Bioresources, Biodata and Digital Health
The infrastructure supports researchers in areas such as biomaterials, medical data and bioinformatics. In addition to analysis tools for modern research, it also offers tools, documents and templates for evaluations, study planning and biomaterial collections.
We, the infrastructure “Bioresources, Biodata, and Digital Health” (BBD), are building a comprehensive biomedical service structure at the DZIF. Our goal is to standardize biomedical data and make database systems interoperable. This will enable translational research at the DZIF to be even more resource-efficient, scientifically high-quality and effective.
Our infrastructure provides DZIF scientists with improved access to information on biosamples and pathogen collections, as well as to databases, analysis tools or apps that are needed more than ever for translational infection research. The new DZIF portal serves as a central meeting point to exchange knowledge and information about services within the DZIF and to strengthen collaboration.
We focus on:
- expanding the data and IT infrastructure for improved information flow
- supporting DZIF scientists in data analysis
- teaching key skills and capacity building through training and consulting
- developing and providing digital tools and services through special projects
Our experts at a glance
The image gallery provides an overview of expertise and suitable contact persons for your concerns:
Services of the infrastructure Bioresources, Biodata and Digital Health
- Pathogen data and tools
- Host-related data and research: clinical and epidemiological data
- Host-related data and research: biobanking
- IT infrastructure
- Training and knowledge transfer
- Methodological support and consultation
- Central links and forms
How can we support your research?
Send us an email
The Central Biosample Register at the DZIF - explained in just under two minutes (only when this video is started will active content be loaded from YouTube and personal data be transferred to YouTube; more information on this can be found in our Privacy Policy).
The BBD experts are located at five of seven DZIF partner sites. At the Munich site, the DZIF Data & Tools Hub (DZIF DT-Hub), the DZIF Metadata Repository (DZIF-MDR) and the Central Biobank Register (DZIF-ZBR) are operated at the Helmholtz Zentrum München. The DZIF-ZBR currently stores information on 10,000 patients and 384,000 biosamples. The short video on the left explains how the DZIF-ZBR works and how DZIF researchers can use this data. In addition to the DZIF-ZBR, the DZIF biobanking for liquid biosamples is also located in Munich.
The Hannover-Braunschweig site is home to experts in bioinformatics and machine learning as well as epidemiology. DZIF researchers can find support here for study planning and data analysis, among other things, but also useful tools for conducting studies, such as offers for digital health, for example the app for health research PIA (Prospective Monitoring and Management App). Furthermore, the DZIF pathogen bank is located at the Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures in Braunschweig.
The Bonn-Cologne, Heidelberg and Tübingen sites provide experts for clinical data and IT infrastructure. The IT experts at the Cologne-Bonn site, for example, have developed the DZIF portal, which, in addition to links to a large part of the research infrastructures offered, provides tools for data management and communication. The DZIF portal is the first point of contact for all DZIF researchers and provides further internal services such as DZIF reporting. At the Heidelberg site, BBD experts supervise the DZIF tissue bank.
Pathogen data and tools
Computer-assisted analyses of large biomedical data sets are an essential part of modern pathogen research. In particular, the rapid development of OMICS technologies has led to an increased demand for informatics methods in biological and clinical research. Collecting and evaluating these data sensibly requires the expertise of bioinformaticians as well as specialized software and hardware.
Bioinformatics is therefore an essential component in the analysis of data within DZIF projects and requires extensive expertise to either develop new methods or identify the best available software tools for a task. In the area of bioinformatics and machine learning, we have extensive expertise in the evaluation of bioinformatic and machine learning methods for analyzing microbial pathogens and microbial communities, the implementation of bioinformatic pipelines, and their application in DZIF-relevant translational research. We provide best practice recommendations for experimental design and computer-aided data analysis. We also support DZIF researchers in selecting suitable methods for specific data analyses from a wide range of available computer-based methods.
