Lao H. Saal 1,3,*, Carl Troein 2,*, Johan Vallon-Christersson 1,*, Sofia Gruvberger 1, Björn Samuelsson 2, Åke Borg 1 and Carsten Peterson 2 Departments of 1 Oncology and 2 Theoretical Physics, Lund University, and 3 MSTP, College of Physicians & Surgeons, Columbia University B A S E Bio Array Software Environment

Outline BASE Project Goals Details of Interface, Platform, & Features Demonstration of Current Functionality Future Directions

Original Goals Backend Production Probe/Reporter Annotation Bacterial Growth Events & Protocols: ie Bacterial Growth, Plasmid Extraction,PCR, etc Gel Bands Microtiter Plates/Parent-Daughters Slide Information (bar codes, batches) Print Design/Print Map Print Batches, Print Conditions Integrate:

Original Goals Backend Production Experimental Data + Raw Images Extracted Data Integrate:

Original Goals Backend Production Experimental Data Biological / Sample Data + + Tissue / Cell Line Treatment / Clinical parameters RNA Extraction / Labeling Integrate:

Original Goals Backend Production Experimental Data Biological / Sample Data + + Integrate: Publication Server Data Analysis Normalization

To create a flexible and open software environment for a microarray lab (not just a database). Local database and analysis engine, not a public repository: Any experiment type (tumor profiling, timecourse, CGH, etc) Any array platform (cDNA glass, nylon, Affy, etc) Any scanner Any normalization algorithm Any analysis and data visualization technique No limitation on # of experiments Multi-user web server, individual access levels, Hyperlinks to relevant public databases (NCBI, etc) Very user-friendly point-and-click interface, follow natural biologist work-flow “MIAME supportive” (MIAME++) Extended Goals

Details OPEN SOURCE under GPL Interface: Entirely Web-accessible, user-friendly User Accounts & defined Workspace and Projects User-level sharing of files, projects, and data Link to other databases (NCBI, UniGene, etc) Secure System Platform: Linux Operating System MySQL Database Apache Webserver PHP, C Dedicated Servers Cost n/a Inexpensive

Details “Plug-Ins”: Architecture for easy addition of your own normalization and analysis modules to BASE Proof-of-concept – we wrote 2 programs and plugged them in: Normalization (LOWESS, mean/median intensity) Multi-Dimensional Scaling (MDS) Import/Export: Import any data format using Import Wizard Export data in standard formats (ie Eisen cluster, J-Express, Expression Profiler, tab delimited, etc) MAGE-ML support soon

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Live Demonstration ER+ ER– Multidimensional scaling ER+ luminal cell type ER– basal cell type

Future Directions MAGE-ML export support (limited import) Beta version available to interested groups Public final release to academia, open source, General Public License Encourage other labs to write and share their own normalization/analysis plug-ins Write more plug-ins Add new features in response to user-feedback