September 2003 Aix en Provence Jonathon Blake EMBL Biochemical Instrumentation.

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Presentation transcript:

September 2003 Aix en Provence Jonathon Blake EMBL Biochemical Instrumentation

EMBL – Biochemical Instrumentation 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 tasks Slide production Medium to large scale feature production Sample preparation Hybridisation Scanning Image processing Data base Custom software tools

Chips 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 & Collaborations Yeast Uni Cologne NIA Mouse Uni Hamburg, Institut Pasteur, Uni Heidelberg,.... Human Uni Heidelberg, RZPD, DKFZ, EMBL, Uni Copenhagen,...

Establishing Data Pipeline to ArrayExpress 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 Laboratory 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 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 MIAMExpress

MIAMExpress Query Output

Api 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 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 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 team ChipsWet lab, Applications Heiko Drzonek Alexandra Ansorge Adolfo 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 LeaderWilhelm Ansorge