News
The latest news regarding the de.NBI network and related activities: upcoming talks, courses, articles, job offers etc. are listed here.
- 2023-09-04
| Issue 03/2023 |
|
|
The life sciences are a major player in the age of big data. Modern high-throughput omics technologies generate large amounts of high-dimensional data. Besides new challenges for the analysis and visualization of this amount of research data, its management and sharing has become an important issue in the daily research process. The main objective of the 2023 de.NBI Summer School is to provide an overview of the possibilities to process, analyze, share and integrate data using different open source platforms. The 8th de.NBI Summer School on Bio Data Analysis for Life Sciences will take place in Bielefeld, Germany. This training event addresses life scientists, bioinformaticians, computer scientists, systems biologists, synthetic biologists and others working with or interested in (bio)research data. The program features lectures and hand-ons about
The Summer School is organized by the de.NBI/ELIXIR DE administration office and the ELIXIR DE Officers at ForschungszentrumJülich. A total of 20 international participants will be welcomed in Bielefeld. |
|
 After the success of the first BioHackathon Germany last year in Lutherstadt Wittenberg, de.NBI and ELIXIR Germany are hosting the 2nd BioHackathon Germany 2023 in Bielefeld from 11-15 December 2023. We hope to attract numerous participants from de.NBI, ELIXIR Germany, other ELIXIR nodes as well as other interested parties and would like to encourage industry involvement.We will offer 11 interesting projects in various areas, e.g. training, single cell omics, Bioschemas, plant bioinformatics, etc. We will offer remote access - available for those who cannot attend the meeting in person. Places for the in-person event are limited, however virtual participation is possible alternatively. Registration is open until 17 November 2023. Selection of participants will be on a first-come, first-served basis. |
|
|
Announcing the Annual Meeting 2023 of the de.NBI Industrial Forum |
 The 4th Annual Meeting of the de.NBI Industrial Forum will take place virtually Thursday, 23 November 2023. The annual meeting connects academic and industrial stakeholders by giving insights in recent research developments in the Life Sciences and showcasing current industrial topics. This year’s meeting will include presentations by academic experts and will feature industrial use cases on "Big Data Handling in the Life Sciences".More information on the agenda as well as relevant organizational information will soon to be provided here. Save the date! |
|
|
|
|
We say goodbye to Andreas Tauch, who has left de.NBI and ELIXIR Germany on 30 June. Andreas has been involved in the planning and development of the German Network for Bioinformatics Infrastructure since the beginning of the conception phase in 2014 and has served as head of the de.NBI Administration Office since the start of the BMBF project in March 2015. Simultaneously, he has also tirelessly promoted the establishment of the German Node of ELIXIR, initially as Deputy Head of Node and after finalisation of the entire contract as HoN from June 2020. |
|
Over 70 international participants attended the „Fellowship of the Data – Research Data Management Trainer Network Meeting“ on-site at the Humboldt University, Berlin, 21 to 22 June 2023. The meeting was jointly organised by ELIXIR DE, ELIXIR NO, and ELIXIR UK in the realm of ELIXIR CONVERGE and the sub-working group training/further education of the DINI/nestor WG Research. The “Fellowship of the Data” meeting will be continued next year 5-7 June 2024 in Jena with ELIXIR DE being once again part of the organisation committee.
|
de.NBI Blog |
 In May 2023, we have launched the new format de.NBI Blog, which comprises 12 articles by now. Topics range from indroductions to the de.NBI network, state-of-the-art services, de.NBI Cloud, benefits of training, deciphering soil metagenome data, microscopy image analysis or differential gene expression to investigation of crop plants. It's worth a read!If you are interested in sharing your experience or describing your tools, please write an email to Johanna ( |
|
Recent updates of services:
|
|
|
|
| The next de.NBI training events are announced on www.denbi.de/training.
Upcoming scheduled events:
|
Impressum |
|
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
If you are interested in receiving regular updates on de.NBI - German Network of Bioinformatics Infrastructure, please subscribe to the de.NBI Quarterly Newsletter here. The mailing list will exclusively be used to distribute the de.NBI Quarterly Newsletter.
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. |
de.NBI Summer School 2023 from 25-29 September 2023
News on the de.NBI Cloud
News on ELIXIR DE
News on Services
Upcoming Events
- 2023-07-11
The Leibniz Institute of Plant Biochemistry (IPB) is located on the Weinberg campus of the Martin-Luther-University Halle-Wittenberg, Germany.
Germany is establishing a long-term national initiative for research data (NFDI) as a dynamic network of services for research data management. The IPB is part of the NFDI4Chem consortium that will support standards-conforming acquisition, storage, analysis and publication of research data in many disciplines in Chemistry.
The Computational Plant Biochemistry research group at the IPB is seeking applications as
Researcher (PostDoc Cheminformatics) (m/f/d)
starting immediately, initially limited until 30.09.2025.
Job description:
The NFDI4Chem consortium is developing standards for research data in chemistry and supporting software and infrastructure. As a computer scientist, cheminformatician or bioinformatician, you will join our research group Computational Plant Biochemistry. As task area leads in NFDI4Chem we take care that research data ("the gold of the 21st century") can be collected in a structured way, processed/analysed and published for efficient re-use. You will develop re-useable workflows to process and transfer e.g. mass spectrometry data to electronic laboratory notebooks or repositories, and to re-analyse public data.
You should hold a degree in computer science, cheminformatics, bioinformatics or a related discipline, with experience in database development, use and development of open source cheminformatics software (e.g., RDKit, CDK, OpenBabel) in several programming environments (e.g., Go, Java, Python, R). Knowledge in mass spectrometry or analytical chemistry are advantageous.
The position is initially limited until 30.09.2025. Salary and social benefits are according to the German Public Service regulation (TV-L E13, 100%).
Further information is available on our web page (http://www.ipb-halle.de) under „Career“. For specific questions regarding this offer, please contact Dr. S. Neumann (
Please notice our data protection information for applicants (m/f/d) according to Article 13 and 14 GDPR concerning data protection processing in the application process:
https://www.ipb-halle.de/en/career/data-protection-information-for-applicants/
The successful applicant with a degree that was not obtained at a German university must submit a certificate assessment for foreign university qualifications (Statement of Comparability for Foreign Higher Education Qualifications) from the Central Office for Foreign Education (https://www.kmk.org/zab/central-office-for-foreign-education).
Please submit your complete application including a cover letter clearly stating the interest in the project and the group, CV, contact details for two referees and transcripts as a single PDF document quoting reference number 10/2023 until August 7th 2023 to
- 2023-06-20
The Institute of Clinical Molecular Biology (IKMB) offers 1 position for a scientist/postdoc in bioinformatics(Biologist, informatician, bioinformatician or similar)
With more than 70 clinics and institutes, the University Medical Center Schleswig-Holstein is one of the largest university hospitals in Europe. It offers outstanding medical treatment and excellence in research and education with nearly 10,000 employees. We provide top research conditions at the interface of medicine, science and technology and maintain research co-operations with universities all over the world.
The Medical Faculty together with the Institute of Clinical Molecular Biology at Kiel University are in the process of establishing a dedicated bioinformatics core facility. This new resource will complement existing local infrastructures, such as a national NGS core facility (“CCGA”), the biobank “Popgen” as well as the recently launched clinical data integration centre “MeDIC”. A primary goal of the platform will be the implementation of best-practices workflows for a range of bioinformatic applications, development of compute and data management infrastructures for clinical “omics” data as well as to provide data analysis support/training to interested researchers in Kiel and elsewhere.
Start in Our Team
We are thus looking for a talented bioinformatician to join our new team and help develop this platform into an integral part of our research landscape.
What we offer:
- The University aims to increase the number of women among faculty staff and therefore explicitly encourages the application of female scientists.
- The contract will be issued for 3 years with the prospect of continuation.
- The salary will be based on the German E 13 TV-L scale if terms and conditions under collective bargaining law are fulfilled.
- Full-time employment, currently 38.5 hours/ week. Part-time employment may be compatible within the framework of certain working time models.
- You are welcome to inform yourself about our benefits under https://www.uksh.de/jobs/Benefits
This awaits you:
- Responsible for the development of bioinformatic pipelines and tools, as well as support research groups with their analytical needs.
- Work with related infrastructures on establishing a campus-wide concept for the standardization and management of omics data.
- The position will be hosted at the Institute of Clinical Molecular Biology (IKMB), which operates one of the four national German DFG-funded sequencing centres and is embedded in multiple high-profile research efforts, including the two DFG Excellence Clusters “Precision Medicine in Chronic Inflammation (PMI) and ROOTS.
- Through this stimulating working environment, the candidate will have an opportunity to interact with colleagues both nationally (e.g., through our membership in the German Network for Bioinformatics, de.NBI) and internationally working on diverse bioinformatic challenges, including clinical diagnostics, genome-wide associations studies and complex data integration as well as related software/infrastructure, to further improve her/his professional profile in these areas.
Your qualifications and skills:
- Strong command of one or several programming languages (Perl, Python, Ruby, etc.) as well as good knowledge of NGS data analysis tools and workflows (e.g., Nextflow) are thus essential prerequisites.
- Skills in the use and development of database applications, web applications, machine learning techniques and data management will be beneficial. Very good knowledge of the English language, both written and orally, is expected.
Contact:
For questions about the position, please contact Prof. Mathieu Groussin and Prof. Andre Franke of the IKMB at
We look forward to receiving your application by 16.07.2023. Please quote the job reference number 21840 in your application.
Disabled candidates who are equally qualified will receive preference.
- 2023-06-02
Educators:
Martin Lang, Martin Braun (HD-HuB)
Date:
23.06.2023 1-5pm
Location:
online
Content:
OpenStack is the underlying infrastructure of the de.NBI Cloud. Participants of this EOSC-Life workshop will learn how to start one or multiple virtual machines by using a graphical interface or via an API and get familiar with basic principles how-to use OpenStack for their projects e.g. assign floating IPs, mount volumes, setup security groups, etc. Learning goals: Get familiar with working with an OpenStack cloud environment.
Prerequisites:
basic terminal knowledge, Linux/OSX Terminal or Windows 10 PowerShell, Browser
Keywords:
Cloud Computing, Linux, de.NBI Cloud
Tools:
Bash, Powershell
Contact:
Registration:
https://www.surveymonkey.de/r/MG2H2T2
- 2023-05-15
| Issue 02/2023 | ||||||||||||||||||
|
||||||||||||||||||
| The Research Data Management (RDM) Trainer Community Meeting entitled “Fellowship of the data” will take place on-site in Berlin, Germany, 21-22 June 2023! This RDM Trainer Community Meeting is organized by de.NBI/ELIXIR DE in the framework of ELIXIR-CONVERGE and the Sub-Working Group Training/Further Education of the DINI/nestor WG Research Data. We invite and encourage everyone interested in research data management and training to join us. Get to know and let’s grow the RDM trainer community! The workshop includes networking opportunities, poster sessions, and keynotes by Rabea Müller (The Carpentries) and Sarah Jones (GÉANT/EOSC), who will shed light on recent developments in the RDM community. Our focal topics also include training materials, implementation, and gamification. Registration is open until 14 June 2023 and the event is free of charge. Please feel free to share this invitation with anyone interested. Find the agenda and the registration link here. We would be delighted to see you there! |
||||||||||||||||||
New de.NBI Blog |
||||||||||||||||||
| On 3 May 2023, we have launched the new format de.NBI Blog. After two weeks of launch where we introduce de.NBI and our subdomains, blog entries will be published bi-weekly. With the de.NBI Blog, we want to intensify direct communication with early career scientists. We aim to promote our services, training courses, and other activities to reach greater visibility. Researchers will have the opportunity to communicate their research or bioinformatic tools and demonstrate how de.NBI state-of-the-art services can be used to answer scientific questions. We kindly invite all members to contribute to the blog. If you are interested in contributing, please write an email to Johanna ( |
||||||||||||||||||
|
||||||||||||||||||
 de.NBI will continue its successful summer school training program with the de.NBI Summer School on Bio Data Analysis for Life Sciences in Bielefeld from 25-29 September 2023. It is organized by the CAU and Team ELIXIR Officers. The life sciences are an important player in the age of Big Data. Modern high-throughput omics technologies produce large quantities of high-dimensional data. Besides new challenges for analysing and visualising this amount of research data, also the management and sharing has become an important point in the daily research process. The main objective of the 2023 de.NBI Summer School is to give an overview of the possibilities to process, analyse, share, and integrate data by using different open source platforms. Application will open on 17 May. |
||||||||||||||||||
|
||||||||||||||||||
|
||||||||||||||||||
|
||||||||||||||||||
| ELIXIR DE and ELIXIR ES, as leading nodes, are pleased to announce a new strategic implementation study entitled ELIXIR LEadership And Diversity mentoring program, starting on 1 June 2023. ELEAD aims to increase the number of women in ELIXIR’s middle management and to support them to develop leadership skills in line with the values of the ELIXIR community. The program consists of a mentoring schema that pairs middle management mentees with senior mentors from ELIXIR and its extended network in combination with professional training events and guidance in key leadership skills. This strategic implementation study is used as a “pilot” project. The experience and results obtained should provide valuable input for the continuation of ELEAD in the upcoming ELIXIR 2024-2028 program. |
||||||||||||||||||
|
||||||||||||||||||
 Soon, ELIXIR's most important event of the year, ELIXIR All Hands 2023, will open its doors. This year's ELIXIR All Hands meeting will take place from 5-8 June in Dublin and bring together members of the community from across all ELIXIR Nodes. ELIXIR Germany contributes to the organization and presentation of several symposia, workshops, and posters shown here at a glance. Don't miss the opportunity to meet us in Dublin!
