# Presentation: 684484

## caTissue SuiteDynamic Extensions

**George Komatsoulis**
**Denise Warzel**
**Poornima Govindrao**
**Ian Fore**

## Outline

**Plenary - 45 mins**
- Introduction
- George Komatsoulis, Denise Warzel
- caTissue overview
- Ian Fore
- caTissue Suite Dynamic Extensions feature
- Poornima Govindrao
- Summary of issues - IF, DW
- The charge for the breakout - GK
**Breakout - 90 mins**
- Summary of XC report on caTissue Dynamic Extensions - Andy Pople
- Detail discussion of issues - All - GK, DW moderated
- Review the spreadsheet - All - IF
- Actions & next steps

## Recognizing  value

**The caBIG toolset is invaluable**
- caCORE Product Line
- caGrid
- Architecture & VCDE processes
- Mentoring
- Reviews processes
**An impressive achievement**
- Useful functionality
- Processes are sound and well managed
- Reviews are thorough
- As seen for caTissue Suite 1.0

## TBPT roll of honor

**Proud adopters of caBIG infrastructure since 2005**
- caCORE SDK
- CSM
- Grid security
**caTissue 1.0 - Mar 2006**
- Silver compatible
**caTissue 1.1 - Feb 2007**
- Silver compatible
**caTissue 1.2 - Jun 2007**
- Silver compatible
**Writable Silver API****	**
- In production use
**Federated query in operation**
- ~20 instances
- Virtual biobank

**caTIES 1.0**
- caGrid 0.5 reference implementation
- Pioneering use cases for grid security
**caTissue Clinical Annotation Module**
- Pushing the envelope!
**All experiencing the bleeding edge!**
- CSM performance
- Writable API before the SDK
**Mandated by workspace management**

**Notes:**
These are our “bragging rights”!

But we need to go beyond this

## Interoperability benefits for  Biospecimens

**Virtual biorepositories**
- The ability to search networked biospecimen databases
**Support for multi site studies**
- Specimens collected at multiple locations
- E.g. Prostate SPORE Biomarker study
**Rare diseases**
- Statistical power only reached through pooling resources
**Biospecimens are the raw material for molecular analysis platforms**
- Need to exchange data with their informatics systems
**Linkage to clinical data on biospecimens**
- Key data on specimens and patients exists in other systems
**Development of common practices for biospecimen handling**
- Establishing common data elements will support this

## The need

**Impossible to imagine research software that isn’t extensible**
**Commercial software for research**
- Dynamically extensible systems are ubiquitous in research software
**The caCORE SDK**
- Illustrated the the point
- Model to implementation in minutes - dynamic
**Semantic integration**
- Takes longer

## Purpose today

**caTissue Suite 1.0**
- In development for 15 months
- Will be released in March
- With dynamic extensions
- Prostate SPOREs will extend model by March
- Needs to be compatible
**Make sure that the XCWS understand the details of the implementation**
**Highlight the issues**
** ****Assessment (over the next few weeks)**
- Whether this meets all of the requirements, or
- Whether modifications are required
- To the implementation - for 1.1
- To its associated processes - in 1.0 - due by March
- To the guidelines - for 3.0? 3.1?
- To their supporting processes - to be revised?

## caTissue Suite 1.0 dynamic extensions

**Overview**
**Demo **
**Movie**

## Some issues

**Tooling focused on the static development use case**
**Central review scalability and turnaround**
**Waterfall**
- And then some
- caCORE SDK - it’s page xxx before you get to executable software
- The Monopoly board
- Somewhere around **Pennsylvania Ave**

## Use cases

**Add an item to a list of permissible values and stay caBIG compatible**
- Site specific
**Get a 4(?) class extension to model up and running as a compatible service in  two weeks**
- Prostate SPORE example
- Need more
**These are meant to be simple**
**Currently can’t be done **

## Implementing compatible extensions

**Handling the areas of compatibility**
**Phases of a dynamic extension implemention**
- Development
- Operation
**Programming and Messaging interfaces**
- Seems all handled during development
**Semantic interoperability**
- Some during development
- Some during operation
**Analysis in spreadsheet mailed to Arch & VCDE lists**

## Good caBIG citizenship

**Extensions implementations should use the caBIG Toolset**
- VCDE APIs
- caCORE SDK
- Grid tools
- Introduce
**These tools may need to adapted extended to support dynamic extensions**

## The plan

**Work with us on the detail**
**Do it as a group with all the domain WS**
**Starting in the breakout here**
**caTissue Suite 1.1 Project Inception meeting**
- Feb 11 and 12 in St Louis
**and elsewhere**

**Notes:**
George...

## For the breakout

## The spreadsheet

**Identifies three things for each guideline**
**Phase where each compatibility requirement is dealt with**
- Development of a system that supports extensions
- Operation of such a system
**Roles involved**
- System developers
- System operators
- Reviewers
**Where a guideline might need to be modified**

## Information models - Silver

***Object-oriented domain information models are expressed in UML as class diagrams and as XMI files, and are reviewed and validated by the VCDE workspace***
**What value do diagrams provide in a dynamic extension scenario**
- Main value is in complex situations
- Picture worth 1000 words
- Superfluous in simple situations?
**Should all models be validated before compatibility?**
- Absolutely
**According to VCDE standards?**
- Absolutely
**By VCDE?**
- Let’s discuss that one
- Domain workspaces contain solid modeling and architectural expertise
- Domain workspaces have domain knowledge

**Notes:**
18 years modeling experience