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21 events found

Scientific topics: Bioinformatics 

and

Keywords: eLearning  or Genome Mapping  or SystemsBiology  or Workflows  or Nextflow  or NGS 

  • Therapeutic Applications of Computational Biology and Chemistry (TACBAC) 2012

    12 - 14 March 2012

    Hinxton, United Kingdom

    Therapeutic Applications of Computational Biology and Chemistry (TACBAC) 2012 https://tess.elixir-europe.org/events/therapeutic-applications-of-computational-biology-and-chemistry-tacbac-2012 2012-03-12 00:00:00 UTC 2012-03-14 00:00:00 UTC Wellcome Trust Wellcome Trust Conference Centre, Hinxton, United Kingdom Wellcome Trust Conference Centre Hinxton United Kingdom Drug metabolism Metabolomics Bioinformatics [] [] [] meetings_and_conferences [] BiotherapeuticsSystemsBiology
  • High-thoughput Omics & Data Integration Workshop

    14 - 16 February 2013

    Barcelona, Spain

    High-thoughput Omics & Data Integration Workshop https://tess.elixir-europe.org/events/high-thoughput-omics-data-integration-workshop 2013-02-14 00:00:00 UTC 2013-02-16 00:00:00 UTC SeqAhead Hospital Duran i Reynals, Barcelona, Spain Hospital Duran i Reynals Barcelona Spain Bioinformatics [] [] [] workshops_and_courses [] NGSdataintegrationmethodologystatisticsEMBnet
  • RNA-Seq Next Generation Sequencing Analysis Workshop

    26 - 28 October 2016

    Leicester, United Kingdom

    RNA-Seq Next Generation Sequencing Analysis Workshop https://tess.elixir-europe.org/events/rna-seq-next-generation-sequencing-analysis-workshop This course will provide an introduction to next generation sequencing (NGS) platforms, data analysis and tools for data quality control, read alignment (mapping), differential expression, de novo and referenced based transcriptome assembly, annotation and gene discovery of RNA sequencing (RNA-Seq) data. The course will be delivered using a mixture of lectures and computer based hands on practical sessions using real data. This course is aimed at wet-lab biologists who are involved in research projects that will require the handling and analysis of NGS data. A significant proportion of the course will be computer-based using command line tools in the Unix environment, therefore, in order to gain maximum benefit from the course all attendees will be required to have basic Unix skills. This means applicants must at a minimum be able to move easily around the file system and make directories (e.g. pwd, cd, ls, mkdir), manage files (e.g. cp, mv, ln, rm, less, head, tail, wc) and search with grep. 2016-10-26 00:00:00 UTC 2016-10-28 00:00:00 UTC University of Leicester University of Leicester - College Court Conference Centre, Leicester, United Kingdom University of Leicester - College Court Conference Centre Leicester United Kingdom LE2 3UF Bioinformatics Sequencing RNA-Seq [] [] [] workshops_and_courses [] NGSRNA-SeqBioinformatics
  • From Functional Genomics to Systems Biology

    12 - 15 November 2016

    Heidelberg, Germany

    From Functional Genomics to Systems Biology https://tess.elixir-europe.org/events/from-functional-genomics-to-systems-biology 2016-11-12 00:00:00 UTC 2016-11-15 00:00:00 UTC EMBL European Molecular Biology Laboratory, Heidelberg, Germany European Molecular Biology Laboratory Heidelberg Germany Systems biology Genomics Bioinformatics [] [] [] meetings_and_conferences [] SystemsBiologyOtherEventsISCB
  • Introduction to Linux and Workflows for Biologists

    24 - 28 April 2017

    Edinburgh, United Kingdom

    Introduction to Linux and Workflows for Biologists https://tess.elixir-europe.org/events/introduction-to-linux-and-workflows-for-biologists Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. 2017-04-24 00:00:00 UTC 2017-04-28 00:00:00 UTC Edinburgh Genomics The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom Bioinformatics [] [] [] workshops_and_courses [] BioinformaticsLinuxWorkflows
  • Common Workflow Language with Michael Crusoe

