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  • Tools for reproducible research - ISMB/ECCB 2019

    21 July 2019

    Basel, Switzerland

    Tools for reproducible research - ISMB/ECCB 2019 https://tess.elixir-europe.org/events/tools-for-reproducible-research-0ed30b48-9c67-48f5-8616-6ca21c78c509 Educators: Bjoern Grüning (RBC), Johannes Köster, Devon Ryan Date: 21.07.2019 Location: ISMB/ECCB Basel Content: The typical data analyst must simultaneously juggle multiple projects, each having its own duration and software requirements. As few analysts have any formal training on structuring or even writing the code necessary to perform an analysis, it is unsurprising that the iterative analytic process can produce a wide assortment of almost identically named files (e.g., “final_results.txt”, “final_results.version2.txt”, “final_results.really_final.txt”), all with unclear origins and produced with a hodge-podge of similarly poorly named scripts. The near impossibility of tracing a results file to the exact process that produced it creates untold difficulties both when it comes time to publish results as well as when planning subsequent experiments months or years later (afterall, which of the “final_results” files was really the “right one”?). These issues are further compounded by software paths and other similar assumptions being hard-coded into scripts, preventing easy analysis replication elsewhere. Performing analyses in a reproducible and traceable manner is clearly needed to combat such problems. Schedule Overview 2:00 - 2:10 pm Installing conda and snakeMake 2:10 - 2:30 pm Intro to conda and bioconda (slides) 2:30 - 3:30 pm Hands-on Session: creating conda envs and installing packages from bioconda repo This practical would require installing hisat, samtools and deeptools via bioconda 3:30 - 4:00 pm Hands-on Session: writing conda recipes Topics in BioVis (including examples) Visualization of sequences, macromolecules, omics data, biological networks 4:00 - 4:15 am Coffee Break 4:15 - 4:35 pm Intro to snakemake Specific tools for visualizing large-scale biological data 4:35 - 6:00 Hands On Session: Writing a snakemake workflow wrapper for mapping, indexing and creating coverage files Learning goals: In this hands-on tutorial, we demonstrate how Conda can be used to deploy specific software versions easily, reproducibly, and without administrator credentials. Moreover, we demonstrate how Conda’s ability to create isolated software environments helps to avoid side-effects between different analyses or different steps of the same analysis. Attendees will also learn how to create conda recipes themselves, so they can contribute new packages to projects such as Bioconda. We further demonstrate how Snakemake can be used in combination with Conda and Containers to create reproducible analysis workflows and execute them on any platform from workstations to clusters and the cloud. Finally, using snakePipes as an example, we demonstrate how Conda and Snakemake can be used to define reproducible and flexible workflows for complex genomics analysis. Prerequisites: - Laptops with Linux or MacOS - Pre-installed Miniconda - install via miniconda : https://conda.io/miniconda.html - Expected audience should have basic familiarity with python, git and the command line. Keywords: Conda, Bioconda, snakemake, Bioconductor, reproducible research Tools: Conda, Bioconda, snakemake, 2019-07-21 09:00:00 UTC 2019-07-21 17:00:00 UTC de.NBI Basel, Basel, Switzerland Basel Basel Basel-Stadt Switzerland [] [] [] meetings_and_conferences [] []
  • ISMB/ECCB 2019

    21 - 25 July 2019

    Basel, Switzerland

    ISMB/ECCB 2019 https://tess.elixir-europe.org/events/ismb-eccb-2019 ISMB/ECCB 2019 is the largest and most high profile annual meeting of scientists working in computational biology and provides an intense multidisciplinary forum for disseminating the latest developments in computational tools for data driven biological research. ELIXIR will be present at this year's ISMB/ECCB 2019 conference with three dedicated Tech Tracks on Monday 22 July and a Special Session on Scalable Plant-Research in Cloud Environments on Wednesday 24 July. ELIXIR will also be have a booth (booth numbers 23 and 24) in the exhibition area with information about our services including Global Alliance, Galaxy, Plants, TeSS and Beacons.  Further details about the conference, including how to register, can be found on the ISMB/ECCB 2019 website. 2019-07-21 10:00:00 UTC 2019-07-25 17:00:00 UTC Congress Center Basel, Basel, Switzerland Congress Center Basel Basel Switzerland 4058 [] [] [] meetings_and_conferences [] []
  • ELIXIR Beacons (at ISMB / ECCB)

