EMMAWiki/StepbyStep

Step by Step tutorial for beginners

• For MGE members
• For GenoMik-Plus members
• For other potential users
• For all users

How to access EMMA for MGE members

• Refer to the MGE homepage to find out if your institution is a member.
• 1) Login to the Portal:
  • If you are a MGE member you should have a login and password for the MGE bioinformatics portal. Your login is usually as follow: Firstname_Surname.
  • Forgot your password? If you have a login to access the MGE bioinformatics portal and have forgotten your password, you can use the following form to submit a password change request.
  • If you don't remember your login, please send a email to mg-bielefeld[at]cebitec.uni-bielefeld.de
• 2) Access to a EMMA project:
  • Once you have logged into the MGE Bioinformatics portal, please check if you can already access a EMMA project by clicking on the link "My Projects" in the Action menu. For more info, have a look at this link.
  • If you don't have access to a EMMA project, either you can have a look at the Demo project or you can request access to a MGE project. The procedure is explained under this MGE wiki link and this GPMS wiki link.
  • Depending on your privileges for the EMMA project(s) you can access, the tasks you can perform inside a EMMA project can be limited. More info can be found under this EMMA guideline Rights and Roles page.
• 3) Use ArrayLIMS and EMMA with your own data:
  • The best is to have your own project as chief. For that you need to request a New Project inside the MGE Bioinformatics Portal. The procedure is explained under this MGE wiki link.
  • Once you have access to your project, please read the ArrayLIMS and EMMA documentations before to start to use EMMA.
• 4) Contact:
  • Please feel free at any time to send us a email to mg-bielefeld[at]cebitec.uni-bielefeld.de if you have any problems and/or comments.

How to access EMMA for GenoMik-Plus members

• Refer to the GenoMikPlus homepage to find out if your institution is a member.
• 1) Login to the GenomikPlus Portal
• 2) Access to an existing EMMA project: see above
• 3) Use ArrayLIMS and EMMA with your own data: see above
• 4) Contact: genomik-support[at]cebitec.uni-bielefeld.de

How to access EMMA for other potential users

• 1) How to get a login and password for using EMMA 2.0? Please send a email to emma[at]cebitec.uni-bielefeld.de
• 2) Login into EMMA: more info under EMMA wiki page.
• 3) Use ArrayLIMS and EMMA with your own data:
  • Request access to an existing project: login to GPMS with your username and password and click Request Project Access.detailed description of the request process
  • We can provide you with your own project as chief. Please send a email to emma[at]cebitec.uni-bielefeld.de for details.
  • Once you have access to your project, please read the ArrayLIMS and EMMA documentations before to start to use EMMA.

Step by Step tutorial for all users

• Basic terms and concepts used in EMMA: more info under this EMMA wiki page.
• What is an arraylayout and why do we need it? More info under this EMMA guideline Arraylayout Guidelines page.
• What data files are required?
  • if ImaGene, two .txt files, one for each channel (versions >= 5.0 supported)
  • if GenePix, one .gpr file (supports versions > 1.x)
  • if Affymetrix, one CEL file per array
  • all other formats: contac emma-devel[at]cebitec.uni-bielefeld.de
  • Dual images or single images? one .tiff file or two .tiff files (one for each channel)
  • .data files containing the images for Affy are not required
• Storage of the hybridization data together with all relevant biological information into our LIMS (Laboratory Information Management System): More info under the ArrayLIMS Guidelines pages.
• Upload and group your hybridized arrays: for that you need to create a new experiment in EMMA. The procedure is explained under this EMMA Guidelines page.
• How to Import Data From the ArrayLIMS system: more info under this EMMA wiki page and under this EMMA Guidelines page.
• Analyzing Data using EMMA: more info under this EMMA Guidelines page.