Do you have questions? Alice McHardy and her team can be reached via bioinformatics@dzif.de
Databases for pathogen data
We develop user-friendly databases for genome sequences and other OMICS data as well as associated metadata. In doing so, we promote the sustainability and FAIRness of data and analyses together with international initiatives. EnteroBase enables web-based genome analysis and is particularly useful for tracking transmission chains, outbreaks and epidemics. BacDive is the world's largest database for standardized information on bacterial strains. An OMICS database is being developed for microbiome-related data from human samples, with a particular focus on data protection.
Pathogen bank
The DZIF Pathogen Bank is located at the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures in Braunschweig. It offers quality-tested microorganisms, associated metadata and scientific services for science and research. At the same time, various options for the safe long-term storage of microorganisms are offered.
DZIF Pathogen Bank - Offer
- Almost 3,000 strains (bacteria, but also fungi and bacteriophages)
- Metadata available via the DSMZ catalog or BacDive
- DNA and other services (DSMZ Services)
- Various options for depositing strains (public collection, internal DZIF collection, security deposit, patent deposit)
- DZIF training courses for the professional handling of pathogens
Key areas
- Microbiome strains from the gastrointestinal tract of mice, pigs, chickens and humans
- Multidrug-resistant bacterial strains (WHO priority pathogen list)
- Multidrug-resistant pathogens from the DZIF transplant cohort
Your contacts for questions about the DZIF pathogen bank: Jörg Overmann is the coordinator. Birte Abt is available to answer questions and suggestions.
Host-related data and research: clinical and epidemiological data
Our metadata repositories provide a comprehensive overview and context of biomedical data to efficiently provide researchers with relevant information.
DZIF Metadata Repository (MDR)
The DZIF Metadata Repository (DZIF-MDR) is a metadata database for core data sets that stores structured information about research data according to the FAIR principles. By providing centralized and harmonized metadata, data sets can be managed more effectively to create new data sets for research purposes. The DZIF-MDR is therefore a valuable tool for standardizing and harmonizing data.
Your points of contact for questions and suggestions regarding the DZIF-MDR are Aloysius Alonso Lubega and Hans Demski.
Click here to go to the DZIF-MDR website.
DZIF Central Biobank Register (ZBR)
Biobanks store biological samples such as human tissue, blood and DNA. These samples and the associated personal data are of particular value for translational research at the DZIF. With their help, the causes of disease can be uncovered and new preventive, diagnostic and therapeutic methods developed in infection research.
In order to make the biological materials stored decentrally at the individual DZIF locations usable for research, the DZIF operates the central biobank registry (DZIF-ZBR) at the Helmholtz Zentrum München. The ZBR brings together the sample data from the local systems, consolidates the data from the various locations and studies, and thus represents a valuable tool for data harmonization. Using individual search queries, the CBR provides DZIF researchers with an overview of the collected biosamples and associated data, thus providing an effective tool for planning projects involving biosamples.
Hans Demski and Manuela Scheuner are the points of contact for questions and suggestions regarding the DZIF-ZBR.
Click here to go to the DZIF-ZBR website.
DZIF clinical core dataset
The DZIF clinical core dataset supports researchers in setting up studies and standardizes datasets. This sustainably promotes both interoperability between different studies and the reusability of the collected data.
The data set was developed on the basis of the iDEx survey and takes into account existing data sets and data collections, including the DZIF-ZBR, MuSPAD, ImmuneBridge and GECCO. In addition, it integrates the elements of the DZG basic data set, which is to be used in DZG-funded studies. This serves the purpose of cross-DZG standardization and data homogenization. An overview of the data elements can be found in the DZIF-MDR.
In parallel to the DZG basic data set, the DZIF clinical core data set is also available for download on the Medical Data Models Portal. The publication process is currently in progress. If you have any questions, please contact Meta Bönniger.
