Data collection and organization Bob Sinkovits AfCS Bioinformatics Lab SDSC

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

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

Ligand GUI

Treatment GUI

GUI deployment – Java web start

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

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

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

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

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 ECD031202A01ECD031202A02ECD031202A RAW cells treated with 10  M UTP (data from BARCODE schema) Ca++ time course data

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

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

Data curation Main curation page provides links to data sets

Data curation Curation of Ca++ assay results