SPAAM Summer School 2023: Introduction to Ancient Metagenomics
The workshop functionality of de.NBI Cloud has been extremely helpful in maximising the accessibility of a global cohort students to consistent software environments to ensure everyone starts on a level playing field. In particular the desktop environments accessible through a web-browser were a great help due to a large number of students with limited command-line experience.
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de.NBI BioHackathon SpaceHack project
How did it work? It was fantastic! I have never organised an event with shared compute that worked so well with regards to helpful consultation, accessibility, scalability and flexibility. We are already organising the follow up of our hackathon project on the de.NBI cloud, and strongly encourage other hackathon and workshop organisers to do the same.
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Computational solutions from data science and machine learning to solve biomedical problems
Our research focuses on developing computational solutions from data science and machine learning to solve biomedical problems. In addition, we aim to develop new methods and algorithms, e.g., for analyzing (meta-)genomic and (meta-)transcriptomic data of microorganisms
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de.NBI Cloud in teaching
Through all of these projects, we have greatly appreciated the interaction with the de.NBI cloud team who has provided tremendous support and responded quickly to various demands for extensions and provided constant expertise to set up the infrastructure.
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Plant Breeding Driven by Big Data Analysis
Plant Breeding is a big numbers game. To enable breeding progress for complex traits like yield and stress tolerance in crop plants, integrated analyses of multi-omics and digitized phenomics data from large plant populations grown in multiple field studies are required. The de.NBI cloud is a great resource which is helping us to extract meaning from large noisy and heterogenous data sets for predicting yield and quality traits from genotypes of crop plants.
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de.NBI Cloud enables Next Generation Plant Science
We integrate genomic, transcriptomic, and metabolomic data of multiple plant species to decipher specialized biosynthesis networks. Plants produce a plethora of specialized metabolites. Understanding the complex connections of biosynthesis pathways requires the analysis of large data sets.
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PhenoMeNal-H2020
Having the de.NBI Cloud, we can easily crunch through some large-scale metabolomics data sets using the containerised workloads we have developed in the PhenoMeNal-H2020.EU project. Scaling up in case of peak usage, e.g. in a training event, works like a charm.
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German Human Genome-phenome Archive (GHGA)
The de.NBI Cloud has been a great resource for GHGA software development team to test the concept in a sandbox project, and utilize state-of-the-art cloud and container tools like OpenStack and Kubernetes.
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MetaProtServ
We use the de.NBI Cloud since 2017 to serve the MetaProteomeAnalyzer software to the metaproteomics community. Now, three times more users analyses their experiments using our software. Our next step is to evolve the software to an analytical platform for mass spectrometry experiments on the de.NBI Cloud using automatic scalable cloud architecture, the SMACK stack.
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Baltic Sea Research
Thanks to de.NBI Cloud, we are able to conduct almost all aspects of large-scale microbial community analyses, such as 16S amplicon analysis, metagenomics, metatranscriptomics and metaproteomics. With the availability and support of de.NBI Cloud, we have created a working and learning environment for undergraduate, PhD students and Postdocs to develop and improve their reproducible workflows and analyses.
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Systems Medicine of the Liver
A major advantage of the de.NBI cloud is that we save time managing hardware and servers and instead focus on the actual science. Compared to other cloud infrastructure the de.NBI cloud provides direct and uncomplicated contact with the support team and admins
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Phased Genome Assembly
The outstanding support during all project phases and the straightforward way of requesting or extending a de.NBI Cloud application make the de.NBI Cloud an ideal platform for data-driven bioinformatic research.
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