RNA-Seq data analysis with Galaxy for clinical applications - GMDS 2019
8 September 2019
Dortmund, GermanyRNA-Seq data analysis with Galaxy for clinical applications - GMDS 2019 https://www.denbi.de/training/662-rna-seq-data-analysis-with-galaxy-for-clinical-applications-gmds-2019 https://tess.elixir-europe.org/events/rna-seq-data-analysis-with-galaxy-for-clinical-applications-gmds-2019 Educators: Andrea Bagnacani, Markus Wolfien (RBC / de.STAIR) Location: Emil-Figge-Straße 44, 44227 Dortmund Date: 08.09.2019, 10:00 - 18:00 Contents: In this workshop, we provide a summary of the applications of Next Generation Sequencing (NGS) technologies in the clinical context. These are presented through a hands-on session on RNA-Seq data analysis, following a use case to tudy a clinical NGS dataset. Leveraging on the Galaxy environment, we guide the participants through all relevant steps for carrying out the analysis, as well as linking the obtained results with current gene-disease-related databases, or other relevant resources to highlight the clinical impact of the technology. Finally, we discuss our audience's NGS experiments, and provide advice on their NGS data analysis approaches. Learning goals: Get familiar with the Galaxy framework (https://usegalaxy.eu) for carrying out scientific data analyses, learn methods for data exploration and quality control of NGS datasets, and get familiar with the concepts underlying genome alignment and data visualization of subsequent results. Prerequisites: This workshop is intended for MSc/PhD students, postdocs, and researchers with a background in Life Science research. Keywords: Galaxy, Reproducibility, Workflow development, RNA-Seq data analysis, Visualization Tools: Galaxy (https://usegalaxy.eu), Galaxy Training material (https://galaxyproject.github.io/training-material/) Contact: email@example.com Registration: https://gmds.de 2019-09-08 09:00:00 UTC 2019-09-08 17:00:00 UTC de.NBI Dortmund, Dortmund, Germany Dortmund Dortmund Arnsberg Germany    meetings_and_conferences  
LIFS Course - ILS 2021 & LipidomicsForum 2021
5 October 2021
Regensburg, GermanyLIFS Course - ILS 2021 & LipidomicsForum 2021 https://www.denbi.de/training/1151-lifs-course-ils-2021-lipidomicsforum-2021 https://tess.elixir-europe.org/events/lifs-course-ils-2021-lipidomicsforum-2021 Educators: Jacobo Miranda Ackerman, Daniel Krause, Nils Hoffmann (de.NBI, BioInfra.Prot / LIFS) Date: October 5th, 2021, 9:00 – 12:00 (CEST) & 13:00 – 17:00 (CEST) Deadline for Workshop Registration: Until capacity is reached. Location: On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise) Contents: In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. In part four, we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology. Morning 09:00 – 09:45 Welcome and Introduction 10:00 – 10:30 Targeted Lipidomics with LipidCreator and Skyline 10:30 – 12:00 LipidCreator and Skyline Exercises Afternoon 13:00 – 14:30 Shotgun Lipidomics with LipidXplorer 14:30 – 15:30 Quantification of Shotgun Lipidomics data with lxPostman 15:30 – 17:00 Lipidome comparison with LUX Score Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score Registration: Please select the “LIFS Training session I & II” in the Workshops section of the conference registration. Capacity is limited to 30 participants. 2G (vaccinated or fully recovered) - with either certificate of full vaccination or certificate of recovery / positive PCR test not older than six months. Nose+mouth protection - FFP2 mask or medical mouth nose protection have to be worn inside of buildings. 2021-10-05 09:00:00 UTC 2021-10-05 17:00:00 UTC de.NBI Regensburg, Regensburg, Germany Regensburg Regensburg Oberpfalz Germany      
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