News
The latest news regarding the de.NBI network and related activities: upcoming talks, courses, articles, job offers etc. are listed here.
![](/images/Quarterly_Newsletter/27/Bildschirmfoto_2022-02-24_um_160509-min.png)
- 2024-06-19
The new de.NBI Quarterly Newsletter, has been published. It reports on main de.NBI activities since March 2024.
Main topics:
- 3rd BioHackathon Germany – Call for project proposals open
- de.NBI/ELIXIR-DE All Hands Meeting - Save the date
- Re-activation of de.NBI working groups
- Reviews of de.NBI Spring School 2024, BrAPI Hackathon, and ELIXIR AHM 2024
- ...and much more!
![](/images/Logos/Jobs2.png)
- 2024-06-14
IT Center (ZDV), High Performance und Cloud Computing Group
Bewerbungsfrist: 14.07.2024
The High Performance und Cloud Computing Group at the IT Center (ZDV) of the Eberhard Karls Universität Tübingen seeks to fill one project position at the earliest possible date for
Scientific Staff (Wissenschaftliche Mitarbeiter (m/w/d; bis zu E 13 TV-L, 100%))
ZDV-09-24
The University of Tübingen is a central partner of the German Network for Bioinformatics Infrastructure (de.NBI) and provides a cloud infrastructure for computation, along with the Universities of Bielefeld, Freiburg, Gießen, Heidelberg, the DKFZ, Charité - BIH and the Research Centre Jülich (https://cloud.denbi.de/). The position focuses on cloud operations and development, collaboration with other cloud sites, and cloud user support.
As part of the de.NBI Cloud team you will be working on:
- Conception, procurement and operation of the hardware infrastructure
- Integration and operation of heterogenous storage resources
- Integration and operation of federated compute resources
- Integration and operation of network components
- Authentication and authorization
- Support of de.NBI Cloud users
- Handling of sensible research data
- Close collaboration with the project partners and the scientific community
- Active support for the broad user community for bioinformatical and technical questions
We expect from you:
- A scientific higher education degree (master, diploma or comparable) in bioinformatics, computer science or a related field
- Experience with an OpenStack-based cloud environment as user and/or administrator
The following competences are considered to be beneficial:
- Python expertise
- DevOps experiences with tools like Ansible, Terraform, Git, Kickstart
- Knowledge about network topologies and concepts like VLAN separation or Software-defined Networking
- Experience with software defined storage systems like Ceph or Quobyte
- Experience with Kubernetes or other container orchestration
- Experience with information security management systems, ideally including certification processes (ISO 27001)
- Experience with Monitoring tools like Prometheus, Grafana or Zabbix
- Team oriented but self-reliant working habits
- Professional interaction with heterogenous user groups
- High motivation, flexibility and team spirit
- Highly proficient in both spoken and written English
- Experience with multidisciplinary scientific working habits
We offer:
- A thorough initial training phase and continuous further training
- A stimulating working environment including space for personal initiative
- Work within a likeable and congenial team
- The opportunity to gain experience in all areas of cloud operation
- Flat hierarchies and the encouragement of own ideas
- Flexible working hours
- Job ticket
- University sport program
The position is initially limited until 31.12.2027. The university seeks to raise the number of women in research and teaching and therefore urges qualified women academics to apply for these positions. Equally qualified applicants with disabilities will be given preference. The employment will be carried out by the central administration of the University of Tübingen.
Have we caught your interest? Please send your application including cover letter, CV, resume and a copy of the certificate of your highest professional qualification, refereeing to reference number ZDV-09-24 until July 14th, 2024 to the director of the ZDV, Prof. Dr. Thomas Walter, 72074 Tübingen, Wächterstraße 76 or in electronic from to
Dr. Jens Krüger (
![](/images/News/FoD.png)
- 2024-05-22
Save the Date for the Fellowship of the Data Meeting 2025!
01.-03. April 2025
Face to face event in Jena with conference fee and: Keynotes! Discussions! Networking! Fun!
For everyone working as Data Steward*, feeling like one, or interested in the topic!
* Data Steward = RDM professional, trainer, data manager, curator, and all similar roles promoting research data management for scientists of any field and discipline from all nations.