    11 May 2017

    University of Melbourne, Australia

    Common Workflow Language with Michael Crusoe https://tess.elixir-europe.org/events/common-workflow-language-with-michael-crusoe 2017-05-11 12:00:00 UTC 2017-05-11 13:00:00 UTC Melbourne Bioinformatics FW Jones Theatre, Level 3, Medical Building , University of Melbourne, Australia FW Jones Theatre, Level 3, Medical Building University of Melbourne Australia Bioinformatics Melbourne BioinformaticsUniversity of Melbourne [] [] [] [] programmingWorkflowsBioinformatics
  • Training Course on Best practices for RNA-Seq data analysis

    27 - 29 September 2017

    Fisciano, Italy

    Training Course on Best practices for RNA-Seq data analysis https://tess.elixir-europe.org/events/training-course-on-best-practices-for-rna-seq-data-analysis Next-generation sequencing (NGS) of RNA libraries (RNA-Seq) has become increasingly common and it largely replaced microarray technology for gene expression profiling. The aim of this course is to get a deeper understanding of RNA-Seq experiments, providing a theoretical introduction to the data processing steps, together with practical sessions illustrating the use of the most popular data analysis tools. The classroom size is limited to 25 participants to optimize the learning and the interaction with the instructors. Starting from the raw sequenced data coming from different phenotypical samples (e.g disease vs healthy control samples), genes which are differentially expressed between the two conditions are determine. Some strategies are illustrated for detecting alternative splicing products, predicting novel isoforms and gene fusion events. Some methods for downstream analysis are described to give insight into how biological knowledge can be generated from RNA-Seq experiments. A lecture on single-cell RNA-Seq will provide an idea of how transcriptome data from individual cells is now emerging as a powerful tool, allowing the study of cell-to-cell gene expression heterogeneity in the same tissue. 2017-09-27 09:15:00 UTC 2017-09-29 16:30:00 UTC Anna Marabotti (University of Salerno and ELIXIR-IIB Training Team, Italy), Roberto Tagliaferri (University of Salerno, Italy), Alessandro Weisz (University of Salerno, Italy), Loredana Le Pera (ELIXIR-IIB Training Team and IIT, Italy), Allegra Via (ELIXIR-IIB Training Coordinator, CNR-IBPM, Italy) Campus di Fisciano, Università degli Studi di Salerno, Via Giovanni Paolo II, n. 132, Fisciano, Italy Campus di Fisciano, Università degli Studi di Salerno, Via Giovanni Paolo II, n. 132 Fisciano Provincia di Salerno Italy 84084 Transcriptomics RNA splicing Sequencing Bioinformatics RNA-Seq Gene expression Campus di Fisciano, University of Salerno, Italy elixir.ita.training@gmail.com, amarabotti@unisa.it ELIXIR Italy PhD students and young researchers in the life science and computational biology field who are planning to use RNA-seq data and are looking for the best practices to analyze these types of data 25 workshops_and_courses first_come_first_servedregistration_of_interest NGSRNA-SeqBioinformaticsData analysisHigh Throughput Sequencing AnalysisGene Expression
  • 3Gb-TEST NGS Course Mexico 2017

    10 - 13 October 2017

    México City, Mexico

    3Gb-TEST NGS Course Mexico 2017 https://tess.elixir-europe.org/events/3gb-test-ngs-course-mexico-2017 The focus of the course is on clinical diagnostics using exome/genome sequences, variant identification and analysis including afternoon practical sessions in dry lab as well as in wetlab. *Event mostly in Spanish 2017-10-10 08:00:00 UTC 2017-10-13 14:30:00 UTC 3Gb-TEST Centro Médico Nacional 20 de Noviembre, México City, Mexico Centro Médico Nacional 20 de Noviembre México City DF Mexico Data quality management Whole genome sequencing Exome sequencing Bioinformatics ISSSTE genomicatraslacional@gmail.com [] [] 200 workshops_and_courses [] NGS bioinformaticsNGSDiagnosisDatabases
  • GOBLET/ELIXIR-EXCELERATE Workshop on e-learning

    21 November 2017

    Oeiras, Portugal

    Elixir node event
    GOBLET/ELIXIR-EXCELERATE Workshop on e-learning https://tess.elixir-europe.org/events/goblet-elixir-excelerate-workshop-on-e-learning GOBLET/ELIXIR-EXCELERATE Workshop on e-learning, Nov 21, 2017 at the Gulbenkian Institute of Science, Oeiras, Portugal 2017-11-21 09:00:00 UTC 2017-11-21 17:00:00 UTC Instituto Gulbenkian, ELIXIR Portugal, GOBLET Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal Bioinformatics Instituto Gulbenkian de Ciência [] Researchersteachers workshops_and_courses registration_of_interest TeachingeLearningEeLPbioinformatics
  • CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF

