Content provider: de.NBI
BioC++ - solving daily bioinformatic tasks with C++ efficiently - ISMB 2020
12 July 2020BioC++ - solving daily bioinformatic tasks with C++ efficiently - ISMB 2020 https://www.denbi.de/training/933-bioc-solving-daily-bioinformatic-tasks-with-c-efficiently-ismb-2020 https://tess.elixir-europe.org/events/bioc-solving-daily-bioinformatic-tasks-with-c-efficiently-ismb-2020 Educators: René Rahn, Marcel Ehrhardt, Svenja Mehringer (CIBI) Date: 12.07.2020 9:00 am - 1:00 pm (Eastern Daylight Time) Location: ISMB 2020: Virtual Conference https://www.iscb.org/ismb2020/4399 Contents: In this half-day tutorial we are going to teach how to use modern C++ and utilise modern C++ libraries to rapidly develop tools and scripts for operating on and manipulating large-scale sequencing data. The high variability and heterogeneity often observed within various genomic data is challenging for many standard tools, for example for read alignment and variant calling. Often, these tools are wrapped in complicated pre- and postprocessing data curation steps in order to obtain results with higher quality. However, these additional steps incur a high maintenance and performance burden to the established work process and often do not scale with larger data sets. Seldomly, C++ is considered as the language of choice for these small processes, although it is the main language used in high-performance computing. We are going to show that implementing modern C++ can be as easy as using other modern high-level languages. Learning goals: Students will develop - skills in developing an application using the C++ programming language - skills in using modern C++ libraries to query large sequence databases (e.g. SeqAn, SDSL, etc.) - knowledge and understanding of modern C++ features, such as ranges and concepts - knowledge and understanding about modern and efficient data structures as well as algorithms crucial for large-scale genomic sequence analysis - knowledge and understanding about how to develop and sustain high-quality software Prerequisites: This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, proteomics, read alignment, variant detection, etc.). A fundamental knowledge about sequencing experiments and the involved data is required. We expect that attendees have an intermediate knowledge in programming with any high-level programming language, e.g. Python, Java or C++. Some basic C++-knowledge is helpful but not mandatory to successfully complete the course. This tutorial is targeting beginners and intermediate C++ developers that want to learn more about modern C++ features like ranges and concepts. Keywords: BioC++, modern C++, bioinformatics, SeqAn, FileIO Tools: - A simple text editor - g++ >= 7 - cmake >= 3.12 - git 2020-07-12 09:00:00 UTC 2020-07-12 13:00:00 UTC de.NBI    meetings_and_conferences  
Introduction to Galaxy and Python with Jupyter Notebook
13 - 27 July 2020Introduction to Galaxy and Python with Jupyter Notebook https://www.denbi.de/training/938-introduction-to-galaxy-and-python-with-jupyter-notebook https://tess.elixir-europe.org/events/introduction-to-galaxy-and-python-with-jupyter-notebook Educators: Julia Scheel, Andrea Bagnacani, Markus Wolfien (RBC) Location: Online Dates: 13.07.2020, 15.07.2020, 27.07.2020 Contents: Life sciences used to be all about wet-lab expertise. Due to fast technical innovations and digitalisation we are now facing the challenge of dealing with vasts amounts of data. Analyses of such data requires advanced statistics and specialized tools to run analyses and to visualize both data and results. Science becomes more and more dependent on bioinformaticians and computer scientists, which creates the additional challenge of interdisciplinary communication. This course introduces the Galaxy framework, an open source, web-based platform for data intensive biomedical research, Python, an interpreted, high-level, general-purpose programming language, and Jupyter Notebook, a multi-language framework for interactive computing. You can chose to use this course as a stepping stone into advanced analyses, or as an opportunity to learn what your bioinformatician of trust is actually doing. Further courses and tutorials for Galaxy and Python are widely available. Both Galaxy and Python have active user communities, making self-paced learning possible. Learning goals: - Know your data: implications of quality control and data preprocessing - Hands-on quality control and data preprocessing - Understanding and programming in Python - Hands-on session with Jupyter Notebooks. Prerequisites: This workshop is intended for PhD students with a background in medicine, engineering and life science research. In order to take part in the hands-on session we recommend one Laptop/PC and a stable internet connection. We further ask you to create a Galaxy account beforehand. Tools: - Galaxy: https://usegalaxy.eu - Python: https://python.org - Jupyter Notebook: https://jupyter.org/ 2020-07-13 09:00:00 UTC 2020-07-27 17:00:00 UTC de.NBI    workshops_and_courses  
Computational genomics course for hands-on data analysis 2020
23 - 25 September 2020
Berlin, GermanyComputational genomics course for hands-on data analysis 2020 https://www.denbi.de/training/806-computational-genomics-course-for-hands-on-data-analysis-2020 https://tess.elixir-europe.org/events/computational-genomics-course-for-hands-on-data-analysis-2020 Educators: Altuna Alkalin, Verdan Franke, Bora Uyar (RBC/deNBI-epi Scientists from Berlin) Date: 15-17 June 2020 Location: BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin. Mitte Campus. Contents: The general aim of the course is to equip participants with practical and technical knowledge to analyze single cell RNA-seq data. With this aim in mind, we will go through unsupervised machine learning methods to analyze high-dimensional data sets, and move on to statistical methods developed to analyze bulk RNA-seq. Lastly, we will introduce analysis techniques used for single cell RNA-seq. There will be theoretical lectures followed by practical sessions where students directly apply what they have learned. The programming will be mainly done in R. Day 1: Intro to machine learning & data visualization for genomics Day 2: Bulk RNA-seq analysis Day 3: Single cell RNA-seq analysis 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: 15th of April 2020-09-23 09:00:00 UTC 2020-09-25 17:00:00 UTC de.NBI Berlin, Berlin, Germany Berlin Berlin Germany    workshops_and_courses  
3rd de.NBI Cloud Usermeeting
8 - 14 October 20203rd de.NBI Cloud Usermeeting https://www.denbi.de/training/936-3rd-de-nbi-cloud-usermeeting https://tess.elixir-europe.org/events/3rd-de-nbi-cloud-usermeeting 3rd de.NBI Cloud Usermeeting Online Educators: de.NBI cloud group including Peter Belmann, Daniel Hübschmann, Peter Ebert, Martin Zurowietz, Kay Schallert, Sven Olaf Twardziok, Jan Krüger, Maximillian Hanussek, Martin Braun, Marius Dieckmann, Björn Grüning etc. Date: 8.10.2020 – 14.10.2020 Location: Online Contents: We are pleased to announce the third de.NBI Cloud User Meeting. In comparison to preceding meetings, this year`s meeting will be organized as an online conference. Over five days users can watch talks of already experienced users and long running projects and thereby learn about best practices in cloud computing. Same as the last years we will try to cover topics for beginners such as virtualization but also topics for software engineers and administrators such as orchestration with Kubernetes. Participants will learn how to scale up their analysis to handle growing input data and how to use workflow managers such as Snakemake in a cloud environment. As every year we are also going to demonstrate the usage of bioinformatics software in the de.NBI Cloud using Docker images or Bioconda packages. Planned Courses: - Running Snakemake Workflows in the de.NBI Cloud - OpenStack Introduction - BioConda and BioContainers - Kubernetes Introduction - Deploying Web Services in the de.NBI Cloud - Extensible Cluster Setup in the Cloud with BibiGrid and Ansible - Using Terraform to define infrastructure as code Learning goals: Working with the de.NBI cloud Prerequisites: We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community. Keywords: de.NBI cloud Tools: de.NBI cloud Webpage: https://cloud.denbi.de/3rd-de-nbi-cloud-user-meeting/ 2020-10-08 09:00:00 UTC 2020-10-14 17:00:00 UTC de.NBI    meetings_and_conferences  
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