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Overview

As an integrating/translational platform, caIntegrator depends on service-level or API interfaces for several other applications in the caBIG suite of tools. Many of these applications have ongoing development and deploy multiple releases each year. In order to better plan for potential breakage or retest necessary in caIntegrator, the team undertook an analysis of these dependencies and the planned release schedules for each. This document highlights dependencies and serves as a place to discuss any breakage to caIntegrator and to schedule this into an iteration.

Application Dependencies

The following applications are used by caIntegrator and require some sort of dependency management.  This table will track upcoming releases and any known changes or retest required for these releases. This work can then be scheduled into an upcoming caIntegrator iteration.

Application / Service

Version
Supported by
caIntegrator 1.3.1

Version
Supported by
caIntegrator 1.4

Next
Planned Version

Projected
Release
Date

Interface Summary / Needed caIntegrator Changes

caArray

2.4

2.5

2.5

7/2012

Use Java RMI-based "external model" API

No data on what will change or a release date.

NBIA

4.4

5.0

TBD

10/31/10

Use caGrid data service for CQL queries and caGrid grid file transfer service.

No changes to the API for 4.5. Version 4.5 does support secure Grid services, so we will need to implement support for secure services sometime in the future.

AIM

1.5

1.5

TBD

TBD

The AIM 3.0 API deprecates the caGrid interface and instead supports only a RESTful interface described here. The API also introduces a new data model. caIntegrator will require integration implementation changes in a future release to support this new API

GenePattern

3.2.1

3.2.1

3.2.3

TBD

caGrid analytical service used for genomic algorithms

caDNAcopy
(part of Bioconductor)

caDNAcopy 1.2
Bioconductor 1.9
(contains DNAcopy 1.8.1)

caDNAcopy 1.2
Bioconductor 1.9
(contains DNAcopy 1.8.1)

TBD

TBD

caGrid anaytical service for caDNAcopy used for copy number data during study deployment.  Deployed as part of Bioconductor. We are examining non-functional changes to improve performance (multi-threading) and logging.

No information on planned future releases of this tool. We do not need to adopt Bioconductor upgrades unless there are fixes to DNAcopy (which is an optional install under Bioconductor).

caBio

4.3

4.3

MAservice 1.0

TBD

REST API used for keyword or pathway based gene search

caBio functionality being replaced by MA service. Meeting with caBio team and caIntegrator scheduled for 11/10/10 to ensure all caIntegrator requirements are met.

caDSR

4.3

4.3

TBD

TBD

NCI Vocabulary Service

UPT

4.2

4.2.3

TBD

2/2012

User Authentication and Authorization management.

caGrid

1.2

1.4

TBD

TBD

core caGrid component

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