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7 events found

Content provider: EMBL-ABR  or de.NBI 

  • ELIXIR FONDUE Datathon

    15 - 28 June 2021

    ELIXIR FONDUE Datathon ELIXIR FONDUE Datathon Online Application: Educators: Sebastian Beier (GCBN/ELIXIR-DE), Anne Fiebig (GCBN/ELIXIR-DE), Matthijs Brouwer (ELIXIR-NL), Martijn van Kaauwen (ELIXIR-NL), Cyril Pommier (ELIXIR-FR), Fuqi Xu (EBI BioSamples), Isuru Liyanage (EBI BioSamples), Sam Holt (EBI ENA), Baron Koylass (EBI EVA) Date: 15th June 2021, 10:00 a.m. – 01:00 p.m. 21st June 2021, 10:00 a.m. – 01:00 p.m. 28th June 2021, 10:00 a.m. – 01:00 p.m. Location: Online Contents: Recent progress in sequencing technologies has produced several large-scale genotyping data sets for crops. The insights afforded by this data have been published in high profile scientific articles, but the underlying raw genotype data and the associated sample and population metadata have not been routinely submitted to appropriate archives. In this workshop we will present best practices on how to format the data and metadata to comply with modern guidelines and help make data resources more long-term stable. Descriptive metadata and the usage of common identifiers shared in different repository is the main tool for that. The course is motivated by the ELIXIR implementation study FONDUE ( and structured in a mix of lectures about the three involved repositories (EBI BioSamples, EBI ENA, EBI EVA) and hands-on test submissions to these repositories. A dedicated time-slot is also allocated for trouble-shooting of own data sets. Learning goals: During this three half-day event participants will learn how to overcome common mistakes during the submission of sample data to BioSamples, sequencing output to ENA and genotyping data to EVA. Prerequisites: The training course is designed not to be restrictive by the experience level of the participants. Beginners will learn how to submit data to the archives, while people with programmatic knowledge will be receive information of updated guidelines and requirements. Keywords: FAIR data, Genotyping, Phenotyping, Genomics, SNPs Tools: Web Browser 2021-06-15 10:00:00 UTC 2021-06-28 13:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • SeqAn Developer Meeting 2021

    28 - 30 June 2021

    SeqAn Developer Meeting 2021 Educators: Marcel Ehrhardt, Enrico Seiler (CIBI) Date: 28 - 30.06.2021 Location: Online Contents: The SeqAn project will hold its SeqAn3 developer meeting and a de.NBI / CIBI workshop online at the end of June (28th to 30th). Goal of the meeting is to kickstart new projects with our collaborators from RKI, MPI, Italy, etc. and for the SeqAn core team to plan the direction of the next SeqAn3 release. Additionally, to working on the release of SeqAn3, the SeqAn team will offer a workshop as part of de.NBI that includes trainings and hands-on sessions so that our project partners and interested guests are the first to learn how to use our new software and related programming techniques. Those parties will be able to come to the meeting with their current research problems or existing applications, and we will do our best to port these or develop new working proto-types with them on-site. Furthermore, the meeting provides a unique opportunity for those parties to present their research and formulate expectations they have of a modern Bionformatics library/framework and thereby influence the future development of SeqAn in a way that benefits their work in the long run. Learning goals: • Software engineering and App development with SeqAn • High-performance computing using SeqAn and the STL • Modern C++ features like Concepts, Ranges, and many more Prerequisites: This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, assembly, read alignment, variant detection, etc.) Attendees must have an intermediate level of programming skills and a strong interest in C++ as well as a fundamental background in the SeqAn3 software library. Attendees must bring their own laptop. Software for the tutorial should be installed beforehand, but we will also dedicate some extra time for setting up the workstations. The following systems/software is required: • MacOS (g++-7 or higher) or Linux or BSD (g++-7 or higher) • Git • Cmake-3.8 or higher Keywords: SeqAn3, Sequence Analysis, modern C++ Tools: SeqAn3 2021-06-28 09:00:00 UTC 2021-06-30 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Computational genomics course for hands-on data analysis 2021 - Machine Learning for Genomics

    2 - 6 August 2021

    Computational genomics course for hands-on data analysis 2021 - Machine Learning for Genomics Educators: Altuna Alkalin, Verdan Franke, Bora Uyar, Jan Dohmen, Artem Baranovsky (RBC/deNBI-epi Scientists from Berlin) Date: August - September 2021 Location: Online Contents: The general aim of the course is to equip participants with practical and technical knowledge to deploy machine learning methods on genomic data sets. With this aim in mind, we will go through certain statistical concepts and move on to unsupervised and supervised machine learning methods to analyze high-dimensional data sets. This will be an online training event which will be mostly asynchronous. A typical module would comprise of lectures followed by hands-on exercises and a quiz. The participants will have a week to complete the lectures and exercises for each module at their own pace and at the time of their choosing within that week. Only the participants who complete the exercises and a quiz in a timely manner and have at least 50% of the tasks in the exercises will be invited to the capstone project. The capstone project tasks are designed using data from a real world problem. The participants who provide the best reports for the capstone projects will be invited to co-author a manuscript with the Akalin lab. Most tasks can be done on a regular laptop. A recent version of R and Rmarkdown is necessary to complete the hands-on exercises. Module 1: Statistics for genomics Module 2: Unsupervised learning and applications in genomics Module 3: Supervised learning and applications in genomics Module 4: Capstone project: Drug response prediction using genomic data Learning goals: The course will be beneficial for first year computational biology PhD students, and experimental biologists and medical scientists who want to begin data analysis or are seeking a better understanding of computational genomics and analysis of popular sequencing methods.r Prerequisites: Some statistics and R programming experience will be good to keep up with the course. Practicals will be done in R. Keywords: Computational genomics, RNA-seq, Machine learing, Tools: R/Bioconductor Application Deadline: 30th of June 2021-08-02 09:00:00 UTC 2021-08-06 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • 5th BioInfra.Prot Tool-Training for Proteomics & Community Meeting

    23 August 2021

    5th BioInfra.Prot Tool-Training for Proteomics & Community Meeting Educators: Anika Frericks-Zipper, Markus Stepath, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2021-08-23 Location: online Contents: In this one-day event we will show some of BioInfra.Prot's tools provided by de.NBI and have a community meeting in the afternoon. The focus of the tool part will be protein inference and boosting of identification performance. In order to do this we will use the tool PIA (Protein Inference Algorithms). PIA allows inspecting and combining the results of proteomics search engines. The focus lays on the integrated inference algorithms for identification and quantification purposes. Besides the tool-based session, we offer a session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. In addition, attendees will get to know the data science platform KNIME. As a novelty, there will be an optional community meeting on the same day (“Current and future use cases for BioInfra.Prot services mentioned by the user community”), where the focus will be on social networking and a relaxed exchange of ideas. In addition, selected use cases for data analysis from the proteomics area with BioInfra.Prot tools or services will be presented in short flash talks. Is your interest sparked? Then simply register with a few clicks via the registration form listed below. Learning goals: Tool-Training (in the morning): Attendees of the course will learn how to use the tools PIA effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud and the data science platform KNIME. Community Meeting (optional in the afternoon): Networking and sharing of ideas in the field of proteomics data analysis and especially the user-oriented development of BioInfra.Prot tools and services. Learning and discussion based on presented use cases for data analysis from the proteomics area with BioInfra.Prot tools or services Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC- MS data are sufficient. Attendees are required to have a computer, headset, camera, and a stable internet connection. Keywords: Proteomics; Data Analysis; de.NBI Cloud; Community Meeting Tools: PIA; KNIME; 2021-08-23 09:00:00 UTC 2021-08-23 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI Summer School 2021 - Proteomics & Lipidomics

    27 September - 1 October 2021

    de.NBI Summer School 2021 - Proteomics & Lipidomics TBA 2021-09-27 09:00:00 UTC 2021-10-01 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • LIFS Course - ILS 2021 & LipidomicsForum 2021

    5 October 2021

    Regensburg, Germany

    LIFS Course - ILS 2021 & LipidomicsForum 2021 TBA 2021-10-05 09:00:00 UTC 2021-10-05 17:00:00 UTC de.NBI Regensburg, Regensburg, Germany Regensburg Regensburg Oberpfalz Germany [] [] [] [] [] []
  • 3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon

    22 - 24 November 2021

    Lutherstadt Wittenberg, Germany

    3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon TBA 2021-11-22 09:00:00 UTC 2021-11-24 17:00:00 UTC de.NBI Lutherstadt Wittenberg, Lutherstadt Wittenberg, Germany Lutherstadt Wittenberg Lutherstadt Wittenberg Germany [] [] [] workshops_and_courses [] []

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