Omics IT and Data Management Core Facility

Omics IT and Data Management Core Facility (ODCF)

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Recent advances have led to an explosion in the use of high-throughput, large-scale experiments in life sciences, including increasing use of omics technologies (genomics, proteomics, epigenomics). These generate huge quantities of data that needs to be stored, shared and analysed effectively.

The Omics IT and Data Management Core Facility (ODCF) at the German Cancer Research Center (DKFZ) provides data management, computing and basic bioinformatics services to groups at the DKFZ and collaborating partners.

The ODCF offers structured data storage of different kinds of raw omics data. Our staff have several years of experience in storing and organizing multiple forms of next-generation sequencing data, and we are constantly working on expanding our portfolio of supported data types to meet the needs of our users.

In addition to storing raw data, the ODCF also provides basic data processing using our automation platform OTP (https://otp.dkfz.de) and our workflow management system RODDY (https://github.com/TheRoddyWMS). Currently, we provide alignments of human and mouse genomics data as well as somatic variant calling for human tumor/control sample pairs using state of the art workflows. We are constantly broadening the scope of our services to include additional data types and workflows. OTP also acts as a database that provides important information about the data and the samples they come from (metadata). These data processing services currently support a wide range of projects, including from the Heidelberg Center for Personalized Oncology (HIPO) and the International Cancer Genome Consortium (ICGC). 

As well as the data processing integrated in OTP, the ODCF also offers a basic bioinformatics service that builds on the interactive analysis tool HUSAR (https://www.dkfz.de/gpcf/hs_husar.html). We provide the infrastructure for sequence analysis and offer further support in analyzing different kinds of sequencing data. This service is mainly aimed at helping small research groups without dedicated bioinformaticians to answer specific research questions.

We operate a computing cluster that is used by the ODCF for data processing, as well as by scientific groups at the DKFZ for downstream analysis. The cluster runs a batch system under Linux. It consists of several thousand cores and is constantly expanded based on demand. In addition to the standard compute nodes we provide some specialized hardware, such as FPGA nodes. All nodes are directly connected to the central storage systems of the DKFZ IT Core Facility. Our goal is to provide a cluster based on the needs of our users, so please feel free to contact us if you have special requirements. 

If you are going to start a new project and want your data managed and processed, if you would like access to the compute cluster, or if you want any more information on the services we offer, please do not hesitate to contact us at odcf-service@dkfz.de

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