1. Data collection and organization Bob Sinkovits AfCS Bioinformatics Lab SDSC

2. Experimental data Data acquisition for the AfCS involves the separate transfer of experimental data and the description of the experiment SDSC Experimental Lab GUIs wget

3. GUIs GUIs based on the Java Swing classes are used to collect information about the experiment. For example Cell prep, mouse, thaw, information Protein, mRNA, lipid extracts Ligands, solutions, reagents, buffers Technician, laboratory, date Protocols and equipment details

4. Ligand GUI

5. Treatment GUI

6. GUI deployment – Java web start

7. Barcoding All experimental samples and materials (protein extracts, gels, cell preps, plasmids, solutions, reagents, etc.) are physically labeled using a 2-d barcode. Zebra Z4M barcode printer Symbol Cyclone scanner

8. Transfer of experimental data Experimental data files transferred on a nightly basis using UNIX wget utility under control of cron job StanfordCaltech SDSC UTSWUCSF Ca++, cAMP phosphoprotein cytokine microarray microscopy single cell Ca++ Ca++ Vanderbilt Lipid MS Myriad Y2H

9. Storage of experimental data Each type/category of experimental data is stored in a separate database schema Easier to work with schemas containing smaller numbers of tables Minimizes possibility of data loss/corruption Avoids confusion due to multiple developers working in a single schema (overlap of namespaces) Easier recovery Privileges granted as needed between schemas

10. Storage of experimental data LIMS (GUI) applications insert data directly into BARCODE database schema Unprocessed experimental results files stored directly in Storage Resource Broker Results files processed using perl scripts and loaded into appropriate schemas cytokine calcium camp western y2h (yeast two-hybrid) lipid_ms m_array

11. Interactions between schemas Experimental results labeled using barcode IDs generated by LIMS. Select privileges granted from BARCODE to experimental schemas so that data can be grouped and analyzed ECD031202A01ECD031202A02ECD031202A03 45.23 54.72 64.98......... RAW 264.7 cells treated with 10  M UTP (data from BARCODE schema) Ca++ time course data

12. Security and access control Access to all restricted areas of AfCS project (including GUIS) controlled through centralized access control system  Access to barcode GUIs  Access to data curation

13. Data authentication All experimental data comes from trusted sources and is downloaded from servers at the participating laboratories For the AfCS data, the main problems are Flagging bad experiments Controlling release of data to public (data not released until it has been verified and replicated) Curation of data done through web interfaces

14. Data curation Main curation page provides links to data sets

15. Data curation Curation of Ca++ assay results