MGE-PortalWiki

MGE-PortalWiki Overview Page

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

In this overview page, you will find the following topics:

• How to access GenDB, SAMS, EMMA, etc...
• Data access
• Supported Web Browsers
• Login to the Portal
• My Projects
• Request Access to the MGE-Portal
• Request New Project to the MGE-Portal
• Information about Tools
• Data integrity, data backup and recovery
• Contact
• Developer Documentation

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.

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

• GenDB Sequence analysis for larger contigs.
• SAMS Sequence analysis for ESTs and shotgun reads.
• EMMA Microarray data storage and analysis.

How to access GenDB, SAMS, EMMA, etc...

The three in-house developed software packages: GenDB (procaryotic genome annotation), SAMS (EST processing and annotation) and EMMA (microarray analysis) are provided by the bioinformatics platform to the whole MGE community. The MGE Portal has been designed to grant MGE members access to these tools and projects. All of them work based on projects that are set up by the bioinformatics team at the platform. Please use the MGE Portal in order to request a new project, or request access to an existing one.

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. More information can be found under this wiki page.

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.

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 is encrypted and thus secure.

Browser Certificates

Unfortunately not all institutions that issue certificates are pre-configured into all browsers. Therefore please accept permanently the CeBiTec certificate. Doing so will only influence your connections to Bielefeld, no other internet connects will be influenced. After accepting the certificate once, this question should not need to be answered again (Technical Information on using Browser certificates)

Forgot your password?

If you have a login to access the MGE bioinformatics portal or one of our web applications and have forgotten your password, you can use the following form to submit a password change request.

My Projects

Once you have logged into the MGE portal, the main page looks like this screenshot: File:MGE-PortalWiki$mge portal overview.png

Click on the link "My Projects" in the Action menu. A page will appear as below where you can see all your projects as a chief. By clicking on the blue arrow on the right inside, you can jump directly to the corresponding EMMA, SAMS or GenDB project: File:MGE-PortalWiki$mge portal myprojects.png

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 by clicking on the link "Request Projects Access" in the Action menu. Then click onto "Request Project Access via GPMS" which allow you to login to the General Project Management System (GPMS). For further information, please go to this wiki page. File:MGE-PortalWiki$mge portal request access.png

Request New Project to the MGE-Portal

By clicking on the link "Request New Project" in the Action menu, a new page will appear as below where you need to fill in the page according to what type of data you have. A email will be sent automatically to the node representative to grant or deny the request. Once the request is granted, we setup your project and let you know by email. File:MGE-PortalWiki$mge portal request newproject1.png File:MGE-PortalWiki$mge portal request newproject2.png

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. File:MGE-PortalWiki$mge portal tools.png

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

• /BLAST
• /EMOWSE

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.

Contact

Please feel free at any time to send us a email to MailTo(mg-bielefeld AT cebitec DOT uni DASH bielefeld DOT de) with questions or suggestions for improvements.