German Crop BioGreenformatics Network (GCBN)
The staff of the Service Center "German Crop BioGreenformatics Network" (GCBN)de.NBI Services offered by GCBN de.NBI Training offered by GCBN
About
The German Crop BioGreenformatics Network (GCBN) is a service center focused on supporting crop research and breeding through specialized bioinformatics infrastructure and plant-specific data resources. GCBN brings together three partners: the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK, BIT, Uwe Scholz), Helmholtz Center Munich (HMGU, PGSB, Klaus Mayer), and Forschungszentrum Jülich (FZJ, IBG-4 Bioinformatics, Björn Usadel). Our collaboration provides researchers and breeders with reliable tools, data, and expertise to advance plant science.
Services
The GCBN consortium offers an extensive suite of bioinformatics tools tailored for plant research, enabling researchers and breeders to efficiently exploit the large genomic and phenomic datasets typical in the field. As part of the consortium's toolkit, raw sequencing data is processed using Trimmomatic to remove low-quality reads and contaminants, ensuring high-quality input for downstream analysis. Helixer, a recent addition to the suite, is an AI-powered tool for structural gene annotation and is accessible online or as a downloadable package. Functional annotation of genes, an important step in gaining biological insight, is supported through the online tool Mercator4. In addition, GCBN offers a tailored Plant Genome Annotation service designed to handle large and complex genomes such as wheat leveraging the latest available tools and methodologies. Functional analysis support is provided by GCBN through tools such as the Crop Analysis Tools Suite (CATS) and MapMan. CATS is an online platform offering a comprehensive collection of tools for plant genome sequence analysis, with a strong focus on crop research. MapMan, a standalone application, maps omics datasets onto plant-specific pathways and provides statistical and clustering tools to support biological interpretation.
GCBN also strongly supports broader initiatives, such as the FAIR principles; findability, accessibility, interoperability, and reusability. The e!DAL-PGP is a registered data repository that stores cross-domain datasets in a persistent manner, thereby providing datasets which have been used in published research. Another major initiative is the EURISCO project, which provides a catalog of passport data for millions of germplasm accessions across many European countries, ensuring access to critical genetic resources.
Through de.NBI, GCBN supports these services by offering training workshops, consulting for researchers and breeders, and streamlined access to germplasm data and annotation resources, thereby creating an integrated framework for crop research.
Developments
GCBN is dedicated to maintaining and improving bioinformatics infrastructure. We focus on expanding access to crop-specific tools and data systems, integrating them into the de.NBI Cloud where applicable. Ongoing efforts aim to enhance tool interoperability, scalability, and accessibility to meet the needs of the plant research and breeding communities.
Project Management
Dr. Uwe Scholz (Service Center Coordinator)
Bioinformatik und Informationstechnologie
Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben
Corrensstraße 3
06466 Stadt Seeland
Prof. Dr. Klaus F. X. Mayer
Plant Genome and Systems Biology
Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH)
Ingolstädter Landstraße 1
85764 Neuherberg
Prof. Dr. Björn Usadel
IBG-4 Bioinformatik
Forschungszentrum Jülich
Wilhelm-Johnen-Straße
52428 Jülich
Posters
