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19 events found

Scientific topics: Informatics  or Bioinformatics 

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Keywords: eLearning  or Genome Mapping  or SystemsBiology  or Workflows  or Nanotechnology  or Medicine  or Docker 

  • 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
  • Global Nanotechnology Congress and Expo

    21 - 23 April 2016

    Dubai, United Arab Emirates

    Global Nanotechnology Congress and Expo https://tess.elixir-europe.org/events/global-nanotechnology-congress-and-expo 2016-04-21 01:00:00 UTC 2016-04-23 01:00:00 UTC Dubai, United Arab Emirates Dubai United Arab Emirates Bioinformatics [] [] [] meetings_and_conferences [] Nanotechnology
  • 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
  • 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
  • Containerised Bioinformatics: Docker and other tools for reproducible analysis

    21 March 2018

    Carlton, Australia

    Containerised Bioinformatics: Docker and other tools for reproducible analysis https://tess.elixir-europe.org/events/containerised-bioinformatics-docker-and-other-tools-for-reproducible-analysis 2018-03-21 13:30:00 UTC 2018-03-21 16:30:00 UTC Melbourne Bioinformatics Melbourne Bioinformatics, 187 Grattan St, Carlton, Australia Melbourne Bioinformatics, 187 Grattan St Carlton Australia 3053 Bioinformatics University of Melbourne [] [] workshops_and_courses [] Docker
  • 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
  • Containerised Bioinformatics: Docker and other tools for reproducible analysis

    21 June 2018

    Carlton, Australia

    Containerised Bioinformatics: Docker and other tools for reproducible analysis https://tess.elixir-europe.org/events/containerised-bioinformatics-docker-and-other-tools-for-reproducible-analysis-8ff6bdae-bc43-4286-b315-af559a6be6dd 2018-06-21 13:30:00 UTC 2018-06-21 15:30:00 UTC Melbourne Bioinformatics Melbourne Bioinformatics, 187 Grattan St, Carlton, Carlton, Australia Melbourne Bioinformatics, 187 Grattan St, Carlton Carlton Australia 3053 Bioinformatics University of MelbourneMelbourne Bioinformatics [] [] workshops_and_courses [] bioinformaticsDocker
  • BITS2018/Eixir-IIB Workshop on Docker and Reproducibility

    25 - 26 June 2018

    Torino, Italy

    BITS2018/Eixir-IIB Workshop on Docker and Reproducibility https://tess.elixir-europe.org/events/bits2018-eixir-iib-workshop-on-docker-and-reproducibility Docker is a container framework for Linux that allows a developer to make easier the creation, deployment and execution of applications by using containers. During the workshop the participant will learn the core concepts of Docker and how to easily embed bioinformatic pipelines/workflows into a docker container. This workshop is a satellite event held jointly with the BITS Annual Meeting 2018. 2018-06-25 09:00:00 UTC 2018-06-26 18:00:00 UTC BITS2018/ELIXIR-IIB Via Nizza, 52 Molecular Biotechonology Center, University of Turin, Torino, Italy Via Nizza, 52 Molecular Biotechonology Center, University of Turin Torino Città Metropolitana di Torino Italy 10126 Computer science Bioinformatics University of Turin beccuti@di.unito.it [] bioinformaticiansBiologists, Genomicists, Computer ScientistsPhD and graduate students, young researchers and PIs in the life science and computational biology field 24 workshops_and_courses first_come_first_servedregistration_of_