MGE-PortalWiki

MGE-PortalWiki Overview Page

This is the primary source of documentation for the the MGE-Portal. The portal gives you access to the Bioinformatics Platform, implementing all activities within the Network of Excellence Marine Genomics Europe.

The Portal contains datasets and tools for the analysis of ESTs, microarrays, genomes etc., and it is run by the "Bioinformatics Resource Facility (BRF)".

Powered by the CeBiTec_Infrastructure, the MGE-Portal contains more than 500 processors and several Terabytes of disk space. MGE has a private set of processors but can use idle resources of the CeBiTec system.

We maintain a list of ./FrequentlyAskedQuestions.

The individual software packages contained in the platform have their own documentation

• GenDB Sequence analysis for larger contigs (GENDB) and ESTs (GenDB!/SAMS).
• EMMA Microarray data storage and analysis.
• SEED Comparative genomics environment.

Login to the Portal

The portal requires a user name and password from every user. The assumption is made that every individual has his/her own private login. If two individuals share one login and use it simultaneously, terrible things will happen to the user settings and data.

Users need to enter user name and password into the login dialog. Since the data is transported via https all traffic encrypted and thus secure.

Logging into the Portal for the first time, you will be prompted by your browser to accept the png. You will receive a message from your browser stating that this certificate is not authenticated by any official site. Nevertheless, the CeBiTec has signed its own certificate that you have to accept if you want to login. For your own convenience, choose to accept this certificate permanently.

Request Access to the MGE-Portal

All MGE members contained in the MGE list in January 2005 have received an automatical e-mail containing their login to the MGE-Portal and password.

If you are a new MGE member (registered after February 2005), you can request access to the Portal by sending an e-mail to the node representative. After the validation by the node representative, the contact person will forward your request to the Bioinformatics Platform. You will receive an automatic mail from our General Project Management System (GPMS) containing your login to the MGE-Portal and password.

Once logged into the Portal, you can request access to any project within MGE. See section "Data Access" below, for details.

Supported Web Browsers

Please note that not all web browsers are supported with the platform. For security reasons we recommend that users use Mozilla/Firefox or Mozilla.

While other browsers might work, we can not test with every browser to ensure compatibility. We strive to use standard D-HTML to ensure maximum compatability.

Data access

There are two major kinds of project "accessibility" within MGE, according to the Data Policy adopted for the Network:

• "your" projects:
  • either you are a project leader and thus have access to your "own" project data,
  • or you have already requested access to this project,
  • or the project has been made public within the whole MGE community
• "MGE" projects:
  • other projects within MGE not yet visible to you, but to which you can request access.

Access to projects is controlled by the project leaders via the GPMS web interface. All MGE members can request access to these datasets directly to the respective project leader via the Portal.

The General Project Management System (GPMS) provides the interface for requesting and granting access to projects.

Data integrity, data backup and recovery

To ensure the existence of the valuable data sets we perform nightly backup of all data on the platform. In the unlikely event of a disasterous system failure all data can be retrieved from backup tape.

Information about Tools

Some public databases are available for analysis with the Platform tools. In addition all sequence data sets created within MGE can be analyzed with the tools.

Please note: Only those data sets that you have access to will be visible within the tool section.

• ./BLAST
• ./EMBOSS

Contact

Please feel free at any time to send us email with questions or suggestions for improvements.