3 Days, 3 Main Topics:
- Data Steward* Newbie Jumpstart: Overview of Landscape, Stakeholders, Support & Networks
- The Life of a Data Steward*: Tips & Tricks, Fails, Task Diversity
- Changing Research Data Management Culture: What, Why, How?
Further information will follow – like & subscribe to our newsletter mailing list: https://www.listserv.dfn.de/sympa/info/datafellows
Note that there will be no event in 2024. Please feel free to forward this Save the Date for 2025 to anyone interested! Please feel free to get in touch for questions or to support us Looking forward to see you all in person! Be a DataFellow!
Your Fellowship-Orga Team Cora (TKFDM), Nils (ELIXIR-DE), Elena (FAIRAgro), Jeanne (Leibniz FLI)
[Event formerly also titled RDM Trainer Network Meeting]
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- 2024-05-13
Position: DevOps Engineer / Cloud Specialist
Department: German Human Genome-Phenome Archive (GHGA)
Code number: 2024-0150
The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research.
The German Cancer Research Center is seeking for the recently launched infrastructure initiative German Human Genome-Phenome Archive (GHGA) a DevOps engineer / cloud specialist.
GHGA is part of the national program for research data infrastructures (NFDI). GHGA will act as a national node within the federated European Genome-Phenome Archive. This infrastructure will support genomics data hubs with software tools for secure data/metadata storage, interactive data portals with data visualization, and streamlined data deposition and acquisition solutions. The GHGA main office, which is coordinated by Prof. Oliver Stegle, is located at DKFZ in close coordination with the European Molecular Biology Laboratory (EMBL).
In order to develop the GHGA software platform into a state-of-the-art infrastructure for the secure exchange of genome data, we are looking for a DevOps engineer / cloud specialist to join the team as soon as possible.
Job description:
We are looking for a team member with substantial experience and/or interest in developing, deploying, and maintaining the cloud platforms for GHGA infrastructure. The successful candidate will be part of an interdisciplinary research, development, and data management team to develop and apply a diverse range of state-of-the-art technologies.
Your responsibilities:
- Build a state-of-the-art infrastructure for deployment of services across multiple data centers
- Design and implement scalable solutions based on modern cloud frameworks and technologies such as Kubernetes, Service & Event Meshes
- Build hybrid cloud solutions that span multiple private or public cloud providers and include edge computing scenarios
- Implementing system security measures and performing penetration testing
- Supporting developers in an agile setting to productionalize their software and make it ready for continuous deployment
- Supporting system administrators of participating academic institutions in migrating from classical HPC environments (Slurm, LSF) to cloud-based settings
Your possibilities:
- Expand your technical skills through curiosity-driven projects in an academic setting that values innovation and supports exploration of new ideas and technologies
- Get exposed to a plethora of fields ranging from AI-guided clinical decision making to modern web development
- Work with an interdisciplinary team of experts bringing state-of-the-art biomedical research closer to clinics and patients
- Take part in international organizations such as the Global Alliance for Genomics and Health (GA4GH), the European Genome-Phenome Archive (EGA) and ELIXIR shaping future of genomics across borders
- Widen your expertise with extensive possibilities of training programs, seminars and conferences
Requirements:
- Bachelor's or master’s degree in computer science or similar technical background
- Extensive experience in building and deploying Docker containers
- Familiarity with infrastructure as code frameworks such as Ansible or TerraForm
- Experience in describing container relations as code using e.g. Helm Charts or Docker Compose
- Experience with CI/CD pipelines such as GitHub Actions
- Experience and/or strong interest in working with Kubernetes clusters
- First hand experience with private OpenStack-based clouds, public providers such as AWS, Azure, and GCS, familiarity with GitOps services like Argo CD, Flux CD, or Jenkins X is a plus
- Enjoy working in an interdisciplinary team and talking to software developers, system administrators, as well as domain experts
- Enjoy working with modern technologies and staying up to date with new tech trends
The ideal applicant should have demonstrated the ability to work independently and creatively. The candidate should have excellent communications skills in English and be able to articulate clearly the technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.
