About the workshop

The interpretation of microarray data often requires mapping large datasets onto a variety of genomic data sources, besides efficient storage, state-of-the-art algorithms and user-friendly interfaces (visualization). The EMMA software developed in the Bielefeld University fulfills these requirements; it is a repository for array-related data as well as a tool for automated analysis using routine pipelines. The participants of the Microarray course in Bielefeld will not only have the chance to talk to the developers themselves, but will mainly learn how to manage and analyze transcriptomics data using the EMMA system, being able to evaluate their own results (achieved from the wet-lab experiments during the week for the MGE network or beforehand in their lab by bringing their own data for the PathoGenoMik network).

Previous workshops

• For the Marine Genomics Europe network of excellence (MGE):
7-11/03/2005: Microarrays - Expression analysis in prokaryotic and eukaryotic systems using microarray techniques.
• For the PathoGenoMik network:
18-19/07/2005: EMMA workshop
• For the Marine Genomics Europe network of excellence (MGE):
10-14/10/2005: Microarrays - Expression analysis in prokaryotic and eukaryotic systems using microarray techniques. workshop links.
• For the PathoGenoMik network:
05-07/12/2005: EMMA workshop

New workshops

• For the GenoMikPlus network:
28-30/06/2007: EMMA workshop in Dresden

Course Material

• Lecture slides will be online for course participants.
• A print of the current "EMMA Documentation Guideline", "ArrayLIMS Documentation Guideline" and a document on "Microarray Introduction" will be given to each participant at the beginning of the course.
• A wet-lab material will be provided.
• The up-to-date presentations, exercises and manuals can be found on our FTP server.

How to get there?

• A page explaining how to arrive at the Uni and in the computer room V6-116.

Accomodation in Bielefeld

For all hotels, to go to the UNI, take the tram line 4 (line from Rathaus to Lohmannshof).

• Youth Hostel (Jugendgästehaus) Hermann-Kleinewächter-Straße 1(almost central, 5-10min walk for tram stop Rathaus).

• Hotel Mercure Bielefeld Am Niederwall 31-35 (central, tram stop Rathaus).

• Comfort Garni Hotel Stadt Bremen am Bahnhofstrasse 32 (central, tram stop Hauptbahnhof).

To use EMMA and ArrayLIMS with your own data

• Account and login

During this year, you should probably have received by email an username and password from the GPMS system. The GPMS system is an online management tool responsible for controlled access of ArrayLIMS, EMMA, GenDB, EMMA and SAMS softwares. Once you get a login and password, you can check which projects you can access under this link: gpms login page.

Please don't forget your login and password for the course!

• What is an arraylayout and why do we need it?

An arraylayout or array design describes the production and layout of your array. An arraylayout is needed for the database storage.

Some arraylayouts are already publicly available on the ArrayExpress web site from the EBI. Check if the array design you used has already been submitted by clicking 'Browse existing array designs' within MIAMExpress, which is a tool for submitting data to the ArrayExpress database. Have a look at the paragraphs below if you need to create your arraylayout.

• How to create an arraylayout (array design)?

More details are available at the ArrayExpress submission site.

• The Array definition file (ADF):

The ADF file provides a general description of the array and any relevant information concerning the manufacturing process. If your array is custom made you need to create an ADF for it.

• Details of how to create an ADF from your spotter output file are available under this link

• Arraylayout file format

• what data files are required? if ImaGene, two .txt files, one for each channel; if GenePix, one .gpr file.

• dual images or single images? one .tiff file or two .tiff files (one for each channel)

Current PDF documentation

• PDF documentation: EMMA documentation guideline, ArrayLIMS documentation guideline and Microarray introduction documentation

Proposed Schedule for the MGE course

• pdf file:microarray course schedule oct05