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GabiPD-Frequently Asked Questions

 

What are the principal tasks of GabiPD?

Principal tasks of GabiPD are, to collect all relevant primary data from different GABI projects, to integrate and to make them available via internet.
Data from different experiments and research groups are linked with each other that a synergistic effect is created in a longer term.
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Which data could be stored in the GabiPD?


Sequence and expression data could be stored as well as results from protein expression profiles, that means MS data and results from 2D gelelectrophoresis, metabolite profiles, that is LC- or GC-MS data, data regarding protein-protein-interactions as just as mapping data and other.
 

How to submit data?


For submitting data to the GabiPD you will first need to register to GabiPD. Please contact us:

Registered users can submit data by secure file upload:
Login to GabiPD, click on "Manage account" and "Send to GabiPD". All data transfer is done encrypted.
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What about the security of the submitted data?


All traffic between the web server and the browser is done encrypted to ensure privacy of the data.
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Which data can be stored in the GabiPD?


Data which should be collected in the GabiPD are, according to the rules laid out by the BMBF, data, which are achieved with materials or services of the GABI resource centers.
But we offer all GABI participants to store their data in GabiPD.
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How to get a registration for GabiPD?


Please contact us to get a password:

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Who has access to the data?


Regarding data, which are achieved with materials and services of GABI resource centers, it is defined by the BMBF rules who gets access to the data to which point of time:
During the first six (optional twelve) month data are only accessed for the owner of the data and owner-defined persons/groups. After this time the patent and licensy agency (PLA) as well as the Wirtschaftsverbund Pflanzengenom (WPG) get privileged access to your data for three month. After this time the data become public.
Regarding all other data, there are no rules concerning the data access. The owner can decide who gets access to his data and when data should become public.
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What are the profits of GabiPD?


Benefits are:

  • Different experiments on the same material and under the same condititons are stored in GabiPD and are available for cross-referencing. Thereby results from different approaches can be compared and linked to complement each other.
  • GabiPD makes a special infrastructure available for storing your experimental data. This facilitates an easy and clear access to your own data and at the same time a standardised and central dissemination node.
  • That the data of other participants are accessible via www interface, that is all groups will profit from the work of each other. You can decide whom to grant special access to parts of your data.
  • That all experimental data in GabiPD are screened for facts worth to be patented prior to publication. Thereby the patent- and licensy agency (PLA) supports the GABI participants. The initial costs or the patent application are covered by the PLA (must be returned in a case of a successful patenting and commercialisation of the investions discovered).
  • That the Wirtschaftsverbund Pflanzengenom (WPG) gets access to your data if you store them in GabiPD. The WPG should ensure that the results of your research find fast access to the industry (plant breeding companies).
  • GabiPD offers a lot of bioinformatics services to the GABI community. For more information, visit our service pages.

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What are the obligations of the financially supported GABI participants towards the GabiPD?


Scientists/research facilities, who make use of the services of any of the GABI resource centers are, according to the rules laid out by the BMBF, obligated to put their data in the GabiPD.
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Is there plant specific biological material available at ImaGenes GmbH (successor of RZPD)??


The support of dissemination biological material is not funded within GABI. Arabidopsis clones and Arabidopsis colony- or PCR-filters can be acquired by purchase. ImaGenes also offers gene expression profiling on all currently available Affymetrix GeneChip® Expression Arrays. For more information on ImaGenes services, please visit ImaGenes webbages.
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Who is the contact person?


If you have questions regarding GabiPD, please contact:

Dr. Björn Usadel (+49-(0)241-80-26634) or Axel Nagel (+49-(0)331-567-8277)
or send email to:

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What is "GreenCards"?


GreenCards is a search and visualization interface to search for sequences, SNPs, mapping information etc. by gene name or function, accession number or clone name etc. Wildcards (*) are allowed.
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How to BLAST via GabiPD?


You are able to blast your sequences by a secure BLAST search via GabiPD.
Copy your sequence inside the textfield, select a program (blastn, blastx, blastp, tblastx, tblastn) from the choice box. Choose also a database against you want to blast your sequence. The default value for the expect value is set to 1E-10; you can change this value.
All selectable databases are mirrored weekly from NCBI or TIGR, respectively. Besides it is possible to make BLAST searches against all sequence data stored in GabiPD.
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