We offer:
- Excellent framework conditions: state-of-the-art equipment and opportunities for international networking at the highest level
- Remuneration according to TV-L incl. occupational pension plan and capital-forming payments
- 30 days of vacation per year
- Flexible working hours
- Possibility of mobile work and part-time work
- Family-friendly working environment, e.g. parent-child room, advisory services caring for elderly relatives
- Sustainable travel to work: subsidized Germany job ticket
- Unleash your full potential: targeted offers for your personal development to further develop your talents
- Our Corporate Health Management Program offers a holistic approach to your well-being
Important notice:
The DKFZ is subject to the regulations of the Infection Protection Act (IfSG). As a consequence, only persons who present proof of immunity against measles may work at the DKFZ.
Earliest Possible Start Date: as soon as possible
Duration: The position is initially limited to 2 years with the possibility of prolongation.
Application Deadline: 30.05.2024
Contact:
Dr. Jan Eufinger
Phone +49 (0)6221/42-3466
Please note that we do not accept applications submitted via email.
![](/images/Logos/Jobs2.png)
- 2024-05-13
The Department of Computer Science is opening a position for a Systems Engineer / DevOps Engineer (m/f/d), bridging development and operations functions within one of the most popular and well-established data analysis platforms for life science. The engineer will be responsible for implementing, supporting, and documenting several large-scale application systems. This role includes but is not limited to, the installation, modification, testing, and upgrades of applications, operating systems, file systems, hardware, and cloud environments. The work will be carried out together with other administrators.
Who we are
The European Galaxy team is a core group within the worldwide Galaxy project. We are an open, passionate, and supportive research group at the University of Freiburg highly involved in many software projects related to the global Galaxy community, including leading the Bioconda and BioContainers projects and developing state-of-the-art computational workflows for genomics, metagenomics, transcriptomics, and pharmacogenomics data.
Based in Freiburg, usegalaxy.eu is the science gateway, providing an open-access computational infrastructure for accessing and running a vast catalog of data resources, tools, and workflows. It is used by nearly 100,000 users worldwide.
Your opportunities
This position will allow the postholder to interact with an interdisciplinary bioinformatics, data science, and software development team, working with cutting-edge cloud infrastructure across Europe and engaged in advanced topics such as distributed heterogeneous computing, encrypted data processing, or smart scheduling of jobs across federated resources.
Your Tasks
- Development & maintenance of the Galaxy server and related infrastructure, e.g., TIaaS (Training Infrastructure as a Service), Pulsar-Network, and the Beacon Service
- Work within the team of Admins to design and improve developed software and deployment pipelines
- Conceptualization of update procedures and software integrations in the running system
- Implementing and maintaining best security practices and adhering to our information security policies and industry standards
- Staying current with industry trends and emerging technologies, e.g., virtualization and infrastructure technologies, automatization, and CI/CD pipelines
- Proactively identifying opportunities to enhance the Galaxy Europe instance as well as general deployment guides for other Galaxy instances
- Integrating infrastructural components like various storage systems and special-purpose computation nodes containing accelerators like GPUs
- Community support and training
- Development of documentation and training material for Galaxy admins and automation workflows
- support of services administrators
- give workshops and train other administrators in live sessions
Your Profile
We are looking for a dedicated and motivated team player with strong communication skills and a good command of the English language.
The successful applicant will be an expert Linux system administrator with proficient knowledge of Python, Git, and SQL databases and a Bachelor or Master in Informatics or equal qualification. He/she is an analytical thinker, problem-solver and reliable, with a strong desire to learn and collaborate with the team.
Additional skills that are advantageous:
- several years experience
- Experience building containerized applications
- Experience configuring continuous integration and continuous delivery (CI/CD) systems
- Proficiency using configuration management tools (Terraform, Ansible)
- Familiarity with cloud technologies (e.g. OpenStack)
- Experience in high-performance computing environments
What we offer
Located in a region that connects Germany, France, and Switzerland, our institute offers an international research environment with outstanding infrastructure facilities and a positive working atmosphere that places a high value on work-life balance.