    22 July 2019

    Basel, Switzerland

    ELIXIR Beacons (at ISMB / ECCB) https://tess.elixir-europe.org/events/elixir-beacons-at-ismb-eccb This workshop will demonstrate the Beacon API, a data discovery protocol that allows users to determine the presence or absence of a particular allele in a dataset, without disclosing any further data differentiating the individuals it contains. The ELIXIR Beacons project is a Driver Project of the Global Alliance for Genomics and Health that provides a simple way to federate data discoverability. The ELIXIR Beacons protocol can allows any variation data back end to be connected to the ELIXIR Beacons network which can then be queried to ask questions like _'does this dataset have any information about allele 'X' at position 'Y' in the genome?'_. This workshop will show how recent extensions to the Beacon API has extended its functionality by adding support for additional types of genomic variants and improved metadata support. Additionally we will also demonstrate the accompanying ELIXIR Beacon reference implementation which utilises risk mitigation strategies by integrating the ELIXIR Authorization and Authentication Infrastructure (AAI), demonstrating to data owners how to light Beacons at different tiers of data access: open, registered, or controlled. 2019-07-22 14:00:00 UTC 2019-07-22 16:00:00 UTC Gary Saunders Congress Center Basel, Basel, Switzerland Congress Center Basel Basel Switzerland [] Gary Saunders <gary.saunders@elixir-europe.org>, Frédéric Haziza <frederic.haziza@crg.eu> [] [] meetings_and_conferencesworkshops_and_courses [] beacon
  • [BC]2 Basel Computational Biology Conference tutorial: Using the Ensembl REST APIs to programmatically access genomic data, 9 September 2019

    9 September 2019

    Basel, Switzerland

    Elixir node event
    [BC]2 Basel Computational Biology Conference tutorial: Using the Ensembl REST APIs to programmatically access genomic data, 9 September 2019 https://tess.elixir-europe.org/events/bc-2-basel-computational-biology-conference-tutorial-using-the-ensembl-rest-apis-to-programmatically-access-genomic-data-9-september-2019 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2019-09-09 09:00:00 UTC 2019-09-09 16:00:00 UTC University of Basel, Basel, Switzerland University of Basel Basel Switzerland 4001 [] Astrid Gall [] [] [] [] HDRUK
  • Protein Structure Fundamentals: Searching – Analyzing – Modeling

    23 - 24 September 2019

    Hamburg, Germany

    Protein Structure Fundamentals: Searching – Analyzing – Modeling https://tess.elixir-europe.org/events/protein-structure-fundamentals-searching-analyzing-modeling Educators: Eva Nittinger (BioData), Matthias Rarey (BioData), Ida Schomburg (BioData), Greg Landrum (CIBI) Date: 23./24.09.2019 Location: Universität Hamburg, ZBH – Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg Contents: In this workshop, you will get to know a combination of tools and webservices for searching and analyzing protein structure data. The focus will be on protein function and related interactions to small molecules. We will work with two web- and two software platforms: BRENDA, the database for enzyme structures will be used to gather information about enzyme structures. The ProteinsPlus web service contains a diverse range of software solution for the analysis of protein structures and its application in molecular modeling approaches. NAOMI ChemBio Suite contains desktop software for cheminformatics and advanced modeling. KNIME offers diverse options for the analysis of biological data and the generation of analytical workflows. Learning goals: This course is designed for life and computer scientists with interest in protein structures, but only very basic experience. Topics include: Finding and selecting protein structure data, evaluating the quality of experimental data, preprocessing structure data for modeling, first modeling steps like the analysis of binding site properties and conformational flexibility. Furthermore, we will introduce basic Cheminformatics tools. Usage of ProteinsPlus, BRENDA, NAOMI ChemBio Suite, and KNIME; all software introduced is available for free for academic use. Prerequisites: General knowledge of proteins and their role in life sciences Keywords: Protein structures, protein-ligand interactions, molecular modeling, structure-to-function relationships, cheminformatics, ProteinsPlus, BRENDA, EnzymeStructures, KNIME Tools: ProteinsPlus, BRENDA, NAOMI ChemBio Suite, KNIME 2019-09-23 09:00:00 UTC 2019-09-24 17:00:00 UTC de.NBI Hamburg, Hamburg, Germany Hamburg Hamburg Germany [] [] [] workshops_and_courses [] []
  • Introduction to RNA-Seq: From quality control to pathway analysis

