September 2003

Aix en Provence

Jonathon Blake

EMBLEMBLBiochemical InstrumentationBiochemical Instrumentation

EMBL – Biochemical EMBL – Biochemical InstrumentationInstrumentation

Development of new instrumentation Introduction and installation of novel

technologies Development of new protocols /

methodologies Development and use of software tools Collaborative pilot application projects EMBO Micro Array Course

Micro array tasksMicro array tasks Slide production Medium to large scale feature production Sample preparation Hybridisation Scanning Image processing Data base Custom software tools

ChipsChips Iron Chip (v1 : 0.5k, v2 : 2k, Martina Muckenthaler ) Yeast ( 6k, Thomas Preiss, Steve Oliver ) Drosophila ( 5k, Giorgos Christofides ) Anopheles ( 5k, George Dimopulous ) NIA Mouse ( 15k, Ruediger Klein ) Alternative splicing ( 4k, Juan Valcarcel )

Human (55k, German Resource Centre, Berlin)

Applications & CollaborationsApplications & Collaborations Yeast

Uni Cologne NIA Mouse

Uni Hamburg, Institut Pasteur, Uni Heidelberg,.... Human

Uni Heidelberg, RZPD, DKFZ, EMBL, Uni Copenhagen,...

Establishing Data Pipeline to Establishing Data Pipeline to ArrayExpressArrayExpress

Packaged data from EMBL labs submitted to ArrayExpress.(2 Sets)

MIAMExpress now installed to automate the process. – Experimental data is now being entered into

local MIAMExpress database.(2 Sets)– Being used during experimental process.

Extending MIAMExpress for Extending MIAMExpress for Laboratory Array Database UsageLaboratory Array Database Usage

Querying facility for MIAMExpress.Data Extraction and transformation api`s for

analysis tools.Batch Uploader for MIAMExpress –

Multiple Hybridisations.Linking of TIFF files to the database.Access Control, Owner, Group, World

levels.

Present PlatformPresent Platform

Based on MIAMExpress. Running on Linux. MySQL database. CGI based Web interface. Developing in PERL. Under Investigation

– Migration to Oracle.– Additional applications in Java.

Generic Query Interface for Generic Query Interface for MIAMExpressMIAMExpress

MIAMExpress Query OutputMIAMExpress Query Output

Api BuildingApi Building

Building api`s based on the Generic Query Interface to allow further analysis of data e.g.– External Normalisation Clustering Tools,– Image Downloading.– Hybridisation Data Averaging/Filtering, ...– ...

Data Annotation Tools Data Annotation Tools

Improvement of Annotation of features spotted on chips.

Construction of crosslinks between feature annotation and established sequence databases.

Integration of enhanced annotation resources with mircoarray data analysis tools.

Migration of LIMS SystemMigration of LIMS System

Automatic generation of ADF files.Linking Experiment to slide production QC.

– Needle quality, Slide position, Library plates,...

Data structure allowing sub library design based on previous experimental results.

Mirco-Array teamMirco-Array team Chips Wet lab, Applications

Heiko Drzonek Alexandra AnsorgeAdolfo Dominguez

Lab automation / Robotics Mechthild Wagner

Jan Selig Ute Wirkner

Software

Data Base Christian Schwager

Jonathon Blake

Christian Schwager Protein Chips

Jan Selig, Frederico DiMasi

Group Leader Wilhelm Ansorge