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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