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  • Metagenomics: Data Analysis and Interpretation

    16 - 19 September 2019

    Norwich, United Kingdom

    Metagenomics: Data Analysis and Interpretation https://tess.elixir-europe.org/events/metagenomics-data-analysis-and-interpretation This course will provide an overview of the main aspects involved in metagenomics data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research. A substantial part of the course will be devoted to hands-on experience with bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start with an overview of NGS technologies, a look at experimental approaches and emerging technologies, including a tour of Earlham Institute’s Genomic Pipelines laboratories. Then the remainder of the course will be spent in front of the computers learning how to produce metagenomic assemblies, and taking participants from data to publication-ready figures. 2019-09-16 09:00:00 UTC 2019-09-19 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ [] training@earlham.ac.uk [] [] workshops_and_courses [] []
  • Microscopy Image Analysis Course

    19 - 20 September 2019

    Heidelberg, Germany

    Microscopy Image Analysis Course https://tess.elixir-europe.org/events/microscopy-image-analysis-course Educators: Karl Rohr, Thomas Wollmann, Manuel Gunkel (HD-HuB), Qi Gao, Leonid Kostrykin Date: 19.-20.9.2019 Location: Heidelberg University IPMB (Institute of Pharmacy and Molecular Biotechnology) Im Neuenheimer Feld 364 Contents: The course gives an introduction into the field of microscopy image analysis for cell biology and the use of software tools for automated processing of image data. Basic methods for computer-based analysis of microscopy images are introduced such as image preprocessing, segmentation, feature extraction, classification, colocalization, and tracking. Concepts of software platforms with focus on ImageJ and their use for analyzing cell microscopy image data are also taught. Workflow systems for automating image analysis pipelines are also considered (e.g., KNIME, Galaxy). The course consists of lectures and practical sessions. Participants should bring their laptops for the practical sessions. The target group are researchers with a background in biology or medicine that need to analyze their data and have little or no experience in automated image analysis. Learning goals: - Introduction into cell microscopy image analysis - Application of software tools for automated analysis of image data Prerequisites: Basic knowledge in using software tools for image analysis is helpful but not mandatory Keywords: Computer-based image analysis, image preprocessing, segmentation, feature extraction, classification, colocalization, tracking Tools: Image J Course fee: Participants will be charged with a course fee of 40 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email. Registration: Please register directly on the HD-HuB website: https://www.hd-hub.de/course-dates/3-all/47-microscopy-image-analysis-course In the "Comments" section of the registration form, please provide some information about yourself and your motivation to attend the training (e.g. Position, Field of study/Background, Topic of work, Knowledge of image analysis methods/tools). Registration closes on August 11, 2019. The capacity is limited to 20 participants and applicants will be selected after registration closed. You will be notified of the outcome by e-mail on August 23, 2019. 2019-09-19 09:00:00 UTC 2019-09-20 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] [] [] []
  • 8th Galaxy workshop on HTS data analysis

    23 - 27 September 2019

    Freiburg im Breisgau, Germany

    8th Galaxy workshop on HTS data analysis https://tess.elixir-europe.org/events/8th-galaxy-workshop-on-hts-data-analysis Educators: RBC Freiburg Date: 23.-27.09.2019 Location: Uni Freiburg Contents: 1-week full-day hands-on workshop in Freiburg. Topics: - Galaxy Introduction - Data analysis of RNA-seq, ChIP-seq, Exome-seq, MethylC-seq data Learning goals: Using Galaxy for data analysis of HTS data. Topics: - Quality control - Mapping - Differential expression analysis - Workflow design - Statistics - Visualization. Prerequisites: No. Beginner training course! Keywords: Galaxy, NGS, HTS, RNA-seq, ChIP-seq, Exome-seq, MethylC-seq Tools: Galaxy 2019-09-23 09:00:00 UTC 2019-09-27 17:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany [] [] [] workshops_and_courses [] []
  • 5th Prague Autumn School - RNASeq Data Analysis Workshop

    7 - 11 October 2019

    Prague, Czechia

    Elixir node event
    5th Prague Autumn School - RNASeq Data Analysis Workshop https://tess.elixir-europe.org/events/5th-prague-autumn-school-rnaseq-data-analysis-workshop 2019-10-07 08:30:00 UTC 2019-10-11 17:00:00 UTC Institute of Molecular Genetics CAS, SEQme s.r.o. Conference Centre, Institute of Molecular Genetics, Videnska 1083, 14220 Prague, Czech Republic, Prague, Czechia Conference Centre, Institute of Molecular Genetics, Videnska 1083, 14220 Prague, Czech Republic Prague Hlavní město Praha Czechia 14220 Institute of Molecular Genetics CASSEQme s.r.o. [] Life Science Researchers 22 workshops_and_courses first_come_first_served Next generation sequencing data analysisnext generation sequencing RNA-Seq
  • Galaxy for linking bisulfite sequencing with RNA sequencing

    9 - 12 October 2019

    Freiburg im Breisgau, Germany

    Galaxy for linking bisulfite sequencing with RNA sequencing https://tess.elixir-europe.org/events/galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing-7b7b1d40-b65b-4694-a5c7-9613dfb3e2c7 Educators: Konstantin Riege (Jena), Steve Hoffmann (Jena), Steffen C. Lott (Freiburg), Wolfgang Hess (Freiburg), Andrea Bagnacani (Rostock), Markus Wolfien (Rostock), Olaf Wolkenhauer (Rostock) (RBC / de.STAIR) Date: 9.-11.10.2019 Location: Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau Contents: In this training course, we introduce the Galaxy framework (https://usegalaxy.eu) for biomedical data analyses, and showcase its tools for data handling and preprocessing, differential gene expression analysis, bisulfite sequencing analysis, and Oxford Nanopore data exploration and usage. Lectures will be provided on the topics of RNA and Bisulfite sequencing, Epigenetics, and basic statistics, and followed by hands-on sessions. Finally, we showcase a Galaxy Docker installation for customized workflow analysis. Learning goals: - Know your data, and the implications of data preprocessing and quality control - Performing differential gene expression analysis using Galaxy - Performing differential methylation analysis using Galaxy - Handling and analyze Oxford Nanopore sequencing data Prerequisites: This workshop is intended for MSc/PhD students, postdocs, and researchers with a background in Life Science research. During registration, please hand over a poster about a research topic of your choosing. Posters will be presented during our poster session, which you can use to exchange experiences with other participants. Keywords: Galaxy, Workflow development, Differential gene expressionanalysis, differential methylation analysis, Epigenetics, Oxford Nanopore Tools: Galaxy (https://usegalaxy.eu), Galaxy Training material (https://galaxyproject.github.io/training-material/) Contact: destair@leibniz-fli.de Register: https://www.leibniz-fli.de/de/news-events/seminare/news-detailpage/news/denbidestair-training-course-galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing-1/ 2019-10-09 09:00:00 UTC 2019-10-12 00:00:00 UTC de.NBI Freiburg im Breisgau, Freiburg im Breisgau, Germany Freiburg im Breisgau Freiburg im Breisgau Freiburg Germany [] destair [at] leibniz-fli.de [] [] [] [] []
  • Software Carpentry Workshop

    16 - 18 October 2019

    Heidelberg, Germany

    Software Carpentry Workshop https://tess.elixir-europe.org/events/software-carpentry-workshop-ab3af408-aa91-49ed-bab2-5db1f2e6d15d Educators: Malvika Sharan, Georg Zeller, Mike Smith, Thomas Schwarzl, Frank Thommen (HD-HuB), Holger Dinkel Date: 16-10-2019 - 18-10-2019 09:00-18:00 Location: ATC Computer Training Lab, EMBL Heidelberg Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2019-10-16 09:00:00 UTC 2019-10-18 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Workshop: Oxford Nanopore long reads - de novo assembly

    6 - 7 November 2019

    Prague, Czechia

    Elixir node event
    Workshop: Oxford Nanopore long reads - de novo assembly https://tess.elixir-europe.org/events/workshop-oxford-nanopore-long-reads-de-novo-assembly 2019-11-06 08:30:00 UTC 2019-11-07 17:00:00 UTC Institute of Molecular Genetics CAS, SEQme s.r.o. Institute of Molecular Genetics, Vídeňská 1083, 1083, Prague 4, Prague, Czechia Institute of Molecular Genetics, Vídeňská 1083, 1083, Prague 4 Prague Hlavní město Praha Czechia 14220 Institute of Molecular Genetics, CASSEQme s.r.o. [] Life Science Researchers 23 workshops_and_courses first_come_first_served Next generation sequencing data analysis
  • Machine Learning in R

    6 - 7 November 2019

    Heidelberg, Germany

    Machine Learning in R https://tess.elixir-europe.org/events/machine-learning-in-r Date Nov 6 - Nov 7 2019 Location EMBL Heidelberg Tutors and helpers - Dr. Malvika Sharan - Prof Bernd Bischl - Martin Binder - Giuseppe Casalicchio Affiliation: Ludwig-Maximilians-University Munich Course Information This two-day course, on the implementation of Machine Learning in R, using mlr package will be delivered as practical sessions on programming and data analysis. The main goal of mlr is to provide a unified interface for machine learning tasks as classification, regression, cluster analysis and survival analysis in R. Sessions will be driven by many practical exercises and case studies. Before this workshop, participants are expected to review the official material introducing the principle of Machine Learning (see the prerequisite). Course Content This 2-day course will cover hands-on sessions using `mlr` and other relevant packages. Daily schedule - 09:30-12:30 3h morning, 90 min Theory + 90 min Practical - 12:30-13:30 1h Lunchbreak - 13:30-16:30 3h afternoon, 90 min Theory + 90 min Practical - 16:30-17:00 Time for general questions Day 1 Introduction to the concepts and Practical with mlr - Performance Evaluation and Resampling (Metrics, CV, ROC) - Introduction to Boosting Day 2 Introduction to the concepts and Practical with mlr - Tuning and Nested Cross-Validation - Regularization and Feature Selection Prerequisite The course is aimed at advanced R programmers, preferably with some knowledge of statistics and data modeling (See prerequisite materials from Day-1, 2, & 4). In this course, our learners will learn more about machine learning and its application and implementation through the hands-on sessions and use cases. Optional: Discussion-Based Session On The Principle of Machine Learning Anna Kreshuk (EMBL Group Leader) will lead a one-day discussion-based session on 14 October 2019 to address your questions on the prerequisite materials on the principle of Machine Learning. This will also allow you to connect with other participants of this workshop informally, and discuss the materials in smaller groups. Please register for this workshop separately: https://bio-it.embl.de/events/machine-learning-discussion-workshop-2019/. Registration Please register on this page: https://bio-it.embl.de/events/machine-learning-in-r-2019/ Please note that the maximum capacity of this course is 40 participants and registration is required to secure a place. If you have any questions, please contact Malvika Sharan. In your registration, please mention your EMBL group name, or institute's name (e.g. DKFZ, Uni-HD) if you are registering as an external participant. Costs 60,00 EUR Keywords: Machine Learning, R 2019-11-06 09:00:00 UTC 2019-11-07 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
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