1. IRWG June 10, 2009

2. Agenda Datatypes and associations Discuss example experiment Scope of LS DAM Discuss the LS DAM Experiment model In context of scope Extensibility Discuss Experiment types Missing Modifications We need to develop concrete recommendations for the LS DAM

3. Agenda Datatypes and associations Discuss example experiment Scope of LS DAM Discuss the LS DAM Experiment model In context of scope Extensibility Discuss Experiment types Missing Modifications We need to develop concrete recommendations for the LS DAM

4. Scope of LS DAM Experiment What is needed to capture the semantics and process of LS research? What are the core objects? Modeled in the DAM Able to be modeled (extensibility)

5. LS DAM vs. caLIMS2 Differences in scope/intent of LS DAM and caLIMS2 LS BAM – Research Lifecycle Identify the Question Identify Experimental System/s Perform Experiment/s Analyze Results Report Findings caLIMS2 – LIMS Project – collection of procedures in a lab toward one goal Method – experimental types (platform, equipment, software, etc) Procedure – steps performed in a method, capture metadata or results Run – actual execution of procedures (inputs, outputs, parameters)

6. Example: SNP Array (Genotyping) 1.Extract DNA samples from biospecimens 2.Perform genotyping 3.Analyze results

7. Example: SNP Array (Genotyping) 1.Extract DNA samples from biospecimens 1.DNA extraction and QC 2.Perform genotyping 1.DNA QC 2.SNP array analysis 3.SNP array QC 3.Analyze results 1.Post-processing 2.Statistical analysis

8. Example: SNP Array (Genotyping) 1.Extract DNA samples from biospecimens 1.DNA extraction and QC 2.Perform genotyping 1.DNA QC 2.SNP array analysis 1.Sty1 digest 2.Sty1 primer ligation 3.Sty1 PCR amplification 4.Nsp1 digest 5.Nsp1 primer ligation 6.Nsp1 PCR amplification 7.etc 3.SNP array QC 3.Analyze results 1.Post-processing 2.Statistical analysis

9. Example: SNP Array (Genotyping) 1.Extract DNA samples from biospecimens 2.Perform genotyping 1.DNA QC 2.SNP array analysis 1.Sty1 digest 1.Equipment 2.References 3.Inputs 4.Steps to perform 5.Outputs

10. Example: Sty1 Digest Protocol Platform/Equipment PE2700, matrix pipettors, clean DNA hood, plate centrifuge References Enzyme digest docs from the manufacturer for recommended protocol Modifications to recommended protocol used by all lab members (lab SOP) Thermocycler settings Inputs Reagents: Sty1 enzyme, NE Buffer 3, BSA, Reduced EDTA TE buffer, Molecular grade water, Affymetrix 6.0 SNP Reagent Kit Supplies: tubes, plates, tips, seals DNA sample(s) to be digested: sample(s) and control(s) Procedure steps Add Specimen DNA to wells on 96-well reaction plate. Check Sty1 concentration. Make Master Mix for Sty1 digestion. Add Sty1 Master Mix to the genomic DNA in the reaction plate. Incubate in thermacycler according to GW5.0.6.0 Digest Program Procedure Place on ice and go immediately to Procedure 2 or seal tightly and store at -20 oC. Outputs Sty1 digest (biological sample)

11. Core Objects Experiment Implementation or execution of a set of protocols Workflow-based (sequential, recursive, conditional) Includes protocols, actual inputs/outputs Includes a name or some type of identifier May reference other experiments or literature Protocol (caLIMS2 calls this "procedure") References (e.g., literature, lab notebook) Steps performed (out of scope?) May refer to other protocols (recursive) Executed protocol (caLIMS2 calls this "run") Platform info (implies or associated to assay type) Inputs (reagents) Outputs LS DAM

12. Core Objects Executed protocol (caLIMS2 calls this "run") Platform info (implies or associated to assay type) equipment (hardware) (what is equipment, what is supply?) e.g., scanner, chip type software version, etc Inputs (Reagents) biological biospecimen chemical supplies (out of scope?) parameters and settings software (analysis) hardware (settings) Outputs biological chemical electronic files hand-written data LS DAM

13. Agenda Datatypes and associations Discuss example experiment Scope of LS DAM Discuss the LS DAM Experiment model In context of scope Extensibility Discuss Experiment types Missing Modifications We need to develop concrete recommendations for the LS DAM

14. Experiment Context Is the current context of the LS DAM "Experiment" classes extensible? Are all core objects represented (or able to be represented)? Scope and intent

15. LS DAM – Superconcepts Core Obj 1Core Obj 2

16. LS DAM – Experiment (Condensed) Core Obj 1Core Obj 2

17. LS DAM – Experiment Core Obj 1Core Obj 2

18. LS DAM – Experiment Core Obj 1Core Obj 2

19. Agenda Datatypes and associations Discuss example experiment Scope of LS DAM Discuss the LS DAM Experiment model In context of scope Extensibility Discuss Experiment types Missing Modifications We need to develop concrete recommendations for the LS DAM

20. Experiment Types caElmir Organism modification/experimental manipulation – Grace, Baris caNanoLab Need characterization experiment type – Sue Homework – top two experiment types