    21 - 22 October 2019

    Basel, Switzerland

    Elixir node event
    Introduction to RNA-Seq: From quality control to pathway analysis https://tess.elixir-europe.org/events/introduction-to-rna-seq-9b1ad1ee-b319-4f6e-bdeb-6b6a297145b2 Overview This two-day course will present the theory and bioinformatics tools required to analyze RNA-seq gene expression data, from the raw data to the biological interpretation. 2019-10-21 09:00:00 UTC 2019-10-22 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Best practices in programming 2019

    5 - 6 November 2019

    Basel, Switzerland

    Elixir node event
    Best practices in programming 2019 https://tess.elixir-europe.org/events/best-practices-in-programming-2019 This workshop is organised by the SIB PhD Training Network. Priority is given to its members, but is open to everyone. 2019-11-05 09:00:00 UTC 2019-11-06 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Ligand-protein docking, and computer-aided drug design

    12 - 14 November 2019

    Basel, Switzerland

    Elixir node event
    Ligand-protein docking, and computer-aided drug design https://tess.elixir-europe.org/events/ligand-protein-docking-and-computer-aided-drug-design-b5c29e56-da43-431c-9283-e0ac2a452322 Overview This workshop aims to present basics on molecular visualization, ligand-protein docking and several computer-aided drug design tools developed at SIB. Numerous case examples are taken from different therapeutic fields. 2019-11-12 09:00:00 UTC 2019-11-14 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to high-performance computing (sciCORE cluster)

    13 November 2019

    Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-515184e9-a4a9-4bca-9273-7caa8f32769a Overview This full-day course has a practical focus, where participants will learn how to use the Linux command line and interact with the sciCORE cluster. All new users of sciCORE are strongly encouraged to follow this course. 2019-11-13 09:00:00 UTC 2019-11-13 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps in Parallelization with OpenMP

    20 November 2019

    Basel, Switzerland

    Elixir node event
    First Steps in Parallelization with OpenMP https://tess.elixir-europe.org/events/first-steps-in-parallelization-with-openmp-e0c0050d-f04e-42b5-a4ae-f1823d2f6f3c Overview We currently live in the era of multicore computers, where almost every computing machine has many CPUs. In order to benefit from this computational power we need to devise programs explicitly written for parallel machines. 2019-11-20 09:00:00 UTC 2019-11-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Python for Life Scientists - along PharmaPy conference

    21 November 2019

    Basel, Switzerland

    Elixir node event
    Python for Life Scientists - along PharmaPy conference https://tess.elixir-europe.org/events/python-for-life-scientists-4b472965-66f4-419e-a282-bc20f5664411 More information soon We were obliged to cancel the 3-day course in Python, initially planned for 18-20 November 2019, and we apologize for this inconvenience. 2019-11-21 09:00:00 UTC 2019-11-21 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • CABANA Workshop: Analysis of Crop Genomics Data

    2 - 6 December 2019

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Analysis of Crop Genomics Data https://tess.elixir-europe.org/events/cabana-workshop-analysis-of-crop-genomics-data This course will introduce crop biologists to methods and approaches for analysing crop genomics data. 2019-12-02 08:30:00 UTC 2019-12-06 12:45:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Marco Cristancho [] [] [] [] HDRUK
  • Statistics for Life Scientists - cancelled

    2 - 4 December 2019

    Basel, Switzerland

    Elixir node event
    Statistics for Life Scientists - cancelled https://tess.elixir-europe.org/events/statistics-for-life-scientists-e25eb89a-c498-4fa4-8a59-fda57cfb60d8 Course Cancelled We were obliged to cancel this 3-day course entitled Statistics to Life Scientists, initially planned for 2-4 December 2019, and we apologize for this inconvenience. We are currently looking for an alternative solution. 2019-12-02 09:00:00 UTC 2019-12-04 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Intermediate R

    9 - 11 December 2019

    Basel, Switzerland

    Elixir node event
    Intermediate R https://tess.elixir-europe.org/events/intermediate-r-ec2abb58-3433-4f1a-9ba4-b04b28549eeb Overview This 3-day intermediate course will move beyond simple scripts/recipes towards a more systematic understanding of R and its data structures. 2019-12-09 09:00:00 UTC 2019-12-11 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
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