- A team of admins to work with
- Professional training and development opportunities
- Challenging tasks in European-wide distributed projects in a modern working environment
- Flexible working hours and trust-based working time
- 30 days holiday a year
- Reduced-cost public transport within the local area
- Family-friendly offers (affiliated daycare center at the institute, family service)
This position is open immediately and funded for two years, with the possibility of extension. The salary will be determined in accordance with TV-L up to E13 if the personal and collective bargaining requirements are met.
More information about the European Galaxy project is available at https://galaxyproject.eu.
Ready to join our team?
Please submit your complete application documents, including a 1-page motivation summary, CV and contact details.
We are particularly pleased to receive applications from women for the position advertised here.
Application
Please send your application in English including supporting documents mentioned above citing the reference number 00003737, by 10.06.2024 at the latest. Please send your application to the following address in written or electronic form:
University of Freiburg
Institut für Informatik, Bioinformatik
Dr. Björn Grüning
Head of Freiburg Galaxy Team
Georges-Köhler-Allee 106
79110 Freiburg
Germany
E-Mail:
For further information, please contact Frau Dr. Anika Erxleben-Eggenhofer on the phone number +49 761 203-54130 or E-Mail
![](/images/Logos/Jobs2.png)
- 2024-04-08
IT Center (ZDV), High Performance und Cloud Computing Group
Bewerbungsfrist: 14.04.2024
The High Performance und Cloud Computing Group at the IT Center (ZDV) of the Eberhard Karls Universität Tübingen seeks to fill one project position at the earliest possible date for
Scientific Staff (Wissenschaftliche Mitarbeiter (m/w/d; bis zu E 13 TV-L, 100%))
ZDV-07-24
The University of Tübingen is a central partner of the German Network for Bioinformatics Infrastructure (de.NBI) and provides a cloud infrastructure for computation, along with the Universities of Bielefeld, Freiburg, Gießen, Heidelberg, the DKFZ, Charité - BIH and the Research Centre Jülich (https://cloud.denbi.de/). The position focuses on cloud operations and development, collaboration with other cloud sites, and cloud user support.
As part of the de.NBI Cloud team you will be working on:
- Conception, procurement and operation of the hardware infrastructure
- Integration and operation of heterogenous storage resources
- Integration and operation of federated compute resources
- Integration and operation of network components
- Authentication and authorization
- Support of de.NBI Cloud users
- Handling of sensible research data
- Close collaboration with the project partners and the scientific community
- Active support for the broad user community for bioinformatical and technical questions
We expect from you:
- A scientific higher education degree (master, diploma or comparable) in bioinformatics, computer science or a related field
- Experience with an OpenStack-based cloud environment as user and/or administrator
The following competences are considered to be beneficial:
- Python expertise
- DevOps experiences with tools like Ansible, Terraform, Git, Kickstart
- Knowledge about network topologies and concepts like VLAN separation or Software-defined Networking
- Experience with software defined storage systems like Ceph or Quobyte
- Experience with Kubernetes or other container orchestration
- Experience with information security management systems, ideally including certification processes (ISO 27001)
- Experience with Monitoring tools like Prometheus, Grafana or Zabbix
- Team oriented but self-reliant working habits
- Professional interaction with heterogenous user groups
- High motivation, flexibility and team spirit
- Highly proficient in both spoken and written English
- Experience with multidisciplinary scientific working habits
We offer:
- A thorough initial training phase and continuous further training
- A stimulating working environment including space for personal initiative
- Work within a likeable and congenial team
- The opportunity to gain experience in all areas of cloud operation
- Flat hierarchies and the encouragement of own ideas
- Flexible working hours
- Job ticket
- University sport program
The position is initially limited until 31.12.2027. The university seeks to raise the number of women in research and teaching and therefore urges qualified women academics to apply for these positions. Equally qualified applicants with disabilities will be given preference. The employment will be carried out by the central administration of the University of Tübingen.
