1. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 Integration of J-Express with ArrayExpress Partner 20 University of Bergen Inge Jonassen - inge@ii.uib.no Kjell Petersen - kjellp@ii.uib.no

2. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 Introduction ● Role in DESPRAD/TEMBLOR project – Integration of analysis tool J-Express with ArrayExpress – New analysis methods – exploiting integration – Population of database – Dissemination ● Norwegian Microarray Consortium – Cooperation to establish and make available microarray technology in Norway – Bioinformatics solutions and support

3. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 Design for an integrated system – solution for Norwegian Microarray Consortium Scanner Image analysis software, e.g. GenePix J-Express BASE Array Express Goals: - ensure efficient, reliable data handling - comply with standards - integration User

4. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 J-Express ● A fully integrated tool for processing and exploring microarray data ● Graphical user interface, fully portable (Java) ● Powerful but intuitive and simple user interface ● Produces high quality (vector) graphics and full documentation of all steps (meta-data) – “Figure and caption for publication” ● Project management system ● Fully supportive of MAGE-ML standard – both for import and export – Integration with databases and other tools using MAGE-ML or MAGE objects

5. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 Project management window Expression profiles of selected data set Analysis windows Meta data

6. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 MAGE Java framework J-Express core MAGE-OM </MAGE-ML </MAGE-ML </MAGE-ML Java MAGEstk based Import Export Array Express Submit Download Query Retrieval MAGE-ML stream BASE

7. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 MAGE Java framework cont. ● MAGE-ML import to J-Express – Single or several files ● MAGE-ML export from J-Express – Prototype for export of filtered, normalized and clustered data. – Soon to be extended for analysis done in JE's new module for batch pipeline import of raw data. ● URL query for retrieval at object level (instead of whole experiments)

8. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 MAGE-ML export – processes Software Protocol Paramet er Transformation Description Parameter Value Protocol Applicatio n Software Applicatio n Parameter Value Parameter Value Values data process

9. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 MAGE-ML export – data BioAssayData Dimensio n BioDataCub e Data in text file BioAssayDat a Dimensio n BioDataCub e Data in text file BioAssayDat a Dimensio n BioDataCub e Data in text file Transformatio n BioAssayDat a Dimensio n BioAssayDat a Dimensio n Transformatio n

10. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 Helping to populate ArrayExpress ● Upgrading and maintenance of BASE 1.2.x installation ● User training – Internal courses/workshops – Norwegian Microarray Consortium courses ● Contribute to MAGE-ML export from BASE – KP registered for BASE meeting in Lund November 5 th 2003. – Vegard Nygaard (NMC partner in Oslo) – Nicklas Nordborg (Main developer of BASE 2.0). – Participation in “MAGE jamboree” at EBI Dec 2003

11. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 J-Express – progress ● Reworked Meta-Data module ● Suite of tools for quality control of arrays and batch pipeline import (merging of replicates, filters, normalisation etc) ● Additional features – Feature Subset Selection – Class Predictor – Cross Validation – New and improved imputation technique

12. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 J-Express cont. ● Data with reliability estimates – Fundamental extension in J-Express – Several sources for reliability estimates ● Error-model – Initialised with error parameters from spot finding program result files (e.g. GPR) or MAGE-ML files. ● MAGE-ML directly ● Replicates

13. TEMBLOR review meeting - EMBL-EBI, Hinxton, October 20 th 2003 People involved ● Bjarte Dysvik – Main developer of J-Express ● Trond H. Bø – FSS, Statistics ● Ugis Sarkans, Helen Parkinson, Alvis Brazma – Array Express ● Svenn Grindhaug, Vegard Nygård, Nicklas Nordborg - BASE ● Inge Jonassen ● Kjell Petersen