    28 February 2018

    CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF https://tess.elixir-europe.org/events/cwlexec-a-new-open-source-tool-to-run-cwl-workflows-on-lsf The [Common Workflow Language (CWL)](http://www.commonwl.org/) is a community-led specification for describing analysis _workflows_ and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and _high performance computing_ (HPC) environments. [IBM Spectrum LSF](https://www.ibm.com/us-en/marketplace/hpc-workload-management) (formerly IBM Platform LSF) is a complete workload management solution for demanding HPC environments. Featuring intelligent, policy-driven scheduling, it helps organizations accelerate research and design while controlling costs through superior resource utilization. Recognizing the popularity of CWL among LSF users, we introduce a new open source project **CWLEXEC** to support running CWL workflows on LSF. The project will feature smooth integration with LSF with high efficiency and scalability, self-healing of workflows, support user-specified submission options while keeping CWL definitions portable, and other benefits. * **Title**: CWLEXEC: A new open source tool to run CWL workflows on LSF * **Presenter:** Qingda Wang, Principal Architect, IBM Spectrum LSF Family Products and OEM * **Time**: 2018-02-28 14:00 GMT / 15:00 CET 2018-02-28 14:00:00 UTC 2018-02-28 15:00:00 UTC BioExcel Bioinformatics Genomics Workflows University of ManchesterBioExcel CoE Stian Soiland-Reyes http://ask.bioexcel.eu/ [] bioinformaticiansHPC users workshops_and_courses registration_of_interest WorkflowsCWLHPCLSF
  • Introduction to Linux and Workflows for Biologists

    14 - 18 May 2018

    Edinburgh, United Kingdom

    Elixir node event
    Introduction to Linux and Workflows for Biologists https://tess.elixir-europe.org/events/introduction-to-linux-and-workflows-for-biologists-866df86c-a827-433d-9445-af7726bcf5a1 Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. 2018-05-14 09:00:00 UTC 2018-05-18 17:00:00 UTC The King's Buildings, The University of Edinburgh, Edinburgh, United Kingdom The King's Buildings, The University of Edinburgh Edinburgh United Kingdom EH9 3JN Workflows Bioinformatics Edinburgh Genomics Bert Overduin - bert.overduin@ed.ac.uk [] [] workshops_and_courses [] BioinformaticsLinuxWorkflows
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1

    20 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series #### Computational requirements for running the H3ABioNet GWAS workflows The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics: Installing and using Nextflow Installing and using Github Use of containers for packaging and running tools Pulling the GWAS pipeline from Github and running it As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements: Either a Linux machine or an Apple running macOS Ideally you should have machine with at least 2-4 cores and 8GB of RAM. Java 8 Nextflow installed (see installation instructions at https://www.nextflow.io/) Python 3 Please also install either Docker OR the following dependencies using pip3: Pandas, Matplotlib, Openpyxl, SciPy, NumPy PLINK 1.9 [Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]: https://github.com/h3abionet/h3agwas/blob/master/README.md 2018-08-20 15:00:00 UTC 2018-08-20 16:30:00 UTC H3ABioNet Population genomics Genotyping experiment Computational biology Workflows GWAS study Bioinformatics H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chipAnyone who wants to learn more about GWAS workshops_and_courses [] NextflowDockerH3ABioNetGWASWorkflowsGenotyping array analysis bioinformaticsAfricaPopulation GenomicsReproducible ScienceH3Africa genotyping arrayHigh performance computingCloud computingGWAS workflowH3ABioNet GWAS 2018 Lecture Series
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 4

    29 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 4 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-lecture-4 ### Quality control and its importance in GWAS In the fourth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS), the importance of doing good quality control for a GWAS will be discussed. The lecture will cover the types of errors one should control for, the specific bioinformatics tools used for quality control. Specific sample and SNP quality control steps that should be undertaken in a GWAS will be explored using specific examples. 2018-08-29 15:00:00 UTC 2018-08-29 16:30:00 UTC H3ABioNet Genotyping experiment GWAS study Computational biology Bioinformatics Population genomics Population genetics H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses [] Genome Wide Association StudiesGenotype callingH3Africa genotyping arrayAfrican populationsQuality Control for GWASSample Quality ControlSNP Quality ControlPopulation GenomicsGenotypingPLINK formatPrincipal Component AnalysisLow minor allele frequencyMissingnessGWAS workflowDiscordant Sex informationNextflowGenotyping rate callHeterozygosity rateRelated and duplicate individualsIdentity by DescentHardy Weinberg EquilibriumBioinformaticsH3ABioNet GWAS 2018 Lecture Series
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Adelaide)