Have we caught your interest? Please send your application including cover letter, CV, resume and a copy of the certificate of your highest professional qualification, refereeing to reference number ZDV-07-24 until April 14th, 2024 to the director of the ZDV, Prof. Dr. Thomas Walter, 72074 Tübingen, Wächterstraße 76 or in electronic from to
Dr. Jens Krüger (
![](/images/Quarterly_Newsletter/27/Bildschirmfoto_2022-02-24_um_160509-min.png)
- 2024-03-26
The new de.NBI Quarterly Newsletter, has been published. It reports on main de.NBI activities in Q1 2024.
Main topics:
- New de.NBI/ELIXIR-DE consortium – national contract signed
- de.NBI and ELIXIR-DE now led by Oliver Kohlbacher and Alexander Sczyrba
- FAIR training handbook published by the ELIXIR FAIR training focus group
- ...and much more!
![](/images/News/FAIRtrainingHandbook_longversion_logo_lightBG.png)
- 2024-03-20
To encourage the re-use of your training material it helps to ensure Findability, Accessibility, Interoperability and Reusability (FAIR). However, it is often not straightforward to apply the FAIR principles to training material. de.NBI and other ELIXIR members just released a handbook to guide you in this process. This comprehensive book provides examples and guidelines to support anyone that is involved in the creation of training materials, such as trainers, training coordinators and Train-the-Trainer instructors. The book consists of ten chapters that treat amongst others how to choose the material formats, annotate materials with metadata, get a persistent identifier and boost discoverability. It can serve as a reference to learn about general best-practices or to quickly look up specific how-tos. This book is an ongoing effort; databases, registries and best practices are constantly evolving. Therefore, any feedback or contributions from the community are warmly welcomed.
Check it out! https://elixir-europe-training.github.io/ELIXIR-TrP-FAIR-training-handbook/
![](/images/Logos/Jobs2.png)
- 2024-01-17
Opportunity: We are looking for candidates to fill an open staff scientist position with a strong background in data science, data engineering or software development to facilitate and assist with the development of ProteomicsDB. ProteomicsDB is an internationally well-reputed publicly available database that provides information about proteins and other bio-molecules initially centered around human biology. It is designed to integrate data from mass spectrometry-based experiments and other sources to offer a comprehensive view of proteomes. We are continuously expanding the types of data stored in as well as the number of organisms covered. Researchers and scientists can use ProteomicsDB to explore and analyze protein-related data for a better understanding of cellular processes, functions, and disease mechanisms. ProteomicsDB is built on the in-memory system SAP HANA using IBM Power 8/9 hardware.
The successful candidate will become a key member of a strong interdisciplinary team of bioinformatician that focus on the development and application of novel approaches in proteomic research. Depending on the applicant’s skills, this position will strengthen our ongoing development of ProteomicsDB focusing on the backend or frontend development. In light of this, the most important aspects of the job description are:
- Service engineering and infrastructure maintenance for ProteomicsDB
- Full-stack development to enhance ProteomicsDB
- Data import, maintenance, and integration of proteomics, lipidomics, or metabolomics data
Requirements: Candidates must hold a master’s degree in Data Engineering, Data Science, Bioinformatics, Informatics, or a related discipline. Essential skills include a sound understanding of Linux and related systems, software development standards, and hardware management. Additional beneficial skills include a theoretical knowledge of and practical skills in statistical analysis, data integration, backend or frontend programming and database design. Interest in understanding technologies e.g. proteomics and metabolomics using mass spectrometers is expected. We are looking for a self-motivated and broadly interested individual with high potential and a strong sense of responsibility. Flexibility and the ability to work in a fast-paced environment on multiple scientific and infrastructure projects are essential. Good inter-cultural and inter-personal communication skills as well as the ability to present in English are also important.
Our offer: You will join a young and highly motivated team of interdisciplinary bioinformaticians that use the latest proteomic approaches to gain insight into the biological processes that govern life. You will further be connected to the Munich Data Science Institute (MDSI) at the Technical University of Munich (TUM) to foster and facilitate exchange. You will also be connected to the SAP University Competence Center (UCC) at the TUM to assist in the hardware/software maintenance of ProteomicsDB, with the option to receive a proof of work with SAP HANA. TUM is one of the best academic institutions in Germany and offers a stimulating work environment and excellent future perspectives.
The position is limited until December 2025 and available as soon as possible. Remuneration is in accordance with the TV-L E13 according to the professional qualification.