Host-related data and research: biobanking
Biobank overview
The biobanks and biosample collections available at the individual sites – including those related to the DZIF – are listed in the “German Biobank Directory” of the “Biobanking and Biomolecular Resources Research Infrastructure” (bbmri). Here you will find information on the biobanks and collections of human biosamples currently available within the DZIF, as well as on biobanks in the DZIF network. A short description and further information on the individual biobanks can be found under the respective acronyms by entering the search term “DZIF” under “Biobank network”.
Go to the participating biobanks
If you would also like to search for biosamples in an international context, you can start your search using the following link:
https://directory.bbmri-eric.eu
Another option for searching for and requesting biosamples can be found at the following link:
https://samplelocator.bbmri.de/
Would you like to have your biobank or biosample collection included in the German Biobank Directory or do you have any requests for changes? Please send an e-mail to Bettina Lorenz-Depiereux.
Biobanking for liquid samples (liquids)
The DZIF biobank is located at the Helmholtz Zentrum München (HMGU) and is responsible for all matters relating to the collection of liquid biosamples. Our goal is to provide safe, high-quality, authenticated and standardized biosamples for DZIF projects and external partners.
The infrastructure's experts are happy to support and advise you in all areas of biobanking - from sample collection and processing to storage and quality management - and offer state-of-the-art processing and analysis methods.
We support you with the following, among other things:
- Preparation of ethics documents, taking into account the reusability of samples and data
- Data management of biosample collections (LIMS, federated data storage)
- Quality management (QM): for the transplant cohort, we have developed a three-tier QM system with SOPs, friendly audits and quality checks on biosamples, which we are happy to adapt to your needs
- Entry of your biosample collection in the German/European biobank registry
We are working on harmonizing and standardizing these topics at all DZIF partner sites and with all cooperation partners. Our leading cooperation project is the Transplantation Cohort (Tx) within the research area Infections in the Immunocompromised Host. For the Munich Tx partners, we store the biosamples centrally in the HMGU Biobank. Another important task of our group is the operation of the Central Biobank Register (ZBR), which provides an up-to-date overview of available biosamples in the DZIF.
Your contact person for questions and services regarding liquid biosamples is Bettina Lorenz-Depiereux.
DZIF Tissue Bank
The central DZIF tissue bank at the Heidelberg site provides collectives of relevant tissue samples for research projects in the DZIF. In this context, the tissue bank offers state-of-the-art analysis and processing methods as well as technologies in the field of tissue banking.
The DZIF Tissue Bank was able to establish a comprehensive COVID-19 collective at the beginning of the SARS-CoV-2 pandemic and to expand this collective over time through ongoing autopsies of deceased COVID-19 patients. Research into the tissue has made it possible, among other things, to analyze the pathophysiological mechanisms of the infectious disease and to adapt the treatment of severe cases.
Your contacts for questions and suggestions regarding tissue samples are Tilman Pfeffer and Peter Schirmacher.
To the website of the DZIF Tissue Bank
IT infrastructure
DZIF portal – where the DZIF meets
The DZIF portal is a central, cloud-based web platform where researchers and experts from all DZIF partner sites and the other German Centers for Health Research (DZGs) can network, exchange ideas and work together.
Developed as part of the BBD's IT infrastructure focus, the DZIF portal combines collaboration tools with links to DZIF-internal research infrastructures. DZIF researchers can access a shared cloud for collaborative work on documents, a chat function and a comprehensive group and authorization management system, among other things, via a single sign-on. Open-source software was used to implement the DZIF portal. The DZIF Data & Tools Hub is also connected to the single sign-on and is thus user-friendly and accessible via the uniform interface.
In addition, DZIF-specific documents such as FlexFunds applications will be available via the portal in the future. Writing and submitting reports will be integrated into a separate tool, enabling standardized submission of reports for the central funding management (FMM).
Click here to go to the DZIF portal.
