1. First Release Requirements Deliverable: –Thick client application that allows the creation of a new project and deployment of that project (edit consists of a delete data, then run the process over) – Potentially silver API for the provided data types Data types: – Clinical Data Input: Text file with column headers for all fields Output: –Clinical query with tabular report. –List management. –KM Plot for Survivability vs. Copy number for one gene or reporter (clinical data must have survivability) Notes: –EVS code can be captured, but is optional. Create “quick search” link to EVS browser. –Attempt to map EVS codes to our domain will be made(?) –SNP Array Data Copy Number Data –Input: caIntegrator copy number data format (text file) –Output: GenePattern SNP viewer. Integration with clinical data for KM plot. – Notes: Data will be stored in R Binary file or netCDF format Annotation File –Input: caIntegrator annotation file format. »One annotation file per array type. –Notes: Stored in database. Will map data into CGOM objects. Notes: Mapping file for patient ID to sample ID is necessary

2. Splash Screen New Project… Adaptive caIntegrator File SPLASH SCREEN HERE Text description, picture, instructions, etc

3. Project Name Location of Project Data Types Header logo Authentication scheme Create new Adaptive caIntegrator

4. Clinical Data Type Upload clinical data (CSV) Data verified: Adaptive caIntegrator ColumnData TypeSearchableEVS Code Subject Id1234 Stage5312 Gender XYZ1231

5. SNP Array Data Type Upload SNP data file (CSV) Upload SNP annotation data (CSV) Data verified: Adaptive caIntegrator

6. Data Mapping Map Clinical Data to SNP Data: Data Verified: Adaptive caIntegrator Clinical Data ColumnSNP Data Column

7. Project details Pane Adaptive caIntegrator File [+] My Proj1 [+] My Proj 2 Textual Summary of My Proj1 Nullam eget diam. Cras et enim. Etiam arcu lectus, dapibus eget, posuere ut, bibendum ac, elit. Cras vitae erat placerat dolor placerat auctor. Proin tortor. Vestibulum vel lacus sed pede aliquet convallis

8. Deployment Note – The following components must be installed: JBOSS version 4.0.4, Oracle 9i+, JDK 1.5+ JBOSS location JBOSS verified: “default” instance verified: Database information: URL Username Password connection verified: schema empty: Application Default User account Application Default Password Adaptive caIntegrator

9. SNP Data File Formats SNP Copy Number File (in caIntegrator copy number data file format) – Patient ID – Sample ID – Reporter ID – Copy Number SNP LOH File (in caIntegrator LOH file format) –Patient ID – Sample ID – Reporter ID – LOH – Call (optional) SNP Annotation Data File – Reporter ID – DB SNP ID (optional) – Chromosome – Physical Location – Gene (optional) Mapping file from patient to sample – Patient ID – Sample ID Snp association file format –Format from cgems (groups, analysis, snp association finding rank, pvalue, scores)

10. Notes – 8/14/2007 Generates a “potentially silver API” for grid-enablement Line connection to EVS to look up concept codes Explicitly ask for the column for the sample ID to link to genomic data Edit project functionality – current solution: drop everything and recreate tables Issue – Dropping user tables may be an issue when editing projects Configurable functionalities – such as KM. Do we do this in the application or have them configure it as well? Annotations and snp array data – current solution is to load into database Can annotations be just flat files or do we need to populate the associations Do we need a rich model for annotations?

11. Actions – 8/14/2007 Screens for SNP array data Think about annotations – rich model vs simplified Alex model Mapping between data types Understanding SNP viewer/gene pattern

12. SNP Input File Format (GenePattern) CN File Format –This is a tab-delimited file format that contains SNP copy numbers. It contains one row for each SNP and one column for each SNP array: the raw copy number value. It is organized as follows: –The first line contains a list of labels identifying the SNP arrays. Line format: SNP (tab) Chromosome (tab) PhysicalPosition (tab) (array_1_name) (tab)... (array_N_name) For example: SNP (tab) Chromosome (tab) PhysicalPosition (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49068 (tab)... MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49084 –The rest of the SNP file contains one row of data for each SNP. Some modules, such as the SNPViewer module, require the data sorted by chromosome and physical position. Line format: (snp) (tab) (chromosome) (tab) (position) (tab) (array_1_cn) (tab)... (array_N_cn) For example: SNP_A-4249904 (tab) 17 (tab) 41420045 (tab) 2.265 (tab)... 1.735 XCN File Format (Allows for LOH display) –This is a tab-delimited file format that is similar to the SNP file format, but contains SNP copy numbers rather than SNP intensity values. It contains one row for each SNP and two columns for each SNP array: the raw copy number value and the call value. It is organized as follows: –The first line contains a list of labels identifying the SNP arrays. Line format: SNP (tab) Chromosome (tab) PhysicalPosition (tab) (array_1_name) (tab) (array_1_name) Call (tab)... (array_N_name) (tab) (array_N_name) Call For example: SNP (tab) Chromosome (tab) PhysicalPosition (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49068 (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49068 Call (tab)... MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49084 (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49084 Call –The rest of the SNP file contains one row of data for each probe, including the raw copy number value and the SNP calls generated by SNP microarray scanning software (such as Affymetrix's GeneChip software). Some modules, such as the SNPViewer module, require the data sorted by chromosome and physical position. Line format: (snp) (tab) (chromosome) (tab) (position) (tab) (array_1_cn) (tab) (array_1_call) (tab)... (array_N_cn) (tab) (array_N_call) For example: SNP_A-4249904 (tab) 17 (tab) 41420045 (tab) 2.265 (tab) AB (tab)... 1.735 (tab) AA