Equal opportunity: TUM is aiming to increase the proportion of women and, therefore, expressly welcomes applications from women. The position is also suitable for severely disabled persons. Severely disabled applicants will be given preference if their suitability, qualifications and professional performance are otherwise essentially equal.
Application process: Applicants should send a dossier containing a motivational statement (max. one page), a curriculum vitae summarizing qualifications and experience, copies of degrees and transcripts of study records, names and the email addresses of at least one referee as a single PDF document to Mathias Wilhelm (via mail
Data Protection Information: When you apply for a position with the Technical University of Munich (TUM), you are submitting personal information. With regard to personal information, please take note of the Datenschutzhinweise gemäß Art. 13 Datenschutz-Grundverordnung (DSGVO) zur Erhebung und Verarbeitung von personenbezogenen Daten im Rahmen Ihrer Bewerbung. (data protection information on collecting and processing personal data contained in your application in accordance with Art. 13 of the General Data Protection Regulation (GDPR). By submitting your application, you confirm that you have acknowledged the above data protection information of TUM.
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- 2023-11-22
Issue 04/2023 | ||||||||||||||||||||||||||||||
Next Event: 23 Nov 2023, Annual Meeting of the de.NBI Industrial Forum |
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![]() Presentations about de.NBI Cloud, an introduction to GAIA-X based Health-X dataLOFT, and data handling in the NFDI4Microbiota consortium will kick off the meeting. Industrial use cases will feature:
Further information, agenda, abstracts, and registration here.
We look forward to welcoming you to the 4th Annual Meeting of the de.NBI Industrial Forum. |
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Andrew Smith as interim ELIXIR Director
Niklas Blomberg will step down as ELIXIR's Director at the end of this year to join the Innovative Health Initiative (IHI) as Executive Director. The ELIXIR Board has approved the recommended candidate for the Director position, and details about the new Director will be confirmed soon. In the meantime, the Board appointed Andrew Smith as interim Director, for an initial term of six months, from December 2023 to May 2024. Alexander Goesmann elected Chair of the ELIXIR Board The ELIXIR Staff Exchange Programme aims to facilitate meaningful networking and engage with experts from various ELIXIR nodes, fostering cross-disciplinary collaboration.ELIXIR's commitment to staff exchanges reflects its recognition of the value in nurturing connections within the scientific community. By facilitating these opportunities, ELIXIR empowers researchers to collaborate on a global scale, contributing to the growth and progress of the bioinformatics field. In 2023, members from ELIXIR Germany particitpate in four projects:
ELIXIR launched the ELIXIR Impact Toolkit |
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Since the initial publication of Galaxy: a platform for interactive large-scale genome analysis in September 2005, a multitude of subsequent papers, authored by both the Galaxy team and its users, have contributed to Galaxy's extensive citation record, exceeding 12,000 globally. This pivotal paper marked the establishment of the global Galaxy community, significantly influencing computational biology and related fields. Congratulations to the inventors, contributors, and supporters on 18 years of success! Here's to looking forward to another 18 years of continuous innovation and collaboration! More details see here. |
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Science communication of a different kind |
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Recent updates of services:
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The next de.NBI training events are announced on www.denbi.de/training.
Upcoming scheduled events:
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Impressum |
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Responsible for contents:
T. Dammann-Kalinowski, I. Maus, D. Wibberg
de.NBI - German Network for Bioinformatics Infrastructure, Forschungszentrum Juelich GmbH - IBG-5, Branch Office at Bielefeld University, 33594 Bielefeld, Germany Phone: +49-(0)521-106-8758
Fax: +49-(0)521-106-89046 Email: Web:https://www.denbi.de
Twitter: #denbi, @denbiOffice LinkedIn: https://www.linkedin.com/company/de-nbi For questions and remarks please contact Subscription
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To unsubscribe from the de.NBI Quarterly Newsletter, please use the unsubscribe link. The de.NBI Quarterly Newsletter is a service of de.NBI - German Network for Bioinformatics Infrastructure for members, partners and interested public. All photos are copyright of the de.NBI administration office unless marked otherwise. |