3^rd BioHackathon Germany - Registration open

After the tremendous success of the first two BioHackathon Germany editions in Lutherstadt Wittenberg and Bielefeld, we are excited to announce that de.NBI and ELIXIR Germany will be hosting the 3^rd BioHackathon Germany in Kassel from 9 - 13 December 2024.

We hope to attract a diverse group of participants from de.NBI, ELIXIR Germany, other ELIXIR nodes, and interested parties from academia and industry. Industry involvement is highly encouraged to foster collaboration and innovation.

• Engaging projects: Dive into 9 different projects spanning areas such as large language models, training, plant bioinformatics, and more. Seven projects will take place on-site with possibility of hybrid participation and two projects will be conducted on-line.
• Participation: on-site or remote. It is desired that on-site participants will attend for the whole week. 
• Networking opportunities: Connect with experts and peers from various fields to share knowledge and ideas.

• Open until: 15 November 2024
• Selection basis: first-come, first-served
• Register here

Don't miss this unique opportunity to collaborate, learn, and innovate with leading experts and fellow enthusiasts in the bioinformatics community. Secure your spot today!

de.NBI/ELIXIR-DE All Hands Meeting, 28-219 Nov 2024 in Berlin 

The de.NBI / ELIXIR-DE All Hands Meeting 2024 will take place in Berlin on 28 - 29 November 2024. This event is intended for all PI and coworkers of de.NBI and ELIXIR-DE and will foster exchange of information and give the opportunity to communicate and to network. Reports on the activities of the network, especially the service centers and working groups, are planned. Information is directly spread through internal network communication channels. Please register! 

Annual Meeting 2024 of the de.NBI Industrial Forum on 19 Nov 2024

This year’s Annual Meeting of the de.NBI Industrial Forum will take place virtually 19 November 2024. Academic and industrial presentations will showcase their research, experience, and views on “AI Ventures in the Life Science”.

The Annual Meeting is the key event of the de.NBI Industrial Forum connecting academic and industrial stakeholders and reflecting insights on recent research developments in the Life Sciences and current industrial topics.

Expand your network, learn about recent research developments in AI in industry and academia, and explore industrial applications in the Life Science!

More information on the agenda, registration as well as relevant organizational information can be found here. 

News from de.NBI/ELIXIR-DE

de.NBI partners active in EOSC Node Concept development 
In an unscheduled meeting on 5 July 2024, the CCU decided that the network would submit an expression of interest (EoI) to participate as a regional thematic node in the development of the EOSC Node and Federations Concept. Furthermore, de.NBI is mentioned in the EoI of the NFDI e.V., which is agreed to represent the national German node, and is involved in the EoI of ELIXIR. This creates the opportunity to be involved in the further development of the concept. An invitation to participate in the workshop in October has already been issued.

  News from ELIXIR

ELIXIR's 12 Internal Projects Awarded €1.6M to support ELIXIR's scientifc strategy

ELIXIR has invested an additional €1.6 million in 12 projects supporting the 2024-28 Scientific Programme priorities: Cellular and Molecular Research, Biodiversity, Food Security and Pathogens, and Human Data and Translational Research. These projects form work packages within the three ongoing Commissioned Services (CoS) for each scientific priority, will start on 1 January 2025, and run for two years. They aim to bring together the expertise of the ELIXIR Nodes, research domains (Communities), and technical areas (Platforms) to drive innovation in bioinformatics. ELIXIR Germany will contribute to 6 of the 12 projects, adding national expertise to strengthen development efforts.

New ELIXIR Cancer Data Community

ELIXIR has launched a new Cancer Data Community, led by Macha Nikolski (ELIXIR France), Eivind Hovig (ELIXIR Norway), and Fátima Al-Shahrour (ELIXIR Spain). Established in early 2024 after the publication of its white paper, the Community focuses on improving the accessibility, quality, and interoperability of cancer data. Additionally, it will serve as a central hub for experts from ELIXIR Nodes, the Cancer Data Community, and external partners to coordinate efforts and expand on ELIXIR’s existing cancer research portfolio.

