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  • Introduction to identifying and characterising somatic variants

    21 April - 21 May 2020

    Sheffield, United Kingdom

    Introduction to identifying and characterising somatic variants https://tess.elixir-europe.org/events/introduction-to-identifying-and-characterising-somatic-variants-907ec326-e958-4c2e-a935-4780254ae845 This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2020-04-21 08:30:00 UTC 2020-05-21 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020

    27 - 29 April 2020

    Magdeburg, Germany

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020 https://tess.elixir-europe.org/events/tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2020 Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio) Date: 27. - 29 April 2020 Location: MPI Magdeburg Sandtorstrasse 1 39106 Magdeburg Contents: Key concepts of stoichiometric and kinetic modeling of biochemical networks: - stoichiometric matrix and stoichiometric networks - steady state flux distributions - principles of constraint-based modeling - metabolic flux analysis and flux optimization (flux balance analysis) - metabolic pathway analysis with elementary flux modes - metabolic network design via minimal cut sets - simulation of dynamic (kinetic) models - sensitivity analysis - carrying out parameter estimation tasks - model exchange using SBML Data and model management: - manual/programmatic access to reaction kinetics data from SABIO-RK - storage and exchange of data and models using FAIRDOMHub/SEEK - modeling specific functionalities in FAIRDOMHub/SEEK Learning goals: During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory. Keywords: CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management Tools: CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK 2020-04-27 09:00:00 UTC 2020-04-29 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Germany [] [] [] workshops_and_courses [] []
  • Ensembl Browser Workshop, DKFZ, 5 May 2020

    5 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl Browser Workshop, DKFZ, 5 May 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-dkfz-5-may-2020 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2020-05-05 09:00:00 UTC 2020-05-05 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl REST API Workshop, DKFZ, 6 May 2020

    6 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl REST API Workshop, DKFZ, 6 May 2020 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-dkfz-6-may-2020 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2020-05-06 09:00:00 UTC 2020-05-06 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • RNA-seq Analysis for Beginners

    13 May 2020

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners-910fd563-0c77-49c8-9f3a-878af00ba1b9 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2020-05-13 08:30:00 UTC 2020-05-13 16:00:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • First Steps with Python in Life Sciences

    18 - 20 May 2020

    Basel, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-d45a8059-cedd-4e69-bcac-8da973f4496d Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-05-18 09:00:00 UTC 2020-05-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps with Python in Life Sciences - streamed

    18 - 20 May 2020

    Basel, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences - streamed https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-402cdbc1-5a65-4f48-8581-994a44441dc5 This course will be streamed only for the registered participants. 2020-05-18 09:00:00 UTC 2020-05-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • ELIXIR All Hands 2020

    8 - 11 June 2020

    Amsterdam, Netherlands

    ELIXIR All Hands 2020 https://tess.elixir-europe.org/events/elixir-all-hands-2020 The ELIXIR All Hands 2020 will be held in the Eye Filmmuseum, Amsterdam. Timeline 21 October - 15 November 2019 Call for workshops and Call for presentations. December 2019 Selection of presentations and workshops. 7 February 2020 Accepted presentations (incl. talks, demonstrations and posters) announced by this date. 24 February 2020 Registration opens for 300 delegates on a first come, first served basis. 1 March 2020 Registration closed, reserve list available. Deadline for poster submissions, or earlier, if capacity is reached. Submission of posters is re-opened. Priority will be given to those participants that have not previously submitted a poster. 31 March 2020 Deadline for poster submissions, or earlier, if capacity is reached. Submission of posters is re-opened. Priority will be given to those participants that have not previously submitted a poster and those already registered. Accommodation For 2020 All Hands meeting, ELIXIR will not have a block reservation for accommodation, but each participant will need to book their own accommodation. The venue is located in central Amsterdam with plenty of options, but keep in mind that June is a busy month in the city and therefore it is recommended to reserve accommodation early. Walking distance hotels from venue Eye Film Museum: Sir Adam Hotel Park Plaza Victoria Ibis Styles Hotel Ibis Amsterdam Central Station Multatuli Hotel Registration The registration to the All Hands meeting is now closed until all speakers have been registered. You can add yourself to the reserve list if you log in to the site and return to this page. You will see the registration link at the top of the page once you are logged in. More spaces may become available later on and will be allocated to people on the reserve list on a first come, first served basis. Code of Conduct The ELIXIR Code of Conduct has been created to ensure that people at ELIXIR events can interact with each other in a respectful and safe environment. It provides ways you can voice your concern if you believe there has been a breach to this Code of Conduct. The ELIXIR Code of Conduct will be in place at this event. Social activities This Google doc lists recommended tourist sites, social activities and things to do in your free time. Note: The All Hands meeting ends on Thursday 11 Jun 2020 at 11:00 CEST. After the end of the meeting, there are two project meetings taking place starting at 11:00 CEST. These are the CONVERGE AGM and the Federated Human Data Strategic Implementation Study meeting. Both of these meetings are restricted to named project partners. 2020-06-08 12:00:00 UTC 2020-06-11 11:00:00 UTC Eye Filmmuseum, Amsterdam, Netherlands Eye Filmmuseum Amsterdam Netherlands 1031 KT [] [] [] meetings_and_conferences [] []
  • First steps in Python, and more!

    9 - 11 June 2020

    Basel, Switzerland

    Elixir node event
    First steps in Python, and more! https://tess.elixir-europe.org/events/first-steps-in-python-and-more Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-06-09 09:00:00 UTC 2020-06-11 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • RNA-seq Analysis for Beginners

    3 July 2020

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners-13c9f173-2fdd-4ea6-9005-58aa798bf289 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2020-07-03 08:30:00 UTC 2020-07-03 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq analysis in R

    13 - 14 July 2020

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-34ffdcbc-a5b7-49ac-afb9-7d338a38ea26 In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. You will also be learning how alignment and counting of raw RNA-seq data can be performed in R. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2020-07-13 08:30:00 UTC 2020-07-14 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Protein Bioinformatics: Sequence-Structure-Function - Dates to be confirmed

    18 - 20 November 2020

    Basel, Switzerland

    Elixir node event
    Protein Bioinformatics: Sequence-Structure-Function - Dates to be confirmed https://tess.elixir-europe.org/events/protein-bioinformatics-sequence-structure-function-dates-to-be-confirmed Overview Sequence-structure-function relationships of proteins are central to a comprehensive understanding of cellular biology. However, many proteins lack direct and detailed information regarding structure, function, and complex formation. 2020-11-18 09:00:00 UTC 2020-11-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

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