles
- Scatter Plots
- Tabular View (w edit)
- Microarray View
- Expression on Pathways
- Cytoscape Expression

- Sequence Analysis
**BLAST (Server)**
**Motifs (SPLASH Server)**
- Promoter Analysis (TRANSFAC)
**Synteny (Server)**
- Sequence Visualization
- Alignment Results
- Motif Visualization
- Motif Histograms
- Dot Plots (Synteny)

## caWorkbench Modules

**Pathways**
**Reverse Engineering**
- caBIO BioCarta
**Cytoscape**
- Pathway Browser
**Genotypic Data Analysis**
**Association Discovery**
**Genotypic Data Visualization**
- Color Mosaic
- Tabular View (w edit)
- Microarray View

**Ontologies**
- Gene Ontology Browser
**Other**
- Project Panel
- Phenotype Sel. Panel
- Gene Selection Panel
- Gene Annotation
- Image Viewer
- Dataset Annotation
- Dataset History
- Experiment Info
- Session Manager (caGRID)
- Visual Builder

## Visualization

- Databases

- Data Management

- Algorithms

## caARRAY integration

- Retrieval using MAGE-OM server and API
- Support for Measured as well as Derived Assays
- Parsing Cube data into caWorkbench BISON (_B_io_I_nformatics _S_tructured _O_ntology _N_otation) data-structures

## Integration Performance Metrics

-  ~20 seconds to retrieve Affymetrix HG_U133b chip related data (about 23k probes)
- More that 2 minutes for retrieval of single feature related data for Measured Assays.

## caARRAY installation at Columbia (issues faced)

- caARRAY JBoss application and MAGE-OM  server installation. Configuration and other files had to be altered
- Create new users using provided SQL fails.
- Query using ‘Public’ user and role fails.
- Large processing and upload times for moderately sized MAGE-ML files
- Batch upload of .chp files hangs with Java Applet providing message: “unable to locate file on file-system”

## caARRAY installation at Columbia (issues faced contd..)

- Database dump provided on NCI website seemed to be malformed
- Web content provided with the JBoss caarray application has default links to NCICB’s application support and other NCI specific links. This could be populated at build time to have site specific information

## Data parsing from MAGE-OM to BISON

## Contributors

**Califano Lab**
- Andrea Califano
- Aner Fust
- Xuegong Wang
- Saroja Hanasoge
- Adam Margolin
- Kelechi Dike
- Behrooz Badii
- Hoomen Ahmadi

**Integrated Genomics Core**
- Aris Floratos
- Ken Smith
- Manjunath Kustagi
- Xiaoqing Zhang
- Pavel Morozov
- Dahai Yu
- Eileen Daly
- Frank Wei Guo
- John Watkinson

**First Genetic Trust**
- Zhong Li
- Frank Kim

## References

- caWorkbench 1.0 download: _[http://](http://ncicb.nci.nih.gov/download)__[ncicb.nci.nih.gov](http://ncicb.nci.nih.gov/download)__[/download](http://ncicb.nci.nih.gov/download)_
- caWorkbench 2.0 download and installation: _[http://amdec-bioinfo.cu-genome.org](http://amdec-bioinfo.cu-genome.org/)_
- caWorkbench 3.0 source: _[http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/caworkbenchcabig/](http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/caworkbenchcabig/)_
- Contact: caworkbench@cu-genome.org