New Focus Group Launched to Advance Domestic Animal Genomics and Phenomics

In early June, ELIXIR introduced the new Focus Group on Domestic Animals Genome and Phenome, aimed at supporting genotype-to-phenotype analysis for farmed and companion animal species. The Focus Group's primary goal is to develop a coordinated, open, and standardized data life cycle, essential for advancing genotype-to-phenotype research and to connect researchers and data scientists across species and countries. The group is led by Emily Clark (UK), Martien Groenen (Netherlands), Peter Harrison (EMBL), and Catherine Larzul (France).

• The budget allocation for the Research Infrastructures programme of FP10 should reflect the fundamental role research infrastructures play in delivering scientific excellence and socio-economic impact
• Open Data should remain the default position for FP10, with greater recognition for the importance of software and other digital assets
• FP10 should enable a better utilisation of research infrastructures by projects funded under other themes, including Partnerships, Missions and the implementation of Data Spaces
• FP10 should provide more fit-for-purpose funding mechanisms for research infrastructures

  News on the de.NBI Cloud

• News on de.NBI Cloud facilities:
  • de.NBI Cloud Gießen has finished their migration to their new datacenter infrastructure. The transition only affected cloud projects for a brief period during the migration of existing projects and VMs.
  • de.NBI Cloud EMBL now offers a Kubernetes environment for services. Please use the project application form’s comment field to request access. 

• de.NBI Cloud activities:
  • The de.NBI Cloud Portal team will present both SimpleVM and the de.NBI Cloud at the EGI conference in 30 Sep -4 Oct 2024 in Lecce, Italy.
  • The SPAAM Ancient Metagenomics Summer School was conducted in August on the de.NBI Cloud infrastructure using the SimpleVM workshop mode with more than 40 participants and VMs.
  • The HAAM Summer School (Human Ancient DNA, Ancestry and Mobility) was conducted in June on the de.NBI Cloud infrastructure using the SimpleVM workshop mode also with more than 40 participants and VMs.

• Current figures on the de.NBI Cloud: Number of users: 3565 (3262), number of active projects: 631 (661), number of publications referencing the use of the de.NBI Cloud: 1096 (1008). This equals an increase of ~9% in users, a decrease of ~4,5% in projects and an increase of ~8,7% in publications, respectively, since June 2024.

• One new testimonial on the use of the de.NBI Cloud for Genomics and Metagenomics of Leaf Microbiome has been published.

News on Services

The Galaxy Community published "The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update" in Nucl. Acids Res. 2024 Jul 5;52(W1):W83-W94.

• CalibraCurve: version 2.0 now includes the KNIME workflow.
• COPASI stable release 4.44 (Build 295) was released. Bugs in the command line and the simulation engine were fixed.
• EURISCO, European Search Catalogue for Plant Genetic Resources, has been extended by national inventory data of four countries.
• UseGalaxy.eu Tool Updates: the tools on UseGalaxy.eu have been updated repeatedly by the automated tool update and installation process in Jenkins Build #469.
• MassBank Release version 2024.06: numerous new spectra have been added and a new contributor of further spectra to MassBank has been welcomed.
• MHCquant 2.6.0: A new rescore module, new support options and some further issues were added. For details see here.
• medbioinf/pia: update 1.5.5 now allows adjusting threads via CLI, and RT problems in mzid were fixed.
• FAIRDOM-SEEK Version 1.15.2 was released. It contained a couple of further bug fixes and improvements, in addition to the major improvement, upgrades and bug fixes that was already addressed in version 1.15.0.
• SILVA: The SILVA taxonomy release 138.2 is a maintenance release with bug fixes and – among others - extensive adoption of the LPSN taxonomy at the genus and phylum level, ongoing adoption of the LPSN taxonomy for families, orders and classes.

Recent Publications by de.NBI partners

• Bielow C, Hoffmann N, et al. Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. J Am Soc Mass Spectrom. 2024 Aug 7;35(8):1875-1882. https://doi.org/10.1021/jasms.4c00174
• Lange E, Kranert L, J Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol. 2024 Jun 19;15:1368377. https://doi.org/10.3389/fmicb.2024.1368377
  Diedrich K, Ehrt C, ..., Rarey M . User-centric design of a 3D search interface for protein-ligand complexes. J Comput Aided Mol Des. 2024 May 30;38(1):23. https://doi.org/10.1007/s10822-024-00563-3
• Witowski A, ..., Weber M, ..., Eisenacher, ..., CovidDataNet.NRW research group. Activation of the MAPK network provides a survival advantage during the course of COVID-19-induced sepsis: a real-world evidence analysis of a multicenter COVID-19 Sepsis Cohort. Infection. 2024 Jun 19. https://doi.org/10.1007/s15010-024-02325-7
• Welten S, ..., Kohlbacher O, Kirsten T. A study on interoperability between two Personal Health Train infrastructures in leukodystrophy data analysis. Sci Data. 2024 Jun 22;11(1):663. https://www.doi.org/10.1038/s41597-024-03450-6
• Dai C, Pfeuffer J, ..., Sachsenberg T, Demichev V, Bai M, Kohlbacher O, et al. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nat Methods. 2024 Jul 4. https://www.doi.org/10.1038/s41592-024-02343-1
• Giurgiu M, ..., Reinert K, Henssen AG. Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Res. 2024 Aug 7:gr.279123.124. https://doi.org/10.1101/gr.279123.124
• Loghmani LG, ..., Kummer U, Fiedler T. Comparing genome-scale metabolic models of the non-resistant Enterococcus faecalis ATCC 19433 and the multi-resistant Enterococcus faecalis V583. J Biotechnol. 2024 Jul 10;392:109-117. https://www.doi.org/10.1016/j.jbiotec.2024.07.006
• Schulz-Mirbach H, ..., Klamt S, Lindner SN. Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules. Nat Commun. 2024 Aug 7;15(1):6725. https://www.doi.org/10.1038/s41467-024-51029-x
• Bueno da Silva M, Wiese-Klinkenberg M, Usadel B, Genzel F. Potato Berries as a Valuable Source of Compounds Potentially Applicable in Crop Protection and Pharmaceutical Sectors: A Review. J Agric Food Chem. 2024 Jul 17;72(28):15449-15462. https://www.doi.org/10.1021/acs.jafc.4c03071
• Santos-Júnior CD, ..., Bork P, et al. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell. 2024 Jul 11;187(14):3761-3778.e16. https://www.doi.org/10.1016/j.cell.2024.05.013
• Holzem M, Boutros M, TW Holstein TW. The origin and evolution of Wnt signalling. Nat Rev Genet. 2024 Jul;25(7):500-512. https://www.doi.org/10.1038/s41576-024-00699-w
• Thiele M, ..., Bork P, ..., MicrobLiver consortium; GALAXY consortium. Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases. J Hepatol. 2024 Aug;81(2):345-359. https://www.doi.org/10.1016/j.jhep.2024.03.035
• Gegner HM , ..., Saez-Rodriguez J, Huber W, Poschet G, Krijgsveld J. A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens. Clin Proteomics. 2024 Jul 5;21(1):49. https://www.doi.org/10.1186/s12014-024-09501-9
• Runge F, ..., Backofen R, Hutter F. Partial RNA design. Bioinformatics. 2024 Jun 28;40(Supplement_1):i437-i445. https://www.doi.org/10.1093/bioinformatics/btae222
• Rautenstrauch P, Ohler U. Liam tackles complex multimodal single-cell data integration challenges. Nucleic Acids Res. 2024 Jul 8;52(12):e52. https://www.doi.org/10.1093/nar/gkae409
• Phan TL, (...), Stadler PF. Reaction rebalancing: a novel approach to curating reaction databases. J Cheminform. 2024 Jul 19;16(1):82. https://www.doi.org/10.1186/s13321-024-00875-4
• Pabba MK, ..., Rohr K, Cardoso MC. DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes. Histochem Cell Biol. 2024 Jul;162(1-2):109-131. https://www.doi.org/10.1007/s00418-024-02285-x 
• Gavriilidis GI, ..., Ishaque N, Psomopoulos F. A mini-review on perturbation modelling across single-cell omic modalities. Comput Struct Biotechnol J. 2024 Apr 25;23:1886-1896. https://www.doi.org/10.1016/j.csbj.2024.04.058
• D Kopczynski D, Ejsing CS ..., Hoffmann N, ..., Schwudke D, Shevchenko A, ..., Ahrends R, Liebisch G. The Lipidomics Reporting Checklist A framework for transparency of lipidomic experiments and repurposing resource data. J Lipid Res. 2024 Aug 14:100621. https://www.doi.org/10.1016/j.jlr.2024.100621

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