# Presentation: 212696

## caBIG  Integrative Cancer Research

- Patrick McConnellDuke Comprehensive Cancer Center
- Duke Bioinformatics Shared Resource
- patrick.mcconnell@duke.edu

## Donate Tools

- Microarray probe designer (beta stage)
- 1 FTE 6 months
- Pluggable Java tools, rankers, filters, printers
- cDNA annotation system (beta stage)
- 2 FTE one year
- Native XML database, Java-based machine processing pipeline, Java (JSP)-based website for curation and public
- Data analysis with R – via Java API and web services (concept stage)
- 1 FTE one year
- (Native?) interface to R, web service wrapper, client interfaces, use cases

## Donate ToolsJProbePicker

## Donate ToolsXML cDNA Annotation System

## Donate ToolsData Analysis with R

**JNI**

## Wrap Common Tools

- Traditional bioinformatics:

**Analysis****Software**

**ATCG...**

- Bioinformatics with caBIO:

**Database ****identifiers**

- What we really need:

**Analysis****Software**

**ATCG...**

## Wrap Common Tools

- Currently: BLAST, ClustalW, BLAT, RepeatMasker (alpha stage)
- XML descriptor for tools (found in jar, home directory, filesystem, etc.)
- Java library for specifying parameters, launching, sending stdinput, and capturing stdout/stderror
- caBIG compliant wrapper: interoperates with caBIO data objects and services
- Time to develop wrapper mechanism – 1FTE 4 months
- Time to develop wrapped tools – 1FTE 1-3 weeks per tool
- Requires API specs from Architecture group

## Web Service Choreography

- Concept stage
- BPEL4WS or WSCI needs to be determined by architecture group
- Example: OrganBlast (working example as proof-of-concept)
- Workflow tool to filter BLAST results by Organ expression
- Based on BPEL4WS, written in Java, hosted in Tomcat
- Services Development for individual tools.
- 1 FTE continuously to wrap/make all services able to be choreographed
- More generic: a graphical tool to link services in a workflow
- 1 -2 FTE’s for 2 years for research and development and to adjust as standards change

## Web Service Choreography

- What genes in the brain are similar to my DNA sequence?

- >gi|6981181|ref|NM_013066.1| Rattus norvegicus microtubule-associated protein 2 (Mtap2), mRNA
- AAAAGAAAGAAGCCAGAACATACCACCAGCCCTTTGAGTATACAACATAACAAACGTCATTACTTTACAA
- CTTGATTAGGAGACAGTACAGAGATCTGAAGGATGGCTGACGAGAGGAAAGACGAAGGAAAGGCACCACA
- CTGGACATCAGCCTCACTCACAGAGGCAGCTGCACACCCCCACTCGCCAGAGATGAAGGACCAGGGTGGC
- TCAGGGGAAGGGCTGAGCCGCAGCGCCAATGGATTTCCATACAGAGAGGAGGAGGAAGGCGCCTTTGGGG
- AGCACGGGTCACAGGGCACCTATTCAGATACCAAAGAGAACGGGATCAACGGAGAGCTGACCTCAGCTGA
- CAGAGAAACAGCAGAGGAAGTGTCTGCAAGGATAGTTCAAGTAGTCACAGCTGAAGCTGTAGCAGTCCTG
- AAAGGTGAACAAGAGAAGGAGGCCCAACACAAGGATCAGCCTGCAGCTCTGCCTTTAGCAGCTGAAGAAA
- CAGTTAATCTGCCACCTTCCCCACCACCATCGCCAGCATCAGAACAAACAGCTGCACTGGAAGAAGCCTC
- GAAGATGGAATTCCCTGAGCAGCAGAAATTGCCTTCCTCATTCGCTGAGCCTTTAGACAAGGAGGAAACG

**BLAST**

**Similar****genes**

## Web Service Choreography

- BPEL4WS (Business Process Execution Language for Web Services)

**invoke****Blast Service**

**while****still more hits**

**invoke****Organ Service**

**switch****hit gene in organ**

**assign****append hit**

**reply****appended hits**

## Develop Proteomics and Metabolomics Tools

- Incorporate emerging standards
- Data representation from Architecture Workspace
- Protein Standard Initiative
- Tools for spectrum analysis (alpha stage)
- R libraries (alpha)
- Wrap for caBIO (for R, re-implement in Java)
- 1 FTE 1 year

## Incorporate External Tools

- Concept stage
- Identify and submit tool suggestions to workspace
- If approved, work with authors to make caBIG compatible
- If authors don’t want to comply, perhaps take source code and convert to caBIG
- Examples:  TIGR’s MEV, VBI’s Pathport, etc.
- 1 FTE continuously as priorities are assigned by the Workspace