1. Call in: 877-416-5524 Participant Passcode: 2627056 Centra: http://ncicb.centra.com Meeting ID: ICR_meetinghttp://ncicb.centra.com April 1, 2009 caArray User Community Meeting Releases 2.2.1 and 2.3.0

2. Agenda Release schedule Items in 2.2.1 Items in 2.3.0 with emphasis on new API New features in analysis phase Announcements Q&A

3. Release Schedule caArray 2.2.1 2.2.1 release candidate starting QA testing this week. 2.2.1 Release: April/May 2009 caArray 2.3.0 2.3.0 Beta release of the new API to Stage: May 2009 2.3.0 Release: July/August 2009

4. Main items in 2.2.1 Change owner of experiments or groups System administrator can pick one of the following: an experiment a collaboration group multiple experiments owned by a particular user multiple collaboration groups owned by a particular user System administrator can set the owner to a new user. Genepix GPR file import GPR data files now require an accompanying SDRF and IDF. Validation error if no MAGE-TAB.

5. Main Items in 2.3.0 New API Grid security Audit trail of permissions changes Ability to download array designs Separation of experiment locking from experiment access

6. New API in 2.3.0 Aids backwards-compatibility from 2.3.0 onwards. 1.0 Client 1.0 Grid Analytical Services 1.0 caArray External Model 1.0 External to 2.3.0 Domain Translator 2.3.0 caArray Internal Domain Model 1.0 External to 2.4.0 Domain Translator 2.4.0 caArray Internal Domain Model 2.0 External to 2.4.0 Domain Translator 2.0 caArray External Model 2.0 Grid Analytical Services 2.0 Client

7. New API in 2.3.0 Faster and more intuitive ways of doing searches. Richer set of services to do new things. Results are unambiguous: No object graph cutting.

8. New API in 2.3.0 Searching for experiments E.g., search for experiments with tissue site = Brain OLD WAY CQLQuery cqlQuery = new CQLQuery(); Object target = new Object(); target.setName("gov.nih.nci.caarray.domain.project.Experiment"); Association termAssociation = new Association(); termAssociation.setName("gov.nih.nci.caarray.domain.vocabulary.Term"); Attribute termAttribute = new Attribute(); termAttribute.setName("value"); termAttribute.setValue("Brain"); termAttribute.setPredicate(Predicate.EQUAL_TO); termAssociation.setAttribute(termAttribute); termAssociation.setRoleName("tissueSite"); Association sourceAssociation = new Association(); sourceAssociation.setName("gov.nih.nci.caarray.domain.sample.Source") sourceAssociation.setRoleName("sources"); sourceAssociation.setAssociation(termAssociation); target.setAssociation(sourceAssociation); cqlQuery.setTarget(target); client.search(cqlQuery);

9. New API in 2.3.0 Searching for experiments E.g., search for experiments with tissue site = Brain NEW WAY ExperimentSearchCriteria searchCriteria = new ExperimentSearchCriteria(); AnnotationCriterion tissueSite = new AnnotationCriterion(); tissueSite.setCategory("OrganismPart"); tissueSite.setValue("Brain"); searchCriteria.getAnnotations().add(tissueSite); Experiment[] experiments = client.searchForExperiments(searchCriteria); Searching for biomaterials Searching for hybridizations Searching for quantitation types

10. New API in 2.3.0 Selecting files for an experiment, a set of samples or a set of hybridizations based on category (RAW or DERIVED) based on type (e.g., AFFYMETRIX_CHP) based on extension (e.g.,.CEL) Downloading file content a single file as a Grid transfer reference multiple files as an array or enumeration of Grid transfer references a zip of files as a Grid transfer reference can opt for server-side compression of individual files or not

11. New API in 2.3.0 Downloading data sets // Get me the data values for these hybridizations. DataSetRequest dataSetRequest = new DataSetRequest(); dataSetRequest.setHybridizations(hybridizationRefs); // Optionally select columns (quantitation types) to retrieve. DataSet dataSet = client.getDataSet(dataSetRequest); Downloading annotation sets // Get me the annotations for these hybridizations. AnnotationSetRequest annotationSetRequest = new AnnotationSetRequest(); annotationSetRequest.setHybridizations(hybridizationRefs); // Optionally select annotations (e.g., tissue site, disease state) to retrieve. AnnotationSet annotationSet = client.getAnnotationSet(annotationSetRequest);

12. New API in 2.3.0 Supporting dictionary methods Get all array providers Get all organisms Get all array designs Get all principal investigators Get all annotation categories (e.g., disease state) Get all annotation values for a category (e.g., tissue site: Brain, Kidney, Lung,…) …. Model and API: latest working copy https://gforge.nci.nih.gov/svnroot/caarray2/trunk/docs/analysis_and_design/m odels/caarray_external_model.eaphttps://gforge.nci.nih.gov/svnroot/caarray2/trunk/docs/analysis_and_design/m odels/caarray_external_model.eap

13. New features in analysis phase Integration with Biospecimen systems Currently working on an Inception effort to identify the use cases and requirements for exchanging data between a biospecimen tracking system (like caTissue) and a molecular assay management system (like caArray) Key requirement is supporting shared biospecimen (sample) identifiers across these systems A goal of this effort is to keep the solution generic enough that other systems could be adapted to use the same solution A parallel Inception effort is underway to create globally unique specimen identifiers to support queries across the grid. Export to GEO While this has always been on the caArray 2 roadmap, as the system is more broadly adopted, this is becoming a more urgent community need Planning for this feature is underway but is likely to be available soon after the 2.3.0 release

14. Announcements New caArray data import demo is now available on the MAT-KC wiki https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/CaArray_Demos More directed demos to come - community suggestions are welcome. The caArray FAQ is growing https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/CaArray_FAQ Revision of the caArray Overview demo is underway

15. Avenues for Feedback Molecular Analysis Tools Knowledge Center Forum GForge Community Change Request tracker: http://gforge.nci.nih.gov/tracker/?atid=1339&group_id=305&func=browse This meeting Next Meeting: Wednesday, May 6, 2:00 PM ET