    25 - 26 September 2019

    Adelaide, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Adelaide) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow 2019-09-25 09:00:00 UTC 2019-09-26 17:00:00 UTC EMBL-ABR Room 4.50 Braggs Building North Terrace Campus, University of Adelaide Adelaide, SA 5000, Adelaide, Australia Room 4.50 Braggs Building North Terrace Campus, University of Adelaide Adelaide, SA 5000 Adelaide Adelaide City Council Australia Bioinformatics University of Adelaide [] [] [] [] bioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Pawsey Supercomputing Centre)

    25 - 26 September 2019

    Perth, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Pawsey Supercomputing Centre) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-3e39d24f-3f89-496f-8d54-479324a373b9 2019-09-25 10:00:00 UTC 2019-09-26 14:00:00 UTC EMBL-ABR Seminar Room Australian Resources Research Centre (ARRC) 26 Dick Perry Avenue Kensington, WA 6151, Perth, Australia Seminar Room Australian Resources Research Centre (ARRC) 26 Dick Perry Avenue Kensington, WA 6151 Perth Australia Bioinformatics Australian Resources Research Centre [] [] [] [] bioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Monash University)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Monash University) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-monash-university 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR L1.02, 44 Exhibition Walk Matheson Library Monash University Clayton, VIC, Melbourne, Australia L1.02, 44 Exhibition Walk Matheson Library Monash University Clayton, VIC Melbourne Australia Bioinformatics Monash University [] [] [] [] SnakemakeNextflowbioinformatics
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Hudson Institute)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Hudson Institute) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-c253f254-38a1-4de9-b3cf-8abf216453db 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Boardroom 1, Level 3 Hudson Institute of Medical Research 27-31 Wright Street Clayton, VIC 3168, Melbourne, Australia Boardroom 1, Level 3 Hudson Institute of Medical Research 27-31 Wright Street Clayton, VIC 3168 Melbourne Australia Bioinformatics [] [] [] [] [] bioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (JCU)

    25 - 26 September 2019

    Townsville, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (JCU) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-b20f419e-63fe-4ad1-a65c-4afe6f988d4c 2019-09-25 12:00:00 UTC 2019-09-26 17:00:00 UTC EMBL-ABR Room 002-107 James Cook University Townsville, QLD, Townsville, Australia Room 002-107 James Cook University Townsville, QLD Townsville Townsville City Australia Bioinformatics James Cook University [] [] [] [] bioinformaticsSnakemakeNextflow
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (UNSW)

    25 - 26 September 2019

    New South Wales , Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (UNSW) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-77dd69fe-1580-410f-86bc-adba3f78eabf 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Squarehouse 217 Kensington Campus (Lower campus near Anzac Parade) UNSW NSW, New South Wales , Australia Squarehouse 217 Kensington Campus (Lower campus near Anzac Parade) UNSW NSW New South Wales Randwick City Council Australia Bioinformatics The University of Sydney [] [] [] [] BioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (UQ)

    25 - 26 September 2019

    Saint Lucia, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (UQ) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-826ee571-b240-4f58-afb8-fd46491db6b1 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Room 505 Axon Building (#47) University of Queensland St Lucia, QLD, Saint Lucia, Australia Room 505 Axon Building (#47) University of Queensland St Lucia, QLD Saint Lucia Australia Bioinformatics University of Queensland [] [] [] [] bioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Melbourne)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Melbourne) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-23941db7-c610-4aaf-8789-f55c938edb0d 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Melbourne Bioinformatics 187 Grattan St University of Melbourne CARLTON, VIC 3053, Melbourne, Australia Melbourne Bioinformatics 187 Grattan St University of Melbourne CARLTON, VIC 3053 Melbourne Australia Bioinformatics University of Melbourne [] [] [] [] bioinformaticsSnakemakeNextflow
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