DZIF Data & Tools Hub - central platform for DZIF resources
The resources and data developed at the DZIF are collected and categorized in the Data & Tools Hub (DZIF-DT-Hub) to make them visible in one place. The platform functions as an independent reference manager and is integrated into the DZIF portal as a one-stop shop. Researchers can thus conveniently access a wide range of biodata, studies, databases including bioinformatic applications, software tools, data protection-compliant linking of routine and study data, documents and templates for evaluations, study planning or biomaterial collections. The efficient exchange of established data and tools streamlines and simplifies workflows and promotes collaboration within the DZIF community.
Your contact person for questions and suggestions regarding the DZIF-DT-Hub is Manuela Scheuner.
Click here to go to the DZIF-Data & Tools-Hub.
Training and knowledge transfer
Our training courses, webinars and workshops provide valuable knowledge and practical skills to support researchers at the DZIF in the best possible way.
Our experts are happy to share their knowledge with both junior and experienced researchers who want to expand their know-how. Whether “deep learning” for the free statistical software “R”, application meetings for biosample registries or outbreak monitoring: specific research methods, among other things, are taught and practiced using concrete examples from everyday research, based on the questions and problems of DZIF researchers. An expansion of the collaboration with the DZIF Academy is being sought.
Current events can be found at the bottom of this page.
Do you and your colleagues have a suggestion for a training course and/or workshop?
We look forward to your suggestions.
Methodological support and consultation
From planning to application to implementation: the BBD experts are at your side throughout many steps of your scientific studies.
For example, we offer comprehensive and independent support for DZIF projects, including advice on FlexFunds applications. Our checklist, which can be found in the DZIF public area on the DZIF portal, provides DZIF researchers with an overview of the services and resources available when they are preparing a FlexFunds application. The confidential review by our experts enables the optimal use of DZIF structures and generates synergies.
In addition, our experts provide best practice recommendations for DZIF researchers on experimental design and computer-aided data analysis. We also support the selection of suitable methods for specific data analyses from a variety of available computer-aided methods.
As part of various collaborations within DZIFs, a series of sample texts, standard operating procedures and templates, as well as recommendations, have been developed and are available on the DZIF portal and on request.
We are happy to advise you on:
Biological materials and pathogens
- Storage and logistics
- Cost calculation for biobank collections
- Quality management, good biobank practice
- SOPs (Standard Operating Procedures)
- Laboratory Information Management System (LIMS)
- Preanalytics
- Compliance with laws, permits
- Ethics, informed consent and patient information
- Nagoya Protocol
Bioinformatic analyses
- Serological evaluations
- Genomic surveillance
- Microbiome data
- Pathogens
- AMR (Antimicrobial Resistance)
Digital tools to support cohort studies
- Health research app (PIA)
- Biobanking Tool HEnRY (HIV Engaged Research Technology)
- Clinical core data sets
Digital tools to support infectious disease surveillance
Epidemiology
- Study design, sample size calculation and data analysis
- Systematic reviews and literature searches
Our experienced team is able to quickly and professionally produce both systematic reviews and systematic literature searches in collaboration with experts in all research areas. We provide support for both “simple” literature searches and the development of extensive systematic reviews. - Dynamic modeling of infectious diseases
We have experience in creating our own infection-dynamic models. We can support modeling through evidence synthesis or methodological capacity. In the context of the COVID-19 pandemic, we have supported public communication and work in expert committees by developing our own models and building a communication platform for the German modeling community. - Meta-analyses and platforms for conducting individual participant data meta-analyses
We conduct meta-analyses both within and outside the framework of systematic reviews. In particular, we specialize in setting up, recruiting for, and maintaining platforms for conducting meta-analyses with individual participant data. In the context of the COVID-19 pandemic, for example, we have established the Serohub, which contains individual participant data from serological studies in Germany.
Do you have any questions? Please feel free to contact us!
Central links and forms
We have summarized important links and forms for you below:
