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  • Introduction to genome-wide association studies (GWAS) 2019

    18 September 2019

    Kiel, Germany

    Introduction to genome-wide association studies (GWAS) 2019 https://tess.elixir-europe.org/events/introduction-to-genome-wide-association-studies-gwas-2019 Educators: David Ellinghaus (Associated partner - CAU) Date: September 18, 2019 Time: 08:30 - 16:30 Location: Kiel, Am Botanischen Garten 1-9, Room E49 This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis. Contents: Over the past decade, genetic epidemiology studies have progressed from studying single genetic variants in candidate genes to investigating millions of common genetic variants in genome-wide association studies (GWAS). Nowadays GWAS studies are moving forward to genome-wide rare variant association studies, gene-gene (GxG) and gene-environment (GxE) interaction studies as well as cross-phenotype studies including several 10k and sometimes even >100k genetic samples. Learning goals: In this one day course we will give guidance for planning of SNP array genotyping and will provide best-practices for large-scale quality control, variant annotation and association analysis of GWAS data. In the practical part of the course will work on real-world data sets and show how to automatically and manually analyze large case-control sample sets and how to annotate phenotype-associated genomic regions. Prerequisites: None Keywords: genome-wide association studies (GWAS); SNP genotype quality control; association testing 2019-09-18 08:00:00 UTC 2019-09-18 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []
  • Eukaryote genome annotation workshop 2019

    19 September 2019

    Kiel, Germany

    Eukaryote genome annotation workshop 2019 https://tess.elixir-europe.org/events/eukaryote-genome-annotation-workshop-2019 Educators: Marc Höppner (Associated partner - CAU) Date: September 19, 2019 - 08:30 - 16:30 Location: Kiel, Am Botanischen Garten 1-9, Room E49 Contents: The constant drop in sequencing prices and the development of easy-to-use assembly programs makes it possible, even for small groups, to embark on a de novo genome project to obtain the full sequence of their species of interest. However, automatically annotating all genetic features in a eukaryotic genome, especially in non-model species with few or no sequenced closely related species, remains a challenge and standard pipelines still do not exist. Learning goals: In this one day course participants will learn about these challenges and the current strategies that can be used to try to obtain the most complete set of genes from a de novo assembled eukaryotic genome. We will also discuss how additional data, such as RNA-seq, assembled transcriptomes or proteomic data, can be used to improve the annotation, which can inform decisions on how best to spend the budget during a genome project. The practical part of the course will explain how to automatically and manually annotate a genomic region and how that information can be immediately translated into biologically relevant data for the species of interest. Prerequisites: None Keywords: eukaryotic genome, annotation, RNAseq proteomic data, assembly Contact: Marc Höppner, m.hoeppner@ikmb.uni-kiel.de This course is designed for 15 participants. If we receive (a lot) more applications, we will choose participants based on the relevance of their application and/or a first-come-first-serve basis. 2019-09-19 09:00:00 UTC 2019-09-19 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []
  • Analyzing and redesigning metabolic networks with CellNetAnalyzer

    15 October 2019

    Valencia, Spain

    Analyzing and redesigning metabolic networks with CellNetAnalyzer https://tess.elixir-europe.org/events/analyzing-and-redesigning-metabolic-networks-with-cellnetanalyzer Date 15.10.2019 Location FOSBE Conference in Valencia http://fosbe2019.ai2.upv.es/workshops/ Educators Steffen Klamt, Philipp Schneider Max Planck Institute for Dynamics of Complex Technical Systems Contact klamt@mpi-magdeburg.mpg.de Duration ca. 3 hours Target audience Students and researchers interested in constraint-based and stoichiometric modeling of metabolic networks. Some basic experiences in constraint-based modeling would be of advantage but is not an absolute requirement. The workshop will focus on the use of the software CellNetAnalyzer. If the participants want to follow the live demonstration or/and take part in the hands-on session, then they should bring their laptops (with MATLAB installed) along. Abstract CellNetAnalyzer (CNA) is a widely used MATLAB package for analyzing biological (metabolic, signaling and regulatory) networks. CNA and supports both command-line based operations as well as a graphical user interface with embedded network visualizations. In the first part of this workshop (1,5h) we will demonstrate key features of CNA for stoichiometric and constraint-based modeling of metabolic networks including flux (balance) analysis, flux and yield optimization, phase plane analysis, elementary mode analysis, computational (re)design of metabolic networks based on minimal cut sets, and many more. The second part of the tutorial (1,5h) will consist of hands-on exercises with example networks where the participants will learn how to use CellNetAnalyzer in practice. 2019-10-15 09:00:00 UTC 2019-10-15 17:00:00 UTC de.NBI Valencia, Valencia, Spain Valencia Valencia Provinz Valencia Spain [] [] [] workshops_and_courses [] []
  • Environmental Genomics training course

    23 - 25 October 2019

    Gießen, Germany

    Environmental Genomics training course https://tess.elixir-europe.org/events/environmental-genomics-training-course Educators: Jochen Blom, Oliver Rupp, Oliver Schwengers, Sebastian Jaenicke (BiGi), Stefanie Glaeser Date: 23.10.2019 – 25.10.2019 Location: Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, Room 0024a Contents: Topic of this three-day-workshop will be sequence data analysis including quality control, assembly, genome annotation and comparative genomics with a focus on microbial taxonomy and phylogenomics and as the usage of the BiGi software tools ASA3P, EDGAR, and MGX. The first day will give a comprehensive introduction to the primary data management in sequencing projects. In this part tools for sequence analysis available via the Galaxy-Server of BIGI will be in the focus of the workshop. • Initial quality assessment and quality control of raw sequencing data • Data preparation, filtering and quality trimming • Assembly strategies for different datasets Furthermore, the basic principles of regional and functional annotation will be introduced, and available tools and algorithms for the different annotation steps will be explained. The ASA3P platform for high-throughput parallel genome annotation and its capabilities in antibiotic resistance and virulence factor detection will be presented in detail. • The basic principles of regional and functional annotation • Genome annotation pipelines for single and multiple genomes • High throughput genome annotation using ASA3P The second day will provide an introduction to the role of genotypic methods in prokaryotic taxonomy including the 16S rRNA gene sequence phylogeny and genome sequences in the identification of environmental isolates. It will will also demonstrate the use of genome sequences to explore the functions of those isolates. • The basic role of 16S rRNA gene sequences in Prokaryotic identification in taxonomic and ecology • Concept of the phylogenetic analysis of environmental 16S rRNA gene amplicon datasets (introduction of SilvaNGS) • Current role of genome sequences in species identification Subsequently the EDGAR platform for comparative genomics will be introduced. One main topic will be its use for phylogenetic analyses based on genome similarity indices and the complete core genome of organisms. All features of EDGAR will be introduced in detail. • Genomic subset calculations (core-genome, pan-genome, singleton genes) • Core-genome-based phylogenetic analyses • Core genome based phylogeny ◦ ANI, AAI, GGDC • Statistical analyses (core/pan/singleton development plots) • The public EDGAR database The third day will show solutions for whole genome shotgun metagenomics. mWGS metagenomics has the potential to address the full spectra of genome-based issues. The focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. The software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated as comprehensive platform for read-based metagenome analysis. • The basic principles of metagenome analysis • Available pipelines for taxonomic and functional analysis • Statistical features: PCA, PCoA, Rarefaction, … The afternoon of the third day will be kept free for custom data analysis consulting. Participants are encouraged to bring their own data which can be discussed with the bioinformatics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi). On all three days the program includes extensive hands-on training to allow participants to become familiar with the presented software. Learning goals: Principles of computational sequence analysis, hands-on experience with de.NBI software services Prerequisites: None Keywords: Sequence data analysis, genomics, annotation, comparative genomics, phylogenetic analysis, metagenome analysis Tools: GenDB, ASA3P, EDGAR, MGX 2019-10-23 09:00:00 UTC 2019-10-25 17:00:00 UTC de.NBI Gießen, Gießen, Germany Gießen Gießen Gießen Germany [] [] [] workshops_and_courses [] []
  • 6th de.NBI Genomics training course

    4 - 6 May 2020

    Gießen, Germany

    6th de.NBI Genomics training course https://tess.elixir-europe.org/events/6th-de-nbi-genomics-training-course Educators: Alexander Goesmann, Sven Griep, Oliver Rupp, Tobias Zimmermann, Oliver Schwengers, Andreas Hoek, Jochen Blom, Sebastian Jaenicke (BiGi) Date: 04.-06.05.2020 Location: Heinrich-Buff-Ring 58, Justus-Liebig-Universität, Gießen, Seminar Rm. 0024a Content: The first day will introduce software tools for the quality control of short read data. For conducting basic sequence read processing steps we will use our local Galaxy server. In the last session we will explain the basic approaches for genome assembly and run various genome assemblers: - Introduction to quality control - Automatic trimming of sequencing reads - The basics of genome assembly On the second day we will take a closer look at the genome assembly results. Afterwards, we provide a comprehensive introduction to microbial genome annotation. Available tools and algorithms for the different genome analysis and annotation steps will be explained and used within Galaxy. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline (ASA3P) that can be used to process thousands of genomes on a single day: - The basic principles of region and function annotation - Genome annotation tools and pipelines in Galaxy - Manual and distributed genome annotation using GenDB - Introduction to the ASA3P software The third day will give an introduction into comparative genomics with a focus on differential gene content analysis using the EDGAR platform. The use of the BLAST score ratio values (SRVs) to measure the similarity between coding sequences and to assess orthology will be introduced. All features of EDGAR will be introduced in detail: - Genomic subset calculations (core-genome, pan-genome, singleton genes) - Core-genome-based phylogenetic analyses - Sequence based phylogeny - ANI, AAI - Statistical analyses (core/pan/singleton development plots) - The public EDGAR database Agenda: Day 1: Quality control & genome assembly 13:00 – 13:15 Welcome & introduction (Alexander Goesmann) 13:15 – 13:30 Transfer of data sets 13:30 – 15:00 Read quality control & trimming incl. hands-on session (Sven Griep, Oliver Rupp) 15:00 – 15:30 Coffee Break 15:30 – 17:00 Introduction to genome assembly incl. hands-on session (Sven Griep, Oliver Rupp) Day 2: Microbial Genome Annotation 9:00 – 10:30 Introduction to microbial genome annotation (Alexander Goesmann) 10:30 – 11:00 Coffee Break 11:00 – 12:30 Genome annotation with Galaxy & GenDB hands-on session (Sven Griep, Oliver Rupp, Tobias Zimmermann) 12:30 – 13:30 Lunch 13:30 – 14:30 Introduction to ASA3P (Oliver Schwengers) 14:30 – 15:00 Coffee Break 15:00 – 17:00 ASA3P practical session (Oliver Schwengers, Andreas Hoek) 17:30 Optional: Tour to Gleiberg castle Day 3: Comparative Genomics 9:00 – 10:30 EDGAR (Jochen Blom) 10:30 – 11:00 Coffee Break 11:00 – 12:00 EDGAR hands-on (Jochen Blom, Sebastian Jaenicke) 12:00 – 12:30 Course evaluation & closing remarks (all hands) During the afternoon of the last day participants are invited to discuss open questions or individual projects or data sets with the course experts. Learning goals: On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software. Participants can bring their own datasets that fit the topics of the workshop. The data can be analyzed in the hands-on sessions. Prerequisites: None Keywords: Quality control, genome assembly, Microbial Genome Annotation, Comparative Genomics Tools: Galaxy, GenDB, ASA3P, EDGAR 2020-05-04 09:00:00 UTC 2020-05-06 17:00:00 UTC de.NBI Gießen, Gießen, Germany Gießen Gießen Gießen Germany [] [] [] workshops_and_courses [] []
  • Phylogenetic reconstruction course 2020

    20 May 2020

    Kiel, Germany

    Phylogenetic reconstruction course 2020 https://tess.elixir-europe.org/events/phylogenetic-reconstruction-course-2020 Educators: Tal Dagan (CAU) Date: 20.05.2019, 08:15 - 16:00 Location: Kiel Contents/Learning goals: The evolutionary history of genes or species is best studied and described by phylogenetic trees. The accumulating sequence data enable the reconstruction of phylogenetic trees for many diverse gene and species. A robust phylogeny is helpful in identifying phyletic groups as well as ancestral relations in the data and lateral gene transfer. Notwithstanding phylogenetic reconstruction is sensitive to various biases in the analysis that originate in alignment and phylogenetic reconstruction artifacts. Students in the workshop will learn to reconstruct multiple sequence alignment and phylogenetic trees of focal sequences. This includes a quantification of possible biases in the phylogenetic reconstruction and ways to counteract their influence on the results. In addition, the students will learn how to identify the root of phylogenetic trees and extract ancestral-descendent relations. The workshop is intended to address scientists from undergraduate to postdoc level and does not expect previous experience in phylogenetics. Basic knowledge on how to work with Linux will be advantageous. Prerequisites: None Keywords: Tree phylogeny, gene homology, rooting, robustness Tools: MAFFT, Guidance, PhyML, IQTree, MAD rooting, FigTree. 2020-05-20 09:00:00 UTC 2020-05-20 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []

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