The Bioinformatics Resource Facility at Bielefeld University provides the common Bioinformatics Platform for the EU Network of Excellence Marine Genomics Europe (MGE) that started in 2004 and ended in summer 2008. The Marine Genomics Europe network will bring high-throughput approaches to the study of marine organisms. Within the platform, the MGE Bioinformatics Portal provides a central point of reference for all data sets and tools. It provides data storage, data analysis and data integration. The Bioinformatics platform also offers training in several areas. To ensure data exchange we suggest a naming convention for sequence data. The MGE final report for the bioinformatics part (pdf file) can be found here: Final report. All MGE projects are still available via the MGE bioinformatics Portal (with your MGE member login and password).

MGE Bioinformatics portal

The tools and data sets available at the MGE bioinformatics platform are organized in a single bioinformatics portal. To access the portal a login is required. All MGE members already have an individual login (account) to access the MGE bioinformatics portal. The data sets are organized into distinct projects. All members of MGE can access the MGE project enabling them to use the tool collection and data visible to the MGE as a whole. If you are a member of MGE and have not yet received an email with your account data, please send an email to your node representative, who should authorize us to give you an account.

New project requests also need to be validated by your node representative. Please go to the wiki pages for detail on requesting new projects.

Please note:
Access to the data is managed by the project leaders themselves using a web interface, not by the Bielefeld Platform. The project leader (owner) can create additional logins for his/her project.

Sequence Analysis

The web-based genome annotation system GenDB and the Sequence Analysis and Management System SAMS will be provided for the automatic analysis of larger contigs and ESTs.

The GenDB system performs gene calling and a subsequent automatic annotation of the genes (afterwards, the user can proceed with manual annotation if needed). We also support the analysis of EST sequence libraries. The sequences are normalized (vector and quality clipping), clustered and subsequently annotated using SAMS. SAMS will also act as a LIMS system for sequencing projects providing quality control if required.

• Naming scheme for reads 

We suggest the following naming convention for high volume sequence data. Complying to this naming scheme will enable effortless integration of data sets.

Name convention for clones and sequences for MGE NoE projects
Xyz	Organism
E01	c=cosmids, b=bacs, f=fosmids, s=shotgun, e=ESTs (library origin should be described separately)
01	MGE Partner ID
01	Group within Partner (1 is added to each further project within the same Partner)
P0001	Plate number
A01	Well position
.x/.y/.z	Extension for forward (.x) or reverse (.y) sequencing - .u for undefined direction
.ext	Extension indicating the type of file: .scf, .abi, .fas




Example: ESTs from Halocynthia roretzi, PartnerID 2 (CNRS):
Hare010201P0001A01.x.scf
Har	Organism
E01	c=cosmids, b=bacs, f=fosmids, s=shotgun, e=ESTs (library origin should be described separately)
02	MGE Partner ID
01	Group within Partner (1 is added to each further project within the same Partner)
P0001	Plate number
A01	Well position
.x	Extension for forward (.x) or reverse (.y) sequencing - .u for undefined direction
.scf	Extension indicating the type of file: .scf, .abi, .fas

• Large volume data submission

We support the automatic submission of large data sets to sequence repositories like EMBL. Upon user request, the system will automatically generate the suitable file formats for sequence submission.

Microarray Data Analysis Tools

For microarray data we provide a web-based system to manage the raw data, and an analysis tool to normalize and cluster the data, compare expression levels, etc.

The ArrayLIMS system was developed to support microarray experiments over the web. Its main goal is to streamline array data acquisition and handling. If required by the project, other members of the project can be allowed to access the experimental data sets by the owners of a respective data set. The system will store the raw experimental data and all relevant biological and technical information.

More and more journals require microarray data to be submitted (identical to sequence data) to public repositories. We support automatic data submission to the ArrayExpress repository. The system will automatically transfer the data in the required MAGE-ML format upon request by the project leader.

The expression profile analysis can be performed with the help of the EMMA system. EMMA provides access to all data sets stored in ArrayLIMS, as well as automated pipelines for data processing, including:

• normalization (reduce noise and systematic errors in data)
• statistical analysis
• clustering

In addition, manual analysis of expression profiles is possible. EMMA can be integrated with other components with additional data sources.

BRIDGE

Training in Bioinformatics

An additional responsibility of the Bioinformatics Platform is the participation in the network's training activities. Bielefeld will cooperate with the Training and Education Platform by providing student courses on applied bioinformatics ( February 2005 and February 2006) and expression profile experiments including the analysis of microrarray data ( March and October 2005).
Additionally, the platform can provide training courses for project teams on the required analysis tools, if needed.

Data Access Policy

The following policy has been discussed at the Scientific Steering Committee (SSC) meeting:

• any result obtained within the NoE will be made public immediately after the data processing period, to maintain the level of accuracy that is required and expected from the scientific community
• each scientist has the chance to disagree before his/her data is released
• the data access policy has to be in conjunction with the IPUDC
• data generated by funding institutes outside the NoE will be considered non-belonging to the Network, and therefore will follow the institutes' policies

This suggestion could not be voted at the meeting, since the required quorum was not met. We expect the SSC to vote on this issue at a later date.

Bioinformatics Committee for Marine Genomics Europe

The Bioinformatics Committee consists of six full members, one representative of the Technology Platform and one guest:

Node contact people (linking people)

The SSC has agreed that each node in the network should name one person to establish the connection to the Bioinformatics Platform. This linking person will be responsible for:

• co-ordinating the activities with Bielefeld
• authenticating new projects requests (channeling requests to Bielefeld)

Nevertheless, project details can still be discussed directly with the team in Bielefeld.

The following linking persons have been named by the nodes:

Contacting Bielefeld and obtaining help

We maintain a MGE-PortalWiki that describes the MGE bioinformatics platform and the MGE portal.

If you want to contact us, please contact the corresponding software mailing lists:

EMMA: emma[at]cebitec.uni-bielefeld.de.

GenDB: gendb[at]cebitec.uni-bielefeld.de.

SAMS: sams[at]cebitec.uni-bielefeld.de.