Mini-Symposia:
Workshops:
Posters:
Additional posters from the German plant community
|
||||||||||||||||||
|
||||||||||||||||||
|
 We are also delighted to welcome Leonid Kostrykin to the Team ELIXIR Officers based at Heidelberg University. Leonid received his PhD in computer science from University in 2022 within the group Biomedical Computer Vision. Currently, he is working in the field of image analysis with a focus on developing new globally optimal methods for biomedical applications. As the ELIXIR Officer of the Heidelberg Center for Human Bioinformatics (HD-HuB), his mission is to bring modern image analysis methods to Bioconda and the Galaxy platform, making them accessible to the life sciences. |
||||||||||||||||||
|
||||||||||||||||||
|
|
||||||||||||||||||
2nd Plant Bioinformatics Community Meeting |
||||||||||||||||||
 2nd Plant Bioinformatics Community Meeting was held on 22 March 2023 in Potsdam as a satellite event to the annual meeting of the BMBF-funded plant research projects PLANT 2030. The meeting was organized by the GCBN Service Center of de.NBI and had 15 participants. The attendees were introduced to the goals of de.NBI and ELIXIR in general, as well as to services and training provided to plant researchers in particular. Additionally, there was a general introduction to the National Research Data Infrastructure NFDI, as well as presentations from the NFDI consortia related to plant research: DataPLANT, FAIRagro and NFDI4Biodiversity. |
||||||||||||||||||
|
||||||||||||||||||
| The de.NBI/ELIXIR DE Hackathon for Data Management Plan (DMP) is going into the next round. During the first hackathon in March 2022, a group of 20 specialists from 11 countries generated training material on the topic DMP. This material has already been successfully used in various workshops (GCB 2022, ECCB 2022 and de.NBI Spring School 2023). The units are available upon request at The 2nd de.NBI/ELIXIR-DE Hackathon for DMP training material took place on 9 May 2023 within the framework of the ELIXIR-CONVERGE project funded by the European Commission to help standardise life science data management across Europe. To achieve this standardisation, Europe’s data management capacity will be strengthened through a comprehensive training programme developed by CONVERGE WP2. The DMP hackathons aim to support this goal by developing new training material for DMP courses, examining gaps and updating existing training material of DMP courses. This workshop aimed at data managers, data stewards, and everyone interested in data management in Germany, ELIXIR and beyond. |
||||||||||||||||||
de.NBI/ELIXIR DE at the German Biotechnology Days 2023 review |
||||||||||||||||||
| The de.NBI administration office (AO) represented the networks de.NBI and ELIXIR as well as the de.NBI Industrial Forum with an information booth at the German Biotechnology Days 2023 in Wiesbaden on 28-29 March. The conference offered the opportunity for the de.NBI AO to get in touch with emerging trends in biotechnology, discussions about data handling in academia and industry as well as connecting to industrial and academic partners. The German Biotechnology Days (DBT) 2023 in Wiesbaden, held by BIO Deutschland e.V., established a national forum for the exchange and communication of industrial, political, entrepreneurial and academic stakeholders. The conference was attended by close to 750 participants discussing current topics in biotechnology ranging from digitalization, application of artificial intelligence, skilled shortages, from innovation to application, start-ups, the effect of the climate crisis and many more. Find more information on the de.NBI profile in the “Exhibition” of the German Biotechnology Days 2023 here. |
||||||||||||||||||
|
||||||||||||||||||
Recent updates of services:
|
||||||||||||||||||
|
||||||||||||||||||
|
||||||||||||||||||
|
||||||||||||||||||
|
The next de.NBI training events are announced on www.denbi.de/training. Next scheduled events:
|
||||||||||||||||||
Impressum |
||||||||||||||||||
|
Responsible for Contents
A. Tauch, T. Dammann-Kalinowski
de.NBI - German Network for Bioinformatics Infrastructure c/o 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
If you are interested in receiving regular updates on de.NBI - German Network of Bioinformatics Infrastructure, please subscribe to the de.NBI Quarterly Newsletter here. The mailing list will exclusively be used to distribute the de.NBI Quarterly Newsletter.
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. |
We welcome Sebastian Schaaf, who started his position as ELIXIR DE Officer on February 1st, 2023. Sebastian comes with a background in molecular biology and bioinformatics with focus on sequencing data analysis and scientific IT infrastructures. With research projects in image analysis, data management and semantics, he can draw on broad experiences covering multiple fields in and around computational biology. He has built and developed a private Galaxy instance in the medical field for several years. After activities in information extraction (text mining) and integration (data model design), Sebastian now returns to Galaxy. As a member of the Freiburg Galaxy team (usegalaxy.eu), he is committed to optimizing interactions and infrastructures in research and is looking forward to bringing together given and future resources in the frames of ELIXIR, EOSC and Galaxy.
The 
- 2023-05-04
In this article, I will first outline the events that led to the establishment of the German Network for Bioinformatics Infrastructure (de.NBI). The establishment of the de.NBI network was made possible through a project of the German Federal Ministry of Education and Research (BMBF), which envisioned several task areas for the network. I will present in detail the task areas that are most important for the bioinformatics infrastructure, such as service, training, cloud computation, international collaboration, and industrial connection, and the successes achieved through these tasks. Finally, I will briefly describe the process that enabled the de.NBI network to be sustained.
The history of the de.NBI network
The development of the German Network for Bioinformatics Infrastructure was initiated by the Bioeconomy Council in 2012. As an independent advisory body to the German government, the Bioeconomy Council deals with recommendations for action to implement the national bioeconomy strategy. The question of whether the bioinformatics established in Germany sufficiently meets the requirements of academia and industry was investigated. This question was discussed within the Bioeconomy Council using the established methods, i.e. a workshop was held on the question raised and its results were written down in a recommendation. Since I was a member of the Bioeconomy Council at that time and had great interest in a powerful bioinformatics input, I agreed to coordinate the workshop and the subsequent statement.
During the preparation of the workshop, it became apparent that in Germany bioinformatics was available to a sufficient extent, but there was a relatively large gap when it came to satisfactory application in the life sciences. The real question to be addressed by a bioeconomy workshop was therefore how to build a bioinformatics infrastructure. The workshop had to consider two possible solutions. One solution path was to establish a new national institute for bioinformatics infrastructure, while the second solution path relied on a network construct. The second solution was chosen because it allowed the establishment of a bioinformatics infrastructure without delay. The basic building blocks of the network, namely potent bioinformatics groups, were sufficiently available and only needed to be networked.
The Bioeconomy Council's statement entitled "Requirements for a Bioinformatics Infrastructure in Germany to Conduct Bioeconomy-Relevant Research" was convincing and the plan to establish a German Network for Bioinformatics Infrastructure was immediately included in the funding catalog of the BMBF. A BMBF project entitled "German Network for Bioinformatics Infrastructure - de.NBI" was announced, which gave all bioinformatics groups located in Germany the opportunity to participate in the establishment of the network. This network to be established was intended to enable experimental life scientists to analyze larger amounts of data. The approach of the BMBF to establish a network for bioinformatics infrastructure by means of a project proved to be a success story from the very beginning. The most powerful of the bioinformatics groups based in Germany participated in the project, which was announced by the BMBF. The establishment of the de.NBI network could thus be started at a high level.
Development, structure and scope of the de.NBI network
As can be seen in Fig. 1, the selection of network partners took place in two stages. After an initial selection of network partners in 2014, a further selection of so-called partner projects was made in 2016. A total of 40 partners were accepted into the de.NBI network and assigned to eight service centers. The distribution of the service centers in Germany and their thematic classification is shown in Fig. 2. The de.NBI network was to be managed by a coordinator with an administration office. Since I signaled that I would be available for such a coordinator role, I was appointed to this position by the BMBF. I carried out the tasks of the de.NBI coordinator from 2015 until the BMBF project ended in December 2021.
Fig. 1: The timeline of the development of the de.NBI network.
Fig. 2: de.NBI service centers in Germany. The lines point to the locations of the eight service centers (large circles). The smaller dots in the same color mark the partners of the respective service center. The location of the administration office is marked by a square.
The various task areas of the de.NBI network are shown in Fig. 3. Service and training represent the basic tasks. In the service area, the various analysis programs for the evaluation of life science data are provided. In the training area, training courses are offered to teach users how to use the analysis programs and how to handle the results obtained.
Fig. 3: The task areas of the de.NBI network
International cooperation with established bioinformatics infrastructures, especially in Europe, is mentioned as a further task of the de.NBI network. This task could be fulfilled by the participation of Germany in the European ELIXIR network. ELIXIR bundles the nationally existing bioinformatics infrastructures in Europe. A contract was made between Germany and ELIXIR in 2016, which regulates the rights and obligations of the German ELIXIR node. The German ELIXIR node is based on the bioinformatics infrastructure implemented by the de.NBI network.
Another task of the de.NBI network is dedicated to the establishment of an adequate compute structure. In 2017 (Fig. 1), the federated de.NBI cloud consisting of initially five sites was launched for this purpose, enabling all researchers from the life sciences to analyze their research data free of charge. To use the de.NBI-Cloud, a simple application is required. Such an application is usually reviewed within a week and the requested computing and storage capacities are allocated. In the meantime, the de.NBI Cloud has become the largest academic cloud in Germany.
Collaboration between industrial companies and the de.NBI network is mediated by the de.NBI Industrial Forum. The Industrial Forum currently consists of more than 35 member companies, all of which work with life science data. Forum members have access to the achievements of the de.NBI network, e.g. they can preferentially participate in training events.
The last item to be mentioned in the de.NBI network's task areas is public relations. First and foremost, the de.NBI website (www.denbi.de) provides information about all events and activitites of the de.NBI network. The public is also informed via Twitter and LinkedIN. The de.NBI Quarterly Newsletter should also be mentioned, which summarizes the current events in a quarterly interval and thus describes the processes in the de.NBI network chronologically.
The successes of the de.NBI network
The presentation of the de.NBI network by means of its task areas facilitates the recognition of de.NBI successes. In the task area of structure and management, the de.NBI coordinator together with the de.NBI administration office succeeded in establishing a well-structured network. The establishment of a de.NBI steering group, in which one representative from each of the eight service centers and the coordinator had a seat, was helpful in this regard. This de.NBI steering committee, which met quarterly, decided on all issues related to the development and progress of the de.NBI network.
A total of about 150 software programs for the analysis of life science data are kept in the service area. These software programs are provided by groups that originally also carried out their development. The software programs offered are the basis for the training area.
The training area offers training courses that focus on the handling of the above-mentioned software programs. Furthermore, the handling of analysis results is also taught. In the training area, approx. 400 training courses have been carried out so far and more than 9,000 researchers from the life sciences have been trained.
The establishment of the de.NBI Cloud has proven to be a flagship for the de.NBI network. The free-of-charge analysis of life science data has been used by a large number of researchers. As a result, there are currently over 700 de.NBI Cloud projects with more than 2,200 registered users.
International cooperation has steadily expanded since 2016. Through ELIXIR membership, joint projects concerning bioinformatics infrastructure - in many cases EU projects - are carried out with numerous national ELIXIR nodes. The German ELIXIR node has also contributed significantly to various ELIXIR committees.
The industry connection is regulated via the de.NBI Industrial Forum. In this task area, the success can be seen by the annual meetings. At the annual meetings with an average of 50 participants, contemporary topics such as COVID 19, artificial intelligence and digital health have been addressed from an academic and industrial perspective.
The successes of the de.NBI network show that the existing network has a high value for a bioinformatics infrastructure, which is currently highly requested and also contains an enormous potential for development in the future.
The continuation of the de.NBI network
BMBF projects are always approved for a certain period of time only. BMBF projects usually address future-oriented research questions, which are then taken over by other research organizations after the project has expired. The de.NBI project was initially granted a period of five years to implement its objectives. This period was sufficient to establish the desired bioinformatics infrastructure in Germany (Fig. 4). A bridging phase of another two years was then granted to find a reasonable continuation solution. The question of a continuation solution for the de.NBI network proved to be difficult. In Germany, the existing research institutions are not suitable for taking over network structures. Only the involvement of the political level led to a solution. After discussing the question of sustainability with members of the Bundestag, they presented a solution. The bioinformatics infrastructure was transferred to the Helmholtz Association and located at the Jülich Research Center. The funding required for the continuation was provided by the federal government and the state of North Rhine-Westphalia. Since the takeover in 2022, Forschungszentrum Jülich has been working to integrate the de.NBI network into the existing research structure in a Jülich-compliant manner. Furthermore, a consortium agreement is to be adopted that focuses on the rights and obligations of the participating institutions. Such a consortium agreement is also necessary to fulfill the contractual obligations with ELIXIR.
Now that the de.NBI network has been made permanent, all the conditions are in place for analyzing the large volumes of data generated in the life sciences. However, the success story of the de.NBI network is far from being completed. The future will show how the established bioinformatics infrastructure will contribute to the development of biotechnology, agriculture and medicine.
Fig. 4: The members of the de.NBI network at its plenary meeting in Berlin in 2020.
- 2023-04-20
Founded in 1607, Justus Liebig University Giessen (JLU) is a research university rich in tradition. Inspired by curiosity about the unknown, we enable around 26,500 students and 5,700 employees to advance science for society. Join us in breaking new ground and writing success stories - your own and those of our university.
Support us as soon as possible in full-time as a
Junior group leader (m/f/d) in the field of bionformatics
focussing on microbial post-genome data analysis
As part of the budget for innovation and structural development by the Hessian Ministry for Science and the Arts, the position is to be filled on a fixed-term basis in accordance with § 2 WissZeitVG and § 72 HessHG with the opportunity for own academic qualification at the Chair of Systems Biology, Department of Biology and Chemistry at the Faculty 08 with the opportunity for own academic qualification. The salary is in accordance with the collective labour agreement of the State of Hessen (E 14 TV-H).
As long as the maximum permissible duration of a fixed-term contract is not exceeded, you will be employed until December 31, 2027.
The junior research group leadership position is part of the Campus+ network at the Research Campus of Central Hessen (FCMH) and promotes the development of new inter-institutional and interdisciplinary collaborations between the universities in Central Hessen and the four non-university research institutions of the region. FCMH combines three strong partners: the two traditional full universities Justus Liebig University Giessen and Philipps University Marburg as well as the Technical University of Central Hesse, which is strongly influenced by engineering sciences. With over 8,000 active researchers and 200 large-scale and specialized research facilities, we offer a network and infrastructures that are otherwise only possible in metropolitan regions. We create cross-university structures and experimental spaces and connect application- and basic-oriented researchers across the entire spectrum of subjects. In this way, we support you in building powerful networks, courageously tackling the big questions of our time and developing your career in a targeted manner.
Our aim is to promote an early-career researcher in the field of microbial bioinformatics in an excellent and highly collaborative research environment and give this young person the chance to develop new subjects and establish his or her own fields of research. We are seeking for a scientist whose bioinformatics approaches, further strengthens and complements our scientific expertise in molecular, synthetic or environmental microbiology at the Justus Liebig University and the Max Planck Institute for Terrestrial Microbiology in Marburg.
Your tasks at a glance
- Development, management and organization of an internationally visible working group in the field of microbial bioinformatics, particularly focusing on the interaction of microorganisms with their environment as well as synthetic microbiology
- Independent scientific work and leadership of a junior research group
- Collaboration with the Core Facilities of the Max Planck Institute for Terrestrial Microbiology in the field of microbial proteomics, metabolomics, as well as the MaxGENESYS Biofoundry
- Supervision of PhD, master and bachelor students as well as student assistants
- Conduction of complex research activities, especially integration of proteomic, metabolomic and other post-genomic data in the microbial research field
- Development and support of sophisticated analysis and evaluation pipelines for standardized high-throughput analysis of post-genomic data
- Independent application, execution and documentation (publication) of research projects and results in the above-mentioned research area
- Acquisition of third-party funds
- Networking and cooperation within the Research Campus of Central Hessen (FCMH), especially in cross-location research projects
- Participation in teaching (e.g. in the M.Sc. Bioinformatics & Systems Biology program)
The provision of academic services (including the processing of a research project financed by third party funds on a temporary basis) also serves the purpose of academic qualification.
Your qualifications and competences
- Candidates are expected to have a scientific university degree and a PhD in bioinformatics or a comparable field (excellent bioinformatics skills are mandatory)
- Broad and sound methodological training, especially in the field of microbial proteomics and metabolomics, extensive experience in the use and development of bioinformatics and statistical methods in this research area
- Proven and extensive knowledge as well as experience in the field of high-throughput data analysis, e.g. in the development of automated workflows
- Proven expertise in bioinformatics software and methods development
- Practical experience and in-depth knowledge in the application of modern machine learning methods, knowledge in the field of deep learning including the use of artificial intelligence methods is desirable
- Ability to work independently and solution-oriented, strong team skills, as well as high competence in comprehensible and structured documentation of the respective processes and procedures
- Strong ability for scientific theory building and appropriate presentation of complex data in the field of microbial bioinformatics
- High willingness to learn new technologies independently and to strengthen own profile
- Active participation in national and international projects of the Research Campus of Central Hessen and collaboration with other academic cooperation partners
- The ability to raise own third-party funding projects is expected
- Fluency in English and German is required
- Proven track record in producing scientific publications in the field of microbial bioinformatics
- Initiative, creativity, team spirit are also required
Our offer to you
- A varied job with flexible working hours
- Personal and individual mentoring offers from leading scientist
- More than 100 training seminars, workshops and e-learning opportunities per year for personal development, as well as a wide range of health and sports activities
- Good compatibility of family and career (certificate "audit familiengerechte hochschule")
- Remuneration according to TV-H, company pension scheme, child allowance and special payments
- Free use of local public transport (LandesTicket Hessen)
If you have any further questions, please do not hesitate to contact Prof. Dr. Alexander Goesmann by e-mail (
JLU aims to employ more women in academic research. We therefore particularly encourage female candidates to apply. JLU is regarded as a family-friendly university. Applicants with children are very welcome. Applications from disabled people of equal aptitude will be given preference.
You want to break new ground with us?
Apply via our online form by May 19th, 2023, indicating reference number 250/08. Please attach to your application a letter of motivation (maximum 2 pages), your curriculum vitae, a list of your publications, a summary of your scientific achievements and future research interests (maximum 2 pages) as well as three potential references, as a single PDF file. We look forward to receiving your application.
- 2023-04-06
Are you a Systems developer with a wish to be part of building lifelong learning in technology- and data-driven life science in Sweden? Then please continue reading! SciLifeLab Data Centre will collaboratively with the SciLifeLab Training Hub build the technical infrastructure needed for the lifelong learning initiative from SciLifeLab as a national Research Infrastructure to be a reality.
One of the advertised three positions as a Systems Developer will be dedicated to focus on establishing the necessary technical solutions for educational purposes. The role will be high in creativity and we would like to be innovative in terms of technical resources and services to be provided to the life science community in order to support their lifelong learning trajectory.
So if you are a Systems developer (or if you know of someone) interested to make a mark on educational technology, if you like to learn beyond your own trait and if you like to thrive in a team science environment do apply to the position. Add emphasis on the interest to contribute to training and technical educational development if this is your cup of tea. We at the Training Hub look forward to meeting you and to begin the journey of establishing the educational technical infrastructure together. Deadline is 28th of April 2023.
For information see: https://lnkd.in/dAZz6xSs
- 2023-03-15
Interdisciplinary research at the IPB, a non-university research institution of the Leibniz Association at the Weinberg Campus of the Martin Luther University Halle-Wittenberg, aims to understand the bio/chemical basis of plant resilience and performance in climate change. The IPB offers excellent research facilities and state-of-the-art infrastructure to investigate the chemical diversity, biochemical interactions, and biological roles of plant and fungal natural products, with an emphasis on specialized metabolites, signaling molecules and relevant molecular networks of functional gene and protein regulation (http://www.ipb-halle.de).
To strengthen its collaborative research activities, the IPB will receive additional core funding for the establishment of a Program Center for Plant Metabolomics and Computational Biochemistry (MetaCom), which will consist of four working units: (i) Metabolomics & Proteomics Technology Platform, (ii) Chemical-analytical Reference Laboratory, (iii) Computational Plant Biochemistry Research Group, and (iv) Independent Junior Research Group.
The Bioinformatics and Scientific Data research group at the IPB is seeking applications to fill the position as
Research associate (computational metabolomics, m/f/d)
initially for three years, starting immediately.
Job description:
As a (bio-) informatician, you will join our research group Bioinformatics and Scientific Data, which focuses on "Computational Metabolomics" and develops methods for processing and interpreting mass spectrometry data in the context of plant biochemistry and biodiversity research. You will develop and evaluate methods for the characterization and identification of metabolites and extraction of statistical relationships and patterns in metabolomics experiments. You will be involved in various projects that bring together different experts and research questions.
You should hold a university degree (master) in bioinformatics or computer science, with experience in algorithm and software engineering and statistics. You are able to program in the statistics framework R, and have worked in Python and Java. Knowledge in metabolomics or chemistry will be an advantage. The position is available for PhD candidates or as a PostDoc position.
Salary and social benefits are according to the German Public Service regulation (TV-L).
Please notice our data protection information for applicants (m/f/d) according to Article 13 and 14 GDPR concerning data protection processing in the application process:
https://www.ipb-halle.de/en/career/data-protection-information-for-applicants/
The successful applicant with a degree that was not obtained at a German university must submit a certificate assessment for foreign university qualifications (Statement of Comparability for Foreign Higher Education Qualifications) from the Central Office for Foreign Education (https://www.kmk.org/zab/central-office-for-foreign-education).
Please submit your complete application including a cover letter clearly stating the interest in the project and the group, CV, contact details for two referees and transcripts as a single pdf document quoting reference number 3/2023 until June 15th 2023 to
For further information please contact Dr. S. Neumann (
Tel.: +49 (0) 345 5582-1470, Fax: +49 (0) 345 5582-1409
- 2023-03-10
The Department Biomedical Informatics, Data Mining and Data Analytics, Prof Dr Matthias Schlesner, at the faculty of Applied Informatics, Augsburg University is offering a position in Biomedical Informatics.
Akademische Rätin/Akademischen Rat auf Zeit (m/w/d)
(BesGr. A 13)
oder für eine/einen
Wissenschaftliche Mitarbeiterin/Wissenschaftlichen Mitarbeiter (m/w/d)
(Entgeltgruppe 13 TV-L)
im Bereich der Medizinischen Bioinformatik
Find more information here:
- 2023-02-28
| Issue 01/2023 | |||||||||||||||
|
|||||||||||||||
 The de.NBI Spring School 2023 - Data Management will take place 13-17 March at the IPK Gatersleben. The training event is jointly organized by the Service Centers BioData, BiGi, GCBN and de.NBI-SysBio as well as by the de.NBI/ELIXIR DE Administration Office. Out of numerous applications 28 candidates have been selected and invited to Gatersleben. The goal of this de.NBI Spring School is to raise awareness for the importance of proper research data management (RDM) in general, but also to provide a practical toolbox for the RDM topics data management planning, FAIR data and reproducibility. Furthermore, a practical training on accessing the data for re-use and integration are part of the learning goals. The detailed program is available here. |
|||||||||||||||
|
|||||||||||||||
|
|||||||||||||||
|
|||||||||||||||
|
The de.NBI/ELIXIR DE training coordinators Daniel Wibberg and Helena Schnitzer lead the Task 6.1. Training. This task will have two main activities with the focus to train and upskill the community: 1) Designing a training collection, agnostic to the use cases, that will address users´ needs while simultaneously facilitating training delivery to stakeholders external to the project. PHENET partners will be invited to take part in the training design process (through hackathons) and co-delivery of workshops, etc. will be offered. 2) Establishing a plant phenotyping train-the-trainer community, using PHENET as the core, and expanding to engage all relevant stakeholders (initiatives, RIs, organizations, efforts). Eventually, this community will be in charge of maintaining and updating the training material to encompass future efforts/services. The Task 6.1 will deliver four Train-the-Trainer courses across the PHENET community. The kick-off meeting took place in Montpellier (FR) on 21-23 February 2023. |
|||||||||||||||
|
|||||||||||||||
|
ELIXIR Germany is deeply involved in ELIXIR Commissioned Services, which are technical projects that guide future service development, drive standards adoption, and connect ELIXIR Nodes. In 2023, ELIXIR Germany will participate in 20 Implementation Studies (IS) by sharing their knowledge to expand Europe's bioinformatics infrastructure further. Among this list are two new community efforts that started this year, namely the Single-Cell Omics Network for ELIXIR (SCONE) study with participation of Naveed Ishaque (Charité Berlin) and the Systems Biology for ELIXIR (SYBEL) study involving Ulrike Wittig (Heidelberg Institute for Theoretical Studies). Furthermore, a strategic implementation study from the ELIXIR Machine Learning Focus Group entitled "A framework to standardize Machine Learning in Life Sciences" with Nils Hoffmann (ELIXIR DE, Forschungszentrum Jülich) representing the German node was also launched in 2023. As the German node, we are proud to be involved in such a number of ELIXIR Commissioned Services and contribute to developing bioinformatics services alongside our European partners. Find the full list of IS with German participation here. |
|||||||||||||||
|
|||||||||||||||
The Global Biodata Coalition (GBC) defines Global Core Biodata Resources representing biodata resources that are of fundamental importance to the wider biological and life sciences community. The GBC aims to ensure sustainable financial support and thus long-term preservation of biological data. Following this strategy, a current list of Global Core Biodata Resources that are crucial for sustaining the broader biodata infrastructure has been identified and published in December 2022. We are more than proud that the de.NBI databases BRENDA and BacDive have been selected in the first set of 37 Global Core Biodata Resources! BRENDA is also an ELIXIR Core Data Resource. |
|||||||||||||||
|
|||||||||||||||
|
In the last edition of the de.NBI Quaterly Newsletter the launch of a new interview series with female data scientists in academia and industry has been announced. In the meantime we have published three new interviews. Find the carreer portraits of Bérence Batut (ELIXIR DE), Katya Nevedomskaya (Bayer), Christina Taylor (Bayer AG) and Eva Alloza (ELIXIR ES) here. Thank you for sharing your stories and experiences. More contributions will follow. |
|||||||||||||||
|
|||||||||||||||
The 1st BioHackathon Germany hosted by de.NBI/ELIXIR DE took place at the Leucorea in Lutherstadt Wittenberg, Germany, from 12-16 December 2022. In this hybrid event 11 hacking projects were carried out with all in all 150 participants, 72 of them on-site. The SpaceHack project — Establishing best practice guidelines for imaging-based spatially resolved transcriptomics data led by Naveed Ishaque (Berlin Institute of Health at the Charité) and Louis Kümmerle (Helmholtz Center Munich) had over 60 active hackers with 30 present at the venue. Several projects made use of de.NBI Cloud resources which was highly appreciated. Find summaries of the SpaceHack project and the Bioshemas4NFDI project led by Steffen Neumann (IPB Halle) and Leyla-Jael Garcia Castro (ZB MED, Cologne) online. The 5-day event was accompanied by a visit to the cosy Wittenberg Christmas market, a guided city tour to historical places of the reformation period, and a party with DJ Tinitus on the last evening giving time for lots of networking. |
|||||||||||||||
de.NBI/ELIXIR DE at the CLIB International Conference 2023 |
|||||||||||||||
|
de.NBI / ELIXIR Germany showcased the de.NBI network, the de.NBI Industrial Forum, and the ELIXIR DE network at the CLIB International Conference 2023, CIC 2023, held in Düsseldorf on 14-15 February. CLIB is the “Cluster Industrielle Biotechnologie” in North Rhine Westphalia. On the first day, the conference focused on “Setting sail for industrial implementation”. Stakeholders from academia and industry discussed how biotechnological ideas and innovations could make use of sustainable resources and be upscaled in industrial implementations. The second day of the conference was revolving around “zero-waste biorefinery concepts”. |
|||||||||||||||
|
|||||||||||||||
| The annual meeting of the de.NBI Industrial Forum with focus on Digital Health took place 24 November 2022. Altogether, more than 50 participants joined the presentations by national and international institutions such as ELIXIR, Berlin Institute of Health (BIH), and EMBL Heidelberg. But also companies from the de.NBI Industrial Forum, Merantix Momentum, Information Technology for Translational Medicine (ITTM), and the Nebion AG – an Immunai Company showcased their activities in the field. The general discussion with selected speakers at the end of the meeting was targeted to the question, which parts of the digital health field are suited for industrial use. Once more, we would like to thank speakers and attendees their contributions and a fruitful discussion.
Find the complete agenda and abstracts here. |
|||||||||||||||
|
|||||||||||||||
|
New de.NBI service:
|
|||||||||||||||
|
|||||||||||||||
|
|||||||||||||||
|
|||||||||||||||
|
The next de.NBI training events are announced on www.denbi.de/training. Next scheduled events:
|
|||||||||||||||
Impressum |
|||||||||||||||
|
Responsible for Contents
A. Tauch, T. Dammann-Kalinowski
de.NBI - German Network for Bioinformatics Infrastructure c/o 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
If you are interested in receiving regular updates on de.NBI - German Network of Bioinformatics Infrastructure, please subscribe to the de.NBI Quarterly Newsletter here. The mailing list will exclusively be used to distribute the de.NBI Quarterly Newsletter.
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. |
The EU project "PHENET — Tools and methods for extended plant PHENotyping and EnviroTyping services of European Research Infrastructures" started 1 January 2023. In this 5-year project, the European Research Infrastructures (RI) on plant phenotyping (EMPHASIS), ecosystems experimentation (AnaEE), long-term observation (eLTER) and data management and bioinformatics (ELIXIR) will join their forces with a diversity of innovative companies to co-develop new tools and methods for the identification of plant species, genotypes and management practices in front of the most likely climatic scenarios across Europe.
WIDS series of interviews with female data scientists expanded
Successful 1st Biohackathon Germany
Review of the 3rd Annual Meeting of the de.NBI Industrial Forum
- 2023-02-17
Monday, 13.03.2023:
11:00-12:00 Arrival & Registration
12:00-13:00 Introduction to the Spring School, de.NBI & IPK Gatersleben (Helena Schnitzer, Daniel Wibberg & Uwe Scholz)
13:00-14:00 Lunch Break
14:00-16:00 Data Management in a Nutshell (Helena Schnitzer & Daniel Wibberg)
16:00-17:00 RDM Games (Helena Schnitzer & Daniel Wibberg)
17:00-19:00 Social Event at IPK Gatersleben (Casino)
19:00-19:30 Transfer to Quedlinburg
Tuesday, 14.03.2023:
08:30-09:00 Transfer to Gatersleben
09:00-10:30 Keynote Talk by Mark Wilkinson - FAIR as a series of vignettes
10:30-11:00 Coffee Break
11:00-13:00 1001 Reasons for a Data Management Plan (Helena Schnitzer & Daniel Wibberg)
13:00-14:00 Lunch Break
14:00-16:00 Introduction to Data Management in the de.NBI Cloud (Sebastian Jünemann)
16:00-16:30 Coffee Break
16:30-18:00 Postersession for the participants & trainers
18:00-18:30 Transfer to Quedlinburg
Wednesday, 15.03.2023:
08:30-09:00 Transfer to Gatersleben
09:00-10:30 Keynote Talk by Harry Enke - Data management support by tools - different views in different communities
10:30-11:00 Coffee Break
11:00-13:00 FAIR Data Deep Dive and the Plant Data Management Infrastructures (ELIXIR, NFDIs) (Sebastian Beier & Daniel Arend)
13:00-14:00 Lunch Break
14:00-16:00 Introduction to Plant Genotyping & Phenotyping and Data Management with MIAPPE, ISA, BrAPI, Bioschemas and e!DAL-PGP Repository (Sebastian Beier & Daniel Arend)
16:00-16:30 Coffee Break
16:30-18:00 Two guided tours in two groups at IPK Gatersleben: Genebank & PhenoSphere
18:00-18:30 Transfer to Quedlinburg
Thursday, 16.03.2023:
08:30-09:00 Transfer to Gatersleben
09:00-10:30 Keynote Talk by Jeanne Wilbrandt - Data Management: Reprise and Chorus
10:30-11:00 Coffee Break
11:00-13:00 Management of Biological Data - the bigger picture (Part I)
Tools and support along the Data Life Cycle in NFDI4Biodiversity (Daniel Tschink, Jimena Linares)
13:00-14:00 Lunch Break
14:00-16:00 Management of Biological Data - the bigger picture (Part II)
Tools and support along the Data Life Cycle in NFDI4Biodiversity
(cont.) plus
Introduction to PANGAEA - Data Publisher for Earth and
Environmental Sciences and Biodiversity Research (Lars Möller & Michael
Oellermann)
16:00-16:30 Transfer to Quedlinburg
16:30-18:00 Historical Sightseeing in Quedlinburg
18:00-20:00 Dinner at Brauhaus
Friday, 17.03.2023:
08:30-09:00 Transfer to Gatersleben
09:00-10:30 Keynote Talk by Susann Auer - Reproducibility for Life Science Researchers
10:30-11:00 Coffee Break
11:00-11:30 Introduction to RDMkit - Research Data Management toolkit (Ulrike Wittig)
11:30-12:30 Introduction to FAIRDOM & the SEEK Data Management platform (Ulrike Wittig)
12:30-13:00 Summary & Goodbye (Uwe Scholz)
13:00-14:00 Lunch & Departure
Organization & Trainer Team:
Daniel Arend (IPK Gatersleben, Gatersleben)
Sebastian Beier (FZ Jülich, Jülich)
Sibille Bettermann (IPK Gatersleben, Gatersleben)
Tanja Dammann-Kalinowski (FZ Jülich, Jülich)
Janine Felden (MARUM/AWI, Bremen)
Frank Oliver Glöckner (MARUM/AWI, Bremerhaven)
Sebastian Jünemann (FZ Jülich, Jülich)
Jimena Linares (GFBio, Bremen)
Lars Möller (MARUM, Bremen)
Michael Oellermann (MARUM, Bremen)
Uwe Scholz (IPK Gatersleben, Gatersleben)
Helena Schnitzer (FZ Jülich, Jülich)
Daniel Tschink (GFBio e.V., Oldenburg)
Daniel Wibberg (FZ Jülich, Jülich)
Ulrike Wittig (HITS, Heidelberg)
Keynote speaker:
Mark Wilkinson (Universidad Politécnica de Madrid)
Harry Enke (Leibniz-Institut für Astrophysik Potsdam)
Jeanne Wilbrandt (Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI))
Susann Auer (TU Dresden)
- 2023-01-24
Educators:
Daniel Arend, Sebastian Beier, Uwe Scholz (GCBN), Ulrike Wittig (de.NBI-SysBio), Helena Schnitzer, Daniel Wibberg (CAU), Sebastian Jünemann (BiGi), Janine Felden, Lars Möller (BioData)
Keynotes:
Susan Auer - TU Dresden
Harry Enke - Leibniz-Institut für Astrophysik Potsdam
Jeanne Wilbrandt - Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)
Mark D. Wilkinson - Universidad Politécnica de Madrid
Date:
13-03-2023 to 17-03-2023, 9:00-18:00
Location:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
OT Gatersleben
Corrensstraße 3
D-06466 Seeland
Contents:
Have you ever wondered what research data management really is? Why is it so important? Then the German Network for bioinformatics infrastructure de.NBI has created the perfect spring school for you!
Data management experts will guide you through the basics of research data management, the dos and don’ts and how to improve the management of the data produced in research projects.
The spring school covers all important aspects of research data management: The data life cycle, the FAIR data principles and reproducibility. In addition, we will explore in hands-on sessions what a data management plan (DMP) is. We will sink our teeth into components, language, and examples of DMPs. In the light of the FAIR principles, we will evaluate possible problems and solutions and self-assess a DMP for our own projects.
Are you ready to boost your knowledge about research data management?
Learning goals:
The goal of this de.NBI spring school is to raise awareness for the importance of proper research data management (RDM) in general, but will also provide a practical toolbox for the RDM topics Data Management Planning, FAIR data and Reproducibility. Furthermore, a practical training on accessing the data for re-use and integration are part of the learning goals.
Prerequisites:
The training course is targeted towards early career scientists like PhD students and Postdocs who want to share, archive and publish their research data.
No programming skills are necessary.
Basic knowledge about research data management would be a plus.
Keywords:
Research Data Management, Data Management Plan, Data Life Cycle, Standards, Data curation, Data archiving and publication, Data licensing
Tools:
GFBio, PANGAEA, e!DAL/PGP, SEEK & FAIRDOM, DSW, RDMKit
Contact:
Application & Registration:
Apply here
Deadline: 15 February
Successful candidates will get free accommodation during the spring school. Breakfast, lunch and social events are also included. Only travel expenses need to be paid the participants.
- 2023-01-06
Opportunity: We invite applications for a PhD position with a strong background or interest in bioinformatics, big data analytics, machine learning, applied mathematics and its application in computational proteomics. The successful candidate will become a key member of an ERC Starting Grant funded project called ORIGIN which aims to answer a fundamental question in biology: To which extent and prevalence are isoforms translated and functionally relevant.
While mass spectrometry-based proteomics is the de-facto standard for measuring proteomes, it is not good at identifying isoforms. Proteins, thus also isoforms, leave a deterministic multi-dimensional fingerprint in each proteomic measurement. The central goal is to discover and quantify protein isoforms systematically by a novel MS-based proteomics data analysis strategy that utilizes these fingerprints. Candidates therefore must have a strong interest in one or more of the following aspects:
- Tap into the wealth of data the proteomics community has already amassed to train deep neural networks that allow the prediction of fingerprints.
- Implement an innovative data analysis strategy that utilizes the predictions to identify and quantify isoforms.
- Demonstrate that the novel approach can be used to address open questions in isoform-biology of varying biological and technical complexity.
The main work duties of the PhD are in research and assisting in the supervision of bachelor and master-level scientist.
Requirements: Candidates must hold an internationally recognized MSc degree in Bioinformatics, Biostatistics or a related discipline. Extensive theoretical knowledge of and practical skills in statistical analysis, data mining, data integration, machine learning, programming and database design are a plus. Additional desirable skills include a sound understanding of proteomic or related technologies as well as basic biological and (bio)chemical concepts. 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 interpersonal communication skills as well as presenting complex data to scientists in English are also important.
Our offer: The position is available for four years. You will join an interdisciplinary team of life scientists and bioinformaticians who use the latest proteomic approaches. The TUM is one of the best academic institutions in Germany, a well worked out international program, offers a stimulating work environment and excellent future perspectives.
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.
Equal opportunity: The Technical University of Munich is an equal opportunity employer. As such, applications from women are explicitly encouraged. Preference will be given to candidates with disabilities who have essentially the same qualifications.
- News
- 2022-12-22
Dear de.NBI and ELIXIR-DE members and friends,
We wish you a peaceful Christmas season and a happy and successful New Year 2023.
your staff of de.NBI and ELIXIR-DE Admin Offices
- 2022-11-22
For more Information see: https://www.dkfz.de/en/datascience/index.html?campaign=phd/nbi</p<
Apply here: https://www.dkfz.de/en/phd-program/index.html?campaign=phd/nbi
- 2022-11-22
| Issue 04/2022 | ||||||||||||||||||||||||||||||
3rd Annual Meeting of the de.NBI Industrial Forum on 24 November 2022 |
||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
 This year's de.NBI Cloud User meeting will take place at the Forschungszentrum Jülich on 6-7 December 2022. The meeting provides the ideal opportunity for our current users to learn more about best practices in cloud computing and showcases the capabilities provided by the de.NBI Cloud that could help accelerate their research in future projects to newcomers and prospective future users. The agenda covers talks and workshops on topics in cloud computing, such as container orchestration using Kubernetes, the application of infrastructure as code technologies but also bioinformatics related workshops such as an introduction to Bioconda and BioContainers as well as introduction to Common Workflow Language (CWL). Take the opportunity to get in personal contact with our cloud staff. Registration is open until 20 November 2022.
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
 Following the success of the BioHackathon Europe organized by ELIXIR Europe, ELIXIR Germany is planning to run the first BioHackathon Germany 2022 in Lutherstadt Wittenberg from 12-16 December 2022. We hope to encourage ELIXIR Germany and non-ELIXIR Germany participants to take part, as well as to attract industry engagement.We will offer 11 interesting projects in different areas, e.g. training, lipidomics, metabolomics, Bioschemas, plant bioinformatics etc. We are planning to hold the BioHackathon Germany with remote access - available for those that cannot attend the meeting in person. We believe this hybrid format will allow everyone to participate in the BioHackathon Germany and deliver optimized outcomes from the selected projects. Seats are limited for face-to-face participation. The registration is based on a first-come, first-served basis. Registration is open until 20 November 2022! |
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
 Steffen Neumann from the Leibniz Institute of Plant Biochemistry in Halle (Saale) has been elected as the new ELIXIR Metabolomics Community co-lead in September 2022 as a representative of ELIXIR Germany. The other new co-lead is Maria Klapa from ELIXIR Greece. The ELIXIR Metabolomics Community joins forces with experimental scientists and developers to provide the resources, analysis tools and infrastructure to analyze and interpret metabolomics data. The community aims to establish an infrastructure of services, standards, and datasets to help researchers discover, annotate and analyze metabolomics data from around Europe. Steffen's contribution to the community is focused on using modern bioinformatics approaches in plant biochemistry research as well as the support of data management according to the FAIR principles. We wish Steffen every success in further developing the Metabolomics Community! Find more information on Steffen’s research here.
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
Team of ELIXIR DE Officers is growing!
|
||||||||||||||||||||||||||||||
New Interview Series with Female Data Scientists from Industry and Academia |
||||||||||||||||||||||||||||||
|
Bérénice Batut, co-lead of the ELIXIR Marine Metagenomics Community representing ELIXIR Germany, is the first woman we interviewed. She shared with us her experiences as a woman in the data science field and gave recommendations on building careers and advancement opportunities. Find out more about Bérénice here. |
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
Three new de.NBI services have been added to our portfolio:
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
||||||||||||||||||||||||||||||
|
The next de.NBI training events are announced on www.denbi.de/training.
Next scheduled events:
|
||||||||||||||||||||||||||||||
Impressum |
||||||||||||||||||||||||||||||
|
Responsible for Contents
A. Tauch, T. Dammann-Kalinowski
de.NBI - German Network for Bioinformatics Infrastructure c/o 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
If you are interested in receiving regular updates on de.NBI - German Network of Bioinformatics Infrastructure, please subscribe to the de.NBI Quarterly Newsletter here. The mailing list will exclusively be used to distribute the de.NBI Quarterly Newsletter.
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.To unsubscribe from the de.NBI Quarterly Newsletter, please use the unsubscribe link. |
de.NBI Cloud User Meeting 2022 on 6-7 December in Jülich
1st BioHackathon Germany 12-16 December 2022 at Leucorea in Wittenberg
New Co-Lead for the ELIXIR Metabolomics Community 
In September this year, Harald Wagener from the Berlin Institute of Health (BIH), has been elected as a new 
We warmly welcome Dirk Winkelhardt, who started his position as 
Within the framework of the joint Bayer AG and de.NBI/ELIXIR Germany of the "Women in Data Science" lecture series, we are proud to launch this new interview collection aimed at celebrating women's achievements in data science for life sciences and bioinformatics. The interviews will promote the work of female researchers and highlight the diversity of research performed and career paths across Bayer AG, de.NBI, and ELIXIR DE and will appear regularly.
News on Services
Upcoming Events
- 2022-10-14
de.NBI welcomes three new services:
The Bioimage ANalysis Desktop (BAND) is a virtual desktop platform aimed at supporting interactive image analysis workflows in the cloud.
https://www.denbi.de/services/1477-band-bioimage-analysis-desktop
Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs
https://www.denbi.de/services/1476-bakta-web-annotation
PLAST is a freely available command line tool enabling the heuristic search for highest scoring local alignments between a nucleotide sequence query and a graphical pangenome consisting of thousands of individual genomes
https://www.denbi.de/services/1491-plast-pangenome-local-alignment-search-tool
- 2022-08-29
| Issue 03/2022 | |||||||||||||||||||||
3rd Annual Meeting of the de.NBI Industrial Forum in November 2022 |
|||||||||||||||||||||
|
This year, the 3rd annual meeting of the de.NBI Industrial Forum will take place in a virtual format on 24 November 2022. As a key topic the meeting will present contributions from the field "Digital Health". Further, it is planned to present the collaboration with the European organization ELIXIR. The agenda as well as the registration of the third annual meeting will be available soon and can be found at https://www.denbi.de/industrial-forum/industrial-forum-activities. Save the date! |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
In March 2022, the Community of Practice (CoP) for data management (DM) and stewardship (DS) training in the life sciences - Developing training and sharing knowledge, best practices, and standards - started with a kick-off meeting hosted by ELIXIR-DE. The essential vision was to bring national and local DM/DS life science communities together to foster the exchange of training materials and knowledge among trainers. |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
ELIXIR Communities bring together experts across Europe to develop standards, services and training within specific life science domains. To coordinate Single-Cell Omics research in Europe and beyond, ELIXIR has recently established the new Single Cell Omics Community, which has been approved by the HoN committee in May 2022. Single-cell technologies have undergone rapid developments in recent years and have revolutionized the way and the level of resolution by which life science research is conducted. The outline of the community´s activities is described in their white paper "Community-driven ELIXIR activities in single-cell omics". Naveed Ishaque (ELIXIR-DE) has been appointed as a co-lead for the ELIXIR Single Cell Omics Community. He recently started his own research group with research focus on applying computational approaches to understand the basis of molecular biological heterogeneity in data of human disease within the unit of Roland Eils at the Berlin Institute of Health. Find more information on Naveed Ishaque‘s research here. |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
We wish Bérénice every success in further developing the Marine Metagenomics Community! |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
Team of ELIXIR-DE Officers is growing
|
|||||||||||||||||||||
|
|||||||||||||||||||||
We are delighted to present our new de.NBI brochure entitled “Development and operation of the federated de.NBI Cloud“. With the life sciences becoming increasingly data-driven, cloud technology will become more important to the sector. Following this trend, the present booklet showcases the power, strength, and range of the de.NBI Cloud for the life science community by providing the ability to unlock research data and better collaborate across the ecosystem. Furthermore, it also sheds light on the role of the de.NBI Cloud in national and international projects such as NFDI, DeCOI, GHGA or EOSC-Life in the European sector of computational biosciences. The editorial team would like to thank all involved authors. We wish you lots of pleasure reading the de.NBI Cloud brochure. |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
At present, the de.NBI Cloud has 2100 registered users and 450 active projects. Two new testimonials on the cloud web page showcase the use of de.NBI cloud resources for plant breeding driven by big data analysis and computational solutions from data science and machine learning to solve biomedical problems. |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
Numerous de.NBI services have been improved in the last quarter:
|
|||||||||||||||||||||
|
|||||||||||||||||||||
|
|||||||||||||||||||||
|
|||||||||||||||||||||
|
The next de.NBI training events are announced on www.denbi.de/training.
Next scheduled events:
|
|||||||||||||||||||||
Impressum |
|||||||||||||||||||||
|
Responsible for Contents
A. Tauch, T. Dammann-Kalinowski
de.NBI - German Network for Bioinformatics Infrastructure c/o 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
If you are interested in receiving regular updates on de.NBI - German Network of Bioinformatics Infrastructure, please subscribe to the de.NBI Quarterly Newsletter here. The mailing list will exclusively be used to distribute the de.NBI Quarterly Newsletter.
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.To unsubscribe from the de.NBI Quarterly Newsletter, please use the unsubscribe link. |
Bérénice Batut from the University of Freiburg has been elected as the new 
Our Twitter channel 
We welcome Simon Gene Gottlieb as an ELIXIR-DE Officer (representing CIBI), active since 1 March 2022. Simon is a profound software engineer with focus on C++ and Linux. He is working on his PhD at the Freie Universität Berlin in the Algorithmic Bioinformatics group focusing on efficient data structures like the bidirectional FMIndex for approximate string searches. Simon also brings special knowledge surrounding the tool framework for SeqAn and OpenMS. As an ELIXIR Officer, one of his goals is to implement CWL support for SeqAn and OpenMS based tools, making these available on the Galaxy platform. If you ever feel like talking about efficient search schemes, newest C++ updates or soccer playing robots, you are welcome to contact Simon. 
- 2022-08-25
We are delighted to present our new de.NBI brochure entitled “Development and operation of the federated de.NBI Cloud“. This brochure showcases the power, strength, and range of the de.NBI Cloud for the life science community by providing the ability to unlock research data and better collaborate across the ecosystem.
The editorial team would like to thank all involved authors! We wish you lots of pleasure reading the de.NBI Cloud booklet!
- 2022-08-24
| Date | Topic | Location |
|---|---|---|
| 2022-08-24 | Research associate (computational metabolomics, m/f/d) | Halle (Saale) |
| 2022-08-24 | Research associate (data scientist, m/f/d) | Halle (Saale) |
- 2022-08-24
| Date | Topic | Location |
|---|---|---|
| 2022-08-24 | Wissenschaftliche/r Mitarbeiter/in (m/w/d) für das Fachgebiet Bioinformatik | Gießen |
| 2022-08-24 | Wissenschaftliche/r Mitarbeiter/in (m/w/d) für das Fachgebiet Informatik/Bioinformatik | Gießen |
- 2022-08-18
| Date | Topic | Location |
|---|---|---|
| 2022-08-18 | Wissenschaftliche/r Mitarbeiter/in (m/w/d) für das Fachgebiet Bioinformatik in de.NBI | Gießen |
| 2022-08-18 | Wissenschaftliche/r Mitarbeiter/in (m/w/d) im Bereich Informatik / Bioinformatik (NFDI in Hessen - Digitalpakt Hochschulen) | Gießen |
| 2022-08-18 | Wissenschaftliche/r Mitarbeiter/in (m/w/d) im Bereich Informatik / Bioinformatik | Gießen |
| 2022-08-18 | Computer scientist for knowledge contextualisation (m/f/d) | Berlin |
- 2022-08-16
- 2022-08-10
| Topic | Location |
|---|---|
| Software Developer in GHGA | Heidelberg |
| Bioinformatician / Computational Biologist | Heidelberg |
| IT Security Specialist | Heidelberg |
| Team Leader Genomics Data Infrastructure | Heidelberg |
- 2022-08-03
Das BioQuant ist das interdisziplinäre Forschungszentrum der Universität Heidelberg für die quantitative Analyse molekularer und zellulärer Systeme. Die Forschung am BioQuant integriert theoretische Modellierungsansätze, Laborexperimente und Technologieentwicklung. Zusammen mit dem Universitätsrechenzentrum betreibt das BioQuant eine Bioinformatik-Cloud an der Universität Heidelberg. Die Cloud ist Teil eines Verbundes wissenschaftlicher Bioinformatik-Cloud Standorte in Deutschland.
Für die Bioinformatik-Cloud an der Universität Heidelberg ist am BioQuant zum nächstmöglichen Zeitpunkt folgende Stelle in Vollzeit, zunächst befristet auf zwei Jahre (eine Fortführung wird angestrebt), zu besetzen:
OpenStack Admin (w/m/d)
Ihre Aufgaben:
- Betreuung der bestehenden OpenStack Cloud Infrastruktur und der dazu gehörigen Speichersysteme
- Wissenschaftlicher Support für Nutzerinnen und Nutzer bei der Erhebung und Verarbeitung von wissenschaftlichen Daten auf zentralen Großgeräten
- Mitwirkung bei wissenschaftlichen Projekten: Projektmanagement, Forschungsdatenmanagement, Einwerbung von Fördermitteln, Erstellung von wissenschaftlichen Publikationen
- Konzeption und Durchführung von Schulungen im Bereich Cloud und OpenStack
- Teilnahme an Cloud Meetings und Zusammenarbeit mit anderen Bioinformatik-Cloud Standorten
- Weiterentwicklung der Bioinformatik-Cloud an der Universität Heidelberg nach den Bedürfnissen der wissenschaftlichen Nutzer*innen.
Ihr Profil:
- Sie haben einen Hochschulabschluss oder vergleichbare Kenntnisse oder eine Ausbildung als Fachinformatiker*in (Systemintegration) mit Berufserfahrung.
- Fundierte Kenntnisse in der Administration von Linux-Servern sind erforderlich.
- Kenntnisse von OpenStack und Cloud Umgebungen
- Idealerweise verfügen Sie über Kenntnisse und Erfahrungen zu den folgenden Punkten oder die Bereitschaft, sich darin einzuarbeiten:
- Administration von Speichersystemen
- Einsatz von Automatisierungswerkzeugen für Server-Konfiguration und Monitoring
- Sehr gute Kenntnisse der deutschen und englischen Sprache in Wort und Schrift sind erforderlich.
- Hohe Kompetenz für Teamarbeit im BioQuant und im Verbund der Bioinformatik-Cloud Standorte sowie in der Kommunikation mit Nutzer*innen und Projektpartner*innen wird erwartet.
Wir bieten:
- Abwechslungsreiche Tätigkeit in einem lösungsorientierten, kommunikativen Team
- Flexible, familienfreundliche Arbeitszeitmodelle
- Vielfältiges universitäres Angebot (Job-Ticket, Hochschulsport, Weiterbildung etc.)
- Möglichkeit zur persönlichen Weiterentwicklung (z.B. Teilnahme an Fortbildungsmaßnahmen) und zur Erlangung von Zertifizierungen
Die Stelle ist grundsätzlich teilbar. Die Vergütung erfolgt nach TV-L.
Wir freuen uns auf Ihre Bewerbung, die Sie bitte mit den üblichen Unterlagen (Lebenslauf, Zeugnisse etc.) unter Angabe des Stichworts „OpenStack Admin“ bis zum 05.09.2022 an das BioQuant, BioQuant-IT, Dr. Nick Kepper, Im Neuenheimer Feld 267, 69120 Heidelberg oder in einer einzigen PDF-Datei per E-Mail an:
Die Universität Heidelberg steht für Chancengleichheit und Diversität. Wir bitten qualifizierte Frauen nachdrücklich um ihre Bewerbung. Menschen mit einer Schwerbehinderung werden bei gleicher Eignung vorrangig berücksichtigt. Informationen zu Stellenausschreibungen und zum Datenschutz finden Sie unter: www.uni-heidelberg.de/stellenmarkt.
- 2022-06-28
Have you ever wondered, what research data management really is? Why is it so important? Then de.NBI / ELIXIR-DE has created the perfect training course for you that will take place in September at GCB (5.9.) and ECCB (18.9) 2022!
More and more funders require the establishment of research data management plans for their grants. Over the course of just three hours, you will get the chance to learn how to transfer research project proposals into proper Data Management Plans (DMPs). The data management experts Helena and Daniel (CONVERGE WP2) will guide you through the basics of research data management, the dos and don’ts and how to improve the management of the data produced in research projects.
After a short introduction to the research data life cycle and the FAIR data principles, we will explore in multiple hands-on sessions what a data management plan (DMP) is. We will sink our teeth into components, language, software and examples of DMPs. In light of the FAIR principles, we will evaluate possible problems and solutions and self-assess a drafted DMP for our own projects. See you in Halle (Saale) or Sitges!
GCB2022: https://www.denbi.de/training/1424-data-management-plan-for-beginners-2
ECCB2022: https://www.denbi.de/training/1425-data-management-plan-for-beginners-eccb-2022
- 2022-08-03
Software Development and Engineering
EMBL Heidelberg
EMBL is seeking a software developer / system architect to join the new EMBL Data Science Centre, co-headed by Jan Korbel, and to actively participate in the recently funded infrastructure initiative German Human Genome Phenome Archive (GHGA, http://www.ghga.de). GHGA is funded within the framework of Germany’s national research data infrastructure (NFDI, https://www.nfdi.de/). The goal of GHGA is to establish a national infrastructure for the archival, analysis and the dissemination of human omics data. GHGA is implemented as a federated infrastructure, which currently connects six data centers across Germany to the federated network of the European Genome Phenome Archive (EGA, https://www.ebi.ac.uk/ega). To enable long-term scalability and respect national data security regulations, the EGA is undergoing a transition to a federated model, with GHGA operating as an EGA node for Germany. GHGA has an ambitious long-term concept with an initial focus on providing technological infrastructure and services for rare disease genetics and oncology. With its 16 partners the GHGA network spans all major omics centers in Germany.
This position can be located at any of the EMBL sites, but may require some travel to EMBL’s five other sites.
Your role
The successful candidate will design, implement, and operate the main GHGA infrastructure, and identify and realise synergies with EMBL’s Data Science data management strategies. As part of an interdisciplinary research, software development, and data management team he or she will develop and apply a diverse range of state-of-the-art technologies.The candidate will take part in national and international collaborations through many partner projects around GHGA. As a young project, GHGA offers its employees room to shape the software development from the start. Your input will help GHGA reach its mission to make omics data more accessible and help drive genome research forwards.
The candidate will be responsible to/for:
- Contribute to the development (backend/frontend) of the GHGA software tools
- Develop a data portal and interface it with underlying software services
- Design and specification of features, aligned with international standards such as GA4GH
- Collaboration with local and international developers
Closing date: 16 July 2022
- Contract duration: 3 years
- Grading: 4, 5 or 6 depending on experience and qualifications
- Reference number: HD02216
Related
You have
- BSc, or alternatively, a higher degree in Computer Science, Bioinformatics statistics, Mathematics, Physics, and/or Engineering, or a degree in biological science with demonstrated experience in Computational Biology/Bioinformatics/Software development.
- Proficiency with python based web frameworks (e.g., FastAPIDjango, Flask, Django)
- Familiarity with database and search engine setups (like PostgreSQL, MongoDB, ElasticSearch)
- Familiarity with test driven software development
- Experience or interest in microservice design patterns and domain-driven design and familiarity with using docker containers for development and deployment is a plus
The ideal applicant should have demonstrated the ability to work independently and creatively. The candidate should have excellent communications skills and be able to articulate clearly the technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.
We encourage candidates with all levels of expertise to apply.
You might also have
- Interest in computational biology and/or data science
- Expertise in informatics
- Expertise in (agile) software development
- Expertise in system architecture
- Expertise in cloud computing
- Expertise in IT-Security
Why join us
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises from a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, and the availability of an excellent child care facility on campus. You will be involved in many ongoing cutting-edge projects and activities and will collaborate with experts from the scientific community and have the possibility to acquire new state-of-the-art skills.
What else you need to know
The Korbel group at the European Molecular Biology Laboratory (EMBL), within the Genome Biology Unit, is a ‘hybrid’ laboratory in which computational biologists and experimentalist collaborate tightly to obtain new insights into human disease and molecular mechanisms. By combining experimental and computational approaches, including single-cell sequencing technology, we aim to unravel determinants and consequences of germline and somatic genetic variation. Our group is using bulk as well as single cell-based omics approaches for investigating mechanisms behind complex phenotypes in humans, ranging from common diseases including cancer to ageing. An overarching theme centers on the formation and selection of germline and somatic genetic variation in health and disease states, in particular genomic structural variation (SV).
- 2022-06-14
Hintergrund
Ihr Aufgabengebiet ist an der Schnittstelle zwischen den drei Bereichen des Rechenzentrums (Systems, Computing und Data) und den wissenschaftlichen Nutzern im AWI und sowie unseren Kooperationspartnern und Nutzenden angesiedelt. Das Ziel ist die IT-Bedarfe der Nutzenden zu erfassen und diese in Absprache mit der Leitung des Rechenzentrums und den Zielen des AWI im Rahmen der Programm orientierten Förderung (PoF) zu operationalisieren. Dazu gehören ausgeprägte Kommunikations- und Koordinationsfähigkeiten sowie ein sehr gutes Verständnis für Ressourceneinsatz und Planung. Sie repräsentieren zudem an vielen Stellen das Rechenzentrum als Dienstleister für die Wissenschaft und Vertreten es in Gremien und im Berichtswesen. Sie erwartet ein abwechslungsreiches Aufgabengebiet mit spannenden technischen und sozialen Herausforderungen in einem Großforschungsinstitut mit internationalen Vernetzungen.
Aufgaben
- Erfassen der IT-Bedarfe von Direktorium, Verwaltung, Fachbereichen und Nutzenden:
- gemeinsam mit Bereichs- und RZ-Leitung
- auch in über das AWI hinausgehenden kollaborativen Kontexten
- Bewertung der Umsetzbarkeit von Projekten und Anträgen unter Berücksichtigung der zur Verfügung stehenden Ressourcen, sowohl hinsichtlich des initialen Aufbaus als auch des dauerhaften Betriebs erforderlicher Dienste
- Vermittlung der technischen, personellen und finanziellen Rahmenbedingungen an die Anfordernden von Infrastrukturen oder Services
- Folgekostenabschätzung und mittelfristige Finanzplanung in Zusammenarbeit mit Controlling, Finanz- und Personalabteilung, sowie Budgetverantwortlichen und Gruppenleitungen
- Erarbeiten bzw. Evaluation von Geschäfts- und Nutzungsmodellen für eigene, Community- und kommerzielle Services
- Unterstützung der Rechenzentrums-Bereiche bei Management, Priorisierung und Qualitätssicherung der Infrastrukturen und Dienste
- Wahrnehmen der Multiplikatorfunktion zu weiteren zu beteiligenden Personen oder Einheiten
- Nachverfolgen offener Diskussionspunkte
- Erwartungsmanagement und Unterstützung der Konsensfindung
- Einbindung und Unterstützung des Project Management Office
- Operationalisierung der Dienste und Projekte des RZ
- Abbilden der Nutzerbedarfe auf technische Lösungen und deren Weiterentwicklung sowie Verbesserung des IT-Service- und Produktportfolios
- Aufstellen und Koordination notwendiger Teams zur Bearbeitung der Projekte
- Vermittlung der Bedarfe an das umsetzende IT-Personal
- Erarbeiten, Überprüfen und Anpassen von Stellenprofilen und Tätigkeitsbeschreibungen, sowie Vorschläge zur Personalentwicklung
- Planung, Dokumentation und Qualitätsmanagement für den sicheren Betrieb und die Weiterentwicklung der Angebote und Dienste aller Rechenzentrums-Bereiche
- Kommunikation und Berichte
- Aktive Mitarbeit in entsprechenden Gremien der HGF, des AWI und der Universität Bremen
- Gestalten und Durchführen von digitalen und analogen Workshops, Schulungen und Informationsveranstaltungen zu Nutzerservices
- Regelmäßige Berichte und Informationen zu Nutzer- und Serviceangeboten des Rechenzentrums für das bzw. im IT-Board, (erweiterten) Direktorium und anderen AWI-Veranstaltungen
- Mitarbeit bei Berichten zum Thema Digitalisierung für das AWI
- Mitarbeit bei der Erarbeitung von Zentrums-, Forschungsbereichs- und HGF-weiten Konzepten in den Bereichen Digitalisierung, Informationsinfrastrukturen, Forschungsdaten und Software
Voraussetzungen
- Master, Diplom oder Promotion in der Informatik oder einer vergleichbaren technischen Fachrichtung
- Hohe Bereitschaft, sich laufend aktuelle Kenntnisse und einen umfassenden Überblick im IT-Sektor zu erarbeiten
- Sehr gute Kenntnisse und tiefgehendes Verständnis für IT-Serviceaufgaben, Funktionen und Leistung von Rechenzentren und IT-Infrastrukturen
- Expertise in der Gestaltung und Steuerung von produktorientierten Systementwicklungsprozessen
- Ausgeprägte Fähigkeit zum konzeptionellen und analytischen Arbeiten sowie zur Lösung komplexer Fragestellungen
- Selbstständige und systematische Arbeitsweise, Planungskompetenz und Zielorientierung
- Hohes Maß an Einsatzbereitschaft und Eigeninitiative, Flexibilität und Belastbarkeit
- Sehr gute Kommunikations- und Teamfähigkeit, verbunden mit einem ausgeprägten Verantwortungsbewusstsein für den gesamten Arbeitsbereich
- Souveränes Auftreten bei internen und externen Gesprächsterminen und Sitzungen
- Bereitschaft zur Teilnahme an (inter)nationalen Workshops und Mitarbeit in überregionalen Arbeitsgemeinschaften
Wünschenswerte Fähigkeiten und Kenntnisse
- Sehr gute IT-Kenntnisse in den Bereichen Netzwerk, Server, Storage und Basisdienste
- Sehr gute Kenntnisse im Bereich Projektmanagement
- Einschlägige Erfahrungen im Bereich IT-Projektmanagement
- Gute Kenntnisse im Personal- und Budgetmanagement
- Grundlegende kaufmännische und Controlling-Kenntnisse
- Sehr gute Deutsch- und Englischkenntnisse in Wort und Schrift
- Sehr gute Kenntnisse im Umgang mit den gängigen Office-Produkten
Weitere Informationen
Weitere Informationen erhalten Sie bei Prof. Dr. Frank Oliver Glöckner (
Die Stelle ist unbefristet und wird in Vollzeit ausgeschrieben. Die Tätigkeit eignet sich auch für eine Beschäftigung in Teilzeit. Die Vergütung ist abhängig von Ihrer Qualifikation sowie den Ihnen übertragenen Aufgaben bis Entgeltgruppe 14 möglich und richtet sich nach dem Tarifvertrag für den öffentlichen Dienst des Bundes (TVöD-Bund). Der Dienstort ist Bremerhaven.
Wir bieten
- exzellente Forschung
- Zusammenarbeit und Kooperation - institutsintern, national und international, interdisziplinär
- Chancen, sich zu entwickeln – auf der eigenen Stelle, auf andere Stellen hin und aus dem AWI heraus
- eine gelebte Kultur der Vereinbarkeit von Beruf und Familie – auditiert, und noch mehr als das
- herausragende Forschungsinfrastruktur – Schiffe, Stationen, Flugzeuge, Labore und mehr
- ein internationales Umfeld – alltägliche Kontakte zu Menschen aus aller Welt
- Grundlagenforschung mit gesellschaftlicher und politischer Relevanz
- flache Hierarchien – Freiheit und Verantwortung
- spannende Themen – auch in Technik, Verwaltung und Infrastruktur
Chancengleichheit ist ein fester Bestandteil unserer Personalpolitik. Das AWI strebt die Erhöhung des Frauenanteils an und ermutigt daher qualifizierte Interessentinnen ausdrücklich zur Bewerbung.
Schwerbehinderte Bewerber/innen werden bei gleicher fachlicher und persönlicher Eignung bevorzugt. Über verschiedene Maßnahmen wird gezielt die Vereinbarkeit von Beruf und Familie gefördert. Aufgrund unserer familienbewussten Personalpolitik wurde uns das Zertifikat zum Audit „Beruf und Familie“ verliehen.
Wir freuen uns auf Ihre Bewerbung!
Bewerben können Sie sich bis zum 31. Juli 2022 ausschließlich online.
Referenznummer: 22/97/G/RZ-u
https://recruitingapp-5442.de.umantis.com/Vacancies/1110/Description/1
- 2022-05-31
The German Research Foundation (DFG) funded RTG „MeInBio – BioInMe: Exploration of spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods” (www.meinbio.uni-freiburg.de) successfully bridges bioinformatics and wet laboratory methods to analyse high-throughput sequencing data at single cell level and in small cell numbers. The RTG provides interdisciplinary education in modern bioinformatics methods and the underlying biological research questions to PhD students in 13 research groups of the University of Freiburg and the Max Planck Institute of Immunobiology and Epigenetics Freiburg.
From July 2022, MeInBio offers 1 Postdoc position (100%, 4 years)
Your tasks:
- You will develop and test software for multi-scale integrative analysis of various high-throughput data sources (e.g. ChIP-seq, ATAC-seq, metabolomics) as needed in individual research projects of the RTG. This includes e.g. defining and codifying best practices based on established software packages, using supervised and unsupervised methods for parallel dimensional reduction of heterogeneous data, implementation of published methods and project-specific optimization of workflows.
- You will be involved in training, e.g. in Galaxy courses, for the members of the RTG and will ensure transferability, scalability and documentation of data and analysis workflows.
- You will advise RTG PhD students in the process of research data management according to the guidelines of the University of Freiburg.
You are convincing through:
- an excellent PhD in informatics/bioinformatics
- documented experience in high-throughput data analysis including single cell data and software development
- a strong interest to acquire biological knowledge and work together with life scientists in different projects
- very good communication skills in English
- motivation to teach and assist PhD students in the usage of various software tools as well as data management
- a strong motivation and enthusiasm for multiple facets of the life sciences
- the ability to work independently and synergistically in a team of different project leaders and PhD students
We offer:
- exciting research projects in integrative data analysis and close collaboration with several life science groups with excellent publication and further career prospects
- time for own algorithmic and software development
- the option to participate in RTG courses and gatherings of all research training group members for scientific exchange
- an international work atmosphere
- participation in the RTGs’ equal opportunities actions for female researchers and parents
- an individual career development plan and participation in the universities’ services for postdocs
Employment will be on a fixed term basis for the duration of 4 years starting July 2022.
Please send applications including the usual documentation (CV, degrees, 2 references, short letter of motivation, list of publications) via email to:
GRK2344, Dr. Christine Hacker,
- 2022-05-18
Hintergrund
Das AWI betreibt weltweit Forschungsplattformen wie z. B. die Neumayer-Station III in der Antarktis, die Forschungsschiffe Polarstern, Heincke, Mya II und Uthörn sowie die Polarflugzeuge Polar 5 & Polar 6. Hinzu kommt eine Vielzahl stationärer, mobiler, driftender oder verankerte Instrumente und Observatorien. Auf diesen Plattformen werden mittels Sensoren wichtige Umweltparameter in Wasser, Erde, Luft und Eis digital gemessen, welche eine wichtige Säule für die Erforschung der Erdsysteme bilden. Unsere Ansprüche sind, dass diese wissenschaftlichen Messdaten zuverlässig von Datenerfassungssystemen digital erfasst, im Datenfluss frühzeitig mit Metadaten angereichert, schnell und sicher zum Rechenzentrum transportiert und nachhaltig, FAIR archiviert werden, um die Nachnutzung durch die wissenschaftliche Gemeinschaft und künftige Generationen zu gewährleisten.
Dazu betreiben und entwickeln wir in einem kreativen Team des AWI-Rechenzentrums moderne IT- und Dateninfrastrukturen. Unsere Arbeitsgruppe Data Logistics Support ist damit betraut, den Betrieb von IT, Kommunikation und Datenerfassungssystemen der Forschungsplattformen zu koordinieren und sicherzustellen. Zudem etablieren wir nachhaltige, FAIRe Roh- und Metadatenflüsse, beginnend beim Sensor im Feld über Monitoring-Systeme bis hin zu Datendiensten und Langzeit-Repositorien im AWI-Rechenzentrum.
Sie haben die Möglichkeit, die Systeme für IT, Kommunikation und Datenerfassung auf unseren Forschungsplattformen in einem spannenden Umfeld voranzutreiben und die Datenflüsse zum Institut nachhaltig und FAIR mitzugestalten.
Dabei übernehmen Sie Aufgaben in allen Phasen des Datenmanagements: Beginnend bei Sensoren und Datenerfassungen auf Stationen, Schiffen und Flugzeugen, über geeignete Kommunikations- und Transportsysteme bis hin zu den Diensten und Speichern im AWI-Rechenzentrum.
Aufgaben
Zu Ihren Aufgaben gehören unter anderem:
- Koordination und Weiterentwicklung von IT-, Kommunikations- und Datenerfassungssystemen auf unseren Forschungsplattformen
- Bearbeitung von wiss./techn. Anfragen in Verbindung mit Forschungsreisen
- Integration neuer Sensorik in die vorhandenen Datenerfassungssysteme
- Teilnahme an Werftliege- und Wartungszeiten im In- und Ausland sowie mehrwöchigen Forschungskampagnen
- Konzeption und Weiterentwicklung von Datenflüssen im AWI Datenflusskonzept „Observation to Archive and Analysis“ (O2A)
- Koordination und Verantwortung für einzelne Datenflüsse vom Sensor bis zur Datenarchivierung
- Dokumentation wissenschaftlicher Systeme der Forschungsplattformen in Geräteakten
Voraussetzungen
- Master in technischer Informatik oder vergleichbare Ausbildung oder Berufserfahrung
- Expertenwissen zu Sensorik und Datenerfassungssystemen für wiss. Messdaten
- Sehr gute Kenntnisse von Server- und Speichersystemen, Virtualisierung und Netzwerkinfrastruktur
- Verbindlich-freundliches und sicheres Auftreten in einem von internationaler Zusammenarbeit geprägten Umfeld
- Sehr gute Kommunikations- und Teamfähigkeit
- Sehr gute Kenntnisse in deutscher und englischer Sprache
- Bereitschaft zur Teilnahme an mehrwöchigen, internationalen See- und Landreisen
Wünschenswerte Fähigkeiten und Kenntnisse
- Sehr gute Kenntnisse von elektronischen Schnittstellen
- Gute Kenntnisse satellitengestützter und mobiler Kommunikation
- Gute Kenntnisse gängiger Server-Betriebssysteme inkl. Linux
- Kenntnisse von Virtualisierung sind von Vorteil
- Gute Kenntnisse von Datenbanksystemen
- Gute Kenntnisse von Skriptsprachen wie Python oder Linux-Shell
- Gute Kenntnisse einschlägiger wiss. Datenformate z. B. NetCDF, Shape, GeoTIFF
Weitere Informationen
Weitere Informationen erhalten Sie bei Sebastian Immoor (
Die Stelle ist unbefristet und wird in Vollzeit ausgeschrieben. Die Tätigkeit eignet sich auch für eine Beschäftigung in Teilzeit. Die Vergütung ist abhängig von Ihrer Qualifikation sowie den Ihnen übertragenen Aufgaben bis Entgeltgruppe 13 möglich und richtet sich nach dem Tarifvertrag für den öffentlichen Dienst des Bundes (TVöD-Bund). Der Dienstort ist Bremerhaven.
Wir bieten
- exzellente Forschung
- Zusammenarbeit und Kooperation - institutsintern, national und international, interdisziplinär
- Chancen, sich zu entwickeln – auf der eigenen Stelle, auf andere Stellen hin und aus dem AWI heraus
- eine gelebte Kultur der Vereinbarkeit von Beruf und Familie – auditiert, und noch mehr als das
- herausragende Forschungsinfrastruktur – Schiffe, Stationen, Flugzeuge, Labore und mehr
- ein internationales Umfeld – alltägliche Kontakte zu Menschen aus aller Welt
- Grundlagenforschung mit gesellschaftlicher und politischer Relevanz
- flache Hierarchien – Freiheit und Verantwortung
- spannende Themen – auch in Technik, Verwaltung und Infrastruktur
Chancengleichheit ist ein fester Bestandteil unserer Personalpolitik. Das AWI strebt die Erhöhung des Frauenanteils an und ermutigt daher qualifizierte Interessentinnen ausdrücklich zur Bewerbung.
Schwerbehinderte Bewerber/innen werden bei gleicher fachlicher und persönlicher Eignung bevorzugt. Über verschiedene Maßnahmen wird gezielt die Vereinbarkeit von Beruf und Familie gefördert. Aufgrund unserer familienbewussten Personalpolitik wurde uns das Zertifikat zum Audit „Beruf und Familie“ verliehen.
Wir freuen uns auf Ihre Bewerbung!
Bewerben können Sie sich bis zum 04. Juni 2022 ausschließlich online.
Referenznummer: 22/66/G/RZ-u
https://recruitingapp-5442.de.umantis.com/Vacancies/1070/Description/1
- 2022-04-25
The DKFZ International PhD Program in Heidelberg (also known as the Helmholtz International Graduate School for Cancer Research) is the interdisciplinary structured graduate school for all PhD students working at the German Cancer Research Center (DKFZ). Our PhD students conduct research at the forefront of basic, computational, epidemiological and translational cancer research.
We warmly invite you to apply to join the DKFZ and our many distinguished scientists in cancer research!
Our online system is currently open for applications - the application deadline is 15. May 2022.
Click here for more information on the selection process and how to apply.
- 2022-04-21
The Goesmann group "Bioinformatics and Systems Biology" offers two positions as Bioinformatician, e.g. in the NFDI4Microbiota project. For more information see:
- 2022-04-21
GFBio and NFDI4Biodiversity are looking for bioinformatics research software developer. For more information see:
| 2022-04-21 | Anwendungsentwicklung (m/w/d) in NFDI4Biodiversity | Bremen |
| 2022-04-21 | Anwendungsentwicklung (m/w/d) im Projekt DISC-3D | Bremen |
- 2022-04-11
The Hannover Medical School (MHH), with about 10.000 employees the biggest company of Lower Saxony, is a university institution for research and teaching in the human and dental medicine and a university hospital of supra-maximum medical care. Research, teaching, medical care and administration work hand in hand in the integration model at the MHH-campus.
The RCUG (http://www.mhh.de/genomics) is a research-driven service facility. Since its formation in 2017, the RCUG is open to all departments at the MHH and selected external partners for the realization of sequencing-based projects. The extensive expertise of the personnel in the fields of planning, technical execution, analysis, and publication of genome-wide studies has been acquired during many years of research in their respective fields.
Modern cluster computational infrastructure, various sequencing technology platforms, and data analysis pipelines are established.
Key aspect of the applicant's work will be the analysis of 2nd and 3rd generation sequencing data in various research projects conducted on site (mainly genomics and metagenomics applications).
Your task
- Analysis and visualization of generated sequencing data
- Consultations with clients, discussing study design, technological prospects, provided data formats, and analysis options
- Pipeline development, maintenance and optimization in accordance with offered services, current inquiries, and general advances in the literature
- Participation in the provision of general RCUG services
- Teaching of students and scientists in Genomics-based applications and prospects
- Participation in the administration of our high-performance computing cluster (in close cooperation with our data center)
- Optional participation in various research proposals and possible integration in collaborative projects on site
Our requirements
- PhD in Bioinformatics, Informatics, or equivalent degree in life sciences with strong background/knowledge in bioinformatics processes
- Profound knowledge in 2nd and 3rd generation sequencing data, QC, and analysis
- Experience with scripting languages such as Python or higher languages like Java/C
- Sound knowledge with Linux
- Very good spoken and written English
- Excellent communication skills as a team player, ability to put yourself in the mindset of others (especially ‘non-bioinformaticians’)
- Desired skills: knowledge in R, experience with Galaxy, expertise with large datasets, and profound statistics knowledge
We offer
- A full position (38,5 h/week) in firm perspective as a permanent employment
- Remuneration according to TV-L
- Modern work environment in a multidisciplinary team, composed of bioinformaticians, molecular biologists, biochemists, and technicians
- Work in a highly motivated team with strong emphasis on personal responsibility, knowledge exchange, flat hierarchies, mutual appreciation, and teamwork
- An international team of scientists on campus
We enable you a collegial initial training and diverse training and development opportunities as well as an extensive health program for employees. In addition, we offer reliable family support and there is a day care center for children with emergency childcare. Furthermore, you will find the usual social benefits of the public service.
You have any questions beforehand?
Dr. Oliver Dittrich-Breiholz
+49 511 532 5814
Apply now
Reference number 1292
Apply until: 05/01/2022
https://mhh.hr4you.org/job/apply/1292?page_lang=en
- 2022-04-08
In einer bundesweiten Ausschreibung vergibt die Joachim Herz Stiftung seit 2015 Fellowships für interdisziplinäre Forschung.
Auch in 2022 richtet sich die Ausschreibung an Doktoranden (w/m/d) und Postdocs, die mit Hilfe von fachübergreifenden Ansätzen biologische Forschungsfragen beantworten wollen. Ziel ist es, jungen Nachwuchswissenschaftlern den berühmten „Blick über den Tellerrand“ zu ermöglichen und sie gleichzeitig untereinander zu vernetzen.
Zu diesem Zweck erhalten die Add-on Fellows über einen Zeitraum von zwei Jahren bis zu 12.500 EUR für internationale Vernetzung und Weiterbildungen in einer jeweils anderen Fachrichtung – so können beispielsweise Biologen in die Mathematik und Modellierer in die Biowissenschaften eintauchen. Die individuell und flexibel angepasste Förderung ermöglicht Forschungsaufenthalte, Konferenzbesuche, Anschaffung von Hilfsmitteln wie Laptop oder Software-Lösungen und die Teilnahme an Fellowship-Treffen. Fellows mit Kindern können zusätzliche Mittel zur Vereinbarkeit von Familie und Beruf beantragen.
Der Bewerbungszeitraum endet am 7. Juni 2022
Weitere Informationen hier
Jury 2022:
Rudi Balling, Systems Biomedicine, Bonn
Jens Bohne, Molecular Biology, Hannover
Susanne Brakmann, Chemical Biology, Dortmund
Björn Corzilius, Physical Chemistry, Rostock
Martin Fischer*, Computational Biology, Jena
Dhana Friedrich*, Systems Biology, Boston (US)
Linnea Hesse*, Biomechanics, Freiburg
Arjen Jakobi*, Bionanoscience, Delft (NL)
Lars Kaderali, Bioinformatics, Greifswald
Edda Klipp, Theoretical Biophysics, Berlin
Andreas Kremling, Systems Biotechnology, München
Ursula Kummer, Modeling of Biological Processes, Heidelberg
Alexander Löwer, Systems Biology, Darmstadt
Annette Meister, Biophysics, Halle
Matthias Rarey, Structural Bioinformatics and Cheminformatics, Hamburg
Fred Schaper, Systems Biology, Magdeburg
Constanze Schmidt, Cardiology and Cellular Electrophysiology, Heidelberg
Andreas Schuppert, Computational Biomedicine, Aachen
Ulrich Schweizer, Biochemistry, Bonn
Petra Schwille, Biophysics, Martinsried
Tatjana Tchumatchenko, Computational Neuroscience, Bonn
Fabian Theis, Computational Biology, München
Jens Timmer, Systems Biology, Freiburg
Matthias Wilmanns, Structural Systems Biology, Hamburg
Marietta Zille*, Neuroscience and Pharmacology, Wien (AT)
Michael Ziller, Systems Medicine, München
*Alumni der Add-on Fellowships for Interdisciplinary Life Science
- 2022-03-25
de.NBI / ELIXIR-DE will offer a training course at Proteomic Forum / EuPA 2022. Here are the details:
Educators:
Nils Hoffmann (FZ Jülich / ELIXIR-DE / de.NBI)
Date:
Sunday, April 3rd 2022
Location:
On-Site, Leipzig, as part of the educational day of Proteomic Forum / EuPA 2022
Registration:
During conference registration, please register for the “Educational Day” (Session 1)
Contents:
This course will provide participants with the necessary knowledge to conduct a differential analysis of high-throughput quantitative proteomics data using R. As we start with a basic introduction to the popular statistical programming language, no prior knowledge on R is required.
The basic statistical background on utilized methods is explained in order to enable the participants to assess their own as well as published workflows critically. In this regard the course will touch upon
- statistical inference: hypotheses, type I and II error
- location tests (t-test)
- multiple testing
This course introduce participants to the ggplot2 package in R to create informative and beautiful figures to communicate your omics data and analysis results.
We will cover the following topics:
- Usage of the tidyverse for data preprocessing
- Usage of the ggplot2 R package
- Presentation of different types of graphics and when to use them
- Customization of graphics
Learning goals:
- Independent usage of basic R functions including data import and export, basic plots and statistical tests
- Basic understanding of statistical methods applied in differential analyses
- Basics of using the ggplot2 R package to create and customize graphics for omics data
Prerequisites:
- Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences
- No prior knowledge on R required, basic knowledge of R (e.g. data import, basic plots) beneficial
- Laptop (Wifi will be available on-site) with R and preferrably RStudio installed to follow along
Keywords:
R; tidyverse; ggplot2; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing
Tools:
Download and more information on R here:
https://cran.r-project.org/
We recommend using an editor such as RStudio, see
www.rstudio.com
Contact:
- 2022-03-09
Michael Hiller's lab at the LOEWE Center for Translational Biodiversity Genomics (TBG) and Senckenberg in Frankfurt, Germany is looking for an ambitious PostDoc and PhD candidate.
- 2022-02-24
| Issue 01/2022 |
New start for de.NBI |
|
From January 2022 de.NBI is continued under the roof of the Forschungszentrum Jülich, member of the Helmholtz Association. Both, de.NBI and ELIXIR-DE administration offices including de.NBI Cloud Bielefeld and the Bielefeld part of the service center BIGI have changed affiliations and are operating from Bielefeld. Additionally, the ELIXIR communication officers located at the individual service centers have been employed by the FZJ. However, restructuring has not yet been completed and negotiations on the affiliation of the decentralized de.NBI partners are ongoing. In this context, the de.NBI Association (de.NBI e.V.), founded in August 2021, has been legally registered as a non-profit association and we hope that further funding can be acquired via this gateway. We will continue to update the interested public with our quarterly newsletters. |
|
|
ELIXIR Germany will participate in 10 out of 29 new Commissioned Services projects launched 01 January 2022. These projects bring together expertise from across ELIXIR’s Nodes and aim to provide methods to advance ELIXIR services and Platform and Community activities to cover a diverse collection of life-science and bioinformatics disciplines. Please see further information about Commissioned Services with German contributions here. |
|
|
The ELIXIR Board is the decision-making body in the intergovernmental organisation ELIXIR. The Board consist of scientific and administrative representatives from each ELIXIR Member State and EMBL. Board members are authorised to deliberate, negotiate and decide on behalf of the respective ELIXIR members. From January 2019 the Federal Ministry of Education and Research (BMBF) appointed two scientific delegates from ELIXIR Germany to the ELIXIR Board: Prof. Rolf Backofen (University of Freiburg) and Prof. Alexander Goesmann (University Gießen). At this year’s November meeting of the Board Alexander Goesmann was elected as Vice-Chair to the ELIXIR Board for 2022 and 2023. Together with Prof. Ferran Sanz (Spain) and Isabel Rocha (Portugal) he completes the Chair of the ELIXIR Board for the next two years. |
|
|
|
|
|
|
|
|
The de.NBI Cloud portal is ever evolving and our team is working hard on providing you with a better cloud system experience. From now on, we will regurarly update you on changes and new features of our project management system and in particular SimpleVM. Since this is our first feature update, we include some features and changes from the past two years which we think should be brought to your attention. In our update article we highlight As always: Feedback in any form is greatly appreciated and can be sent to us at |
|
|
Some research areas in life sciences touch the topic of sensible data. To offer a reliable environment for the processing of such data in a verifiable way, the IT Center of the Eberhard Karls Universität Tübingen has pursued the certification of the de.NBI Cloud site in Tübingen according to the ISO 27001 standard. As such, well defined procedures have been documented easing the bureaucratic aspects related to sensible data processing. As the third de.NBI Cloud facility, the Albrecht Ludwigs Universtät Freiburg has implemented an information security management system for their de.NBI Cloud site and a achieved an ISO 27001 certifcation to document a secure cloud environment. Preparations of the certification processes took more than two years. |
|
|
In 2021, Bayer AG and de.NBI / ELIXIR Germany organized two virtual public events entitled “Women in Data Science – Perspectives in Industry and Academia” promoting women doing outstanding work in data science across sectors. This lecture series was attended by about 150 participants at the first and 75 at the second event and was born out of the vision to showcase career models for women in data science. All in one, ten fantastic female professionals from academia and industry shared their experience on how to build your own career and showed opportunities for advancement. We are delighted that this series of lectures will be continued and look forward to the third event in spring 2022. Stay tuned! |
|
|
Future oriented analysis of research data applying AI methods exemplified by efforts within the de.NBI consortium have recently been published in gesundhyte.de (p. 42-45). An overview on AI-oriented activities in de.NBI is summarized on the website. |
|
| Numerous improvements of de.NBI services have been reported in the last quarter: Mercator: LipidXplorer: BRENDA: BacDive: |
|
|
The next de.NBI events or training events are announced at https://www.denbi.de/events or www.denbi.de/training. |
Impressum |
Responsible for ContentsA. Puehler, A. Tauch, T. Dammann-Kalinowski Phone: +49-(0)521-106-8750 Web:https://www.denbi.de SubscriptionIf you are interested in receiving regular updates on de.NBI - German Network of Bioinformatics Infrastructure, please subscribe to the de.NBI Quarterly Newsletter here. The mailing list will exclusively be used to distribute the de.NBI Quarterly Newsletter.
|
ELIXIR's activities are generally divided into five areas (Data, Tools, Compute, Interoperability, and Training) that are called Platforms. Each Platform has a Platform Coordinator based at the ELIXIR Hub and is managed by three Platform leads, with the scientific work being carried out by different groups within the Platform. The Platform Leads are collectively responsible for the operations and activities of their respective Platforms and help to drive new developments in these areas. In December 2021 Ulrike Wittig (HITS, Heidelberg) was elected as Platform Lead of the 
Due to the coronavirus pandemic, de.NBI and ELIXIR Germany offered mainly online training courses in 2021. Six years ago, the de.NBI training program started with 17 f2f training courses and 329 participants, constantly increasing to 79 courses with 1,586 participants in 2019. In 2020, the practical conduct of training courses was significantly affected by the pandemic, but it initiated the development of online training courses and materials (40 courses with 1,149 participants). Due to the implementation of these newly designed formats, de.NBI/ELIXIR Germany reached a new attendance record of 2,128 training course participants (49 courses) in 2021. All in all, up to now 9,076 scientists have been trained in 371 courses by our bioinformatics network.
- 2022-02-24
The Freiburg Galaxy Team is looking for an Admin/Systems Engineer/DevOps Engineer and a Bioinformatician working for the Galaxy project.
- Bioinformatician: https://www.denbi.de/jobs/1373-bioinformatician-working-for-the-galaxy-project
- Admin: https://www.denbi.de/jobs/1372-admin-systems-engineer-devops-engineer-working-for-the-galaxy-project
- 2022-02-07
In 2021, due to the global Corona pandemic, de.NBI and ELIXIR-DE offered mainly online training courses. In 2015, de.NBI started with 17 training courses and 329 participants, with increasing numbers in 2016 (40 courses with 882 participants), 2017 (69 courses with 1,489 participants), 2018 (77 courses with 1,520 participants) and 2019 (79 courses with 1586 participants), but a decresase (40 Courses with 1149 Participants) in 2020. Due to the establishment of different online training formats, de.NBI reached a new participant record of 2,128 training course participants (49 courses) in 2021.
The largest course was attended by 595, the smallest one – the only face-to-face course – by three scientists. Approx. 75% of the participants were PhD students or Postdocs. The remaining 25% were PIs, undergraduates, and participants from industry. The gender ratio of the students was 51% male and 49% female. We saw a remarkable high number of international and overseas participants in our courses due to the simplified virtual online participation. About 55% of the participants came from outside Germany. In general, the user survey shows satisfaction values more than 90%.
- 2022-01-17
Institut für Klinische Biochemie und Pathobiochemie (Direktor: Univ.-Prof. Dr. rer. nat. Hadi Al-Hasani)
The German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research at the Heinrich Heine University (HHU) Düsseldorf is an interdisciplinary research institute that links basic and clinical sciences to improve prevention, diagnosis and therapy of Diabetes mellitus and its complications. The Institute for Clinical Biochemistry and Pathobiochemistry (Director: Prof. Dr. Hadi Al-Hasani) investigates the molecular mechanisms of onset and progression of insulin resistance and type 2 diabetes. In a novel precision medicine approach, biosamples from deep-phenotyped patients are analyzed using state-of-the-art omics technologies to develop individualized options for prevention and treatment of the disease. For data analysis of patient profile data, we are looking for a highly motivated and talented
Post-doctoral Researcher Bioinformatics / Data Science
with excellent skills and knowledge in comprehensive analysis of omics data to join our international and collaborative team in an outstanding and competitive scientific environment.
Your tasks
- Conduct omics data analyses (e.g., transcriptomics and/or proteomics).
- Improve existing procedures for measurements and quality control of omics data sets.
- Develop novel tools for multi-omics data analysis, patient profiling, pathway mapping, visualization of omics data, signaling cascades in diabetes and use in precision medicine.
Your profile
- Studies and PhD degree in bioinformatics, data science, computer science, statistics or related.
- Prior experience in computational analysis of large-scale omics data sets.
- Advanced programming skills (e.g. R, Python).
- Knowledge in statistical and machine learning / AI methods.
- Independent and creative thinking.
- Excellent communication skills in English.
Desirable skills and experience
- Analysis of biological networks.
- Multi-omics data analysis.
- Visualization of data and results.
- Methods for feature selection, classification and clustering.
- Methods for data cleaning and data pre-processing.
- Further programming skills (e.g. C++, SQL, web programming, workflow systems).
Our Offer
- Association with the DFG-Research Training Group GRK2576 (vivid.hhu.de), the German Center for Diabetes Research (dzd-ev.de) and the Leibniz PostDoc Network, offering unique access to scientific resources and networks for career development, training and mentoring.
- Support towards independent, responsible and flexible work.
- The position is awarded for 2 years and an extension of the contract period is envisaged.
- Family-friendly working conditions and professional equality. Since May 2011, the DDZ has been certified by the “career and family audit”. The provision of section §7 (1) of the Part-Time and Fixed-Term Act is taken into account.
- Salary is regulated by the collective agreement for the civil service of the state (TV-L) in the version valid for the state of North Rhine-Westphalia.
- Severely handicapped persons will be preferred in case of equal qualification.
- Women are given preference for equal qualifications.
For more information see: https://ddz.de/job/post-doctoral-researcher-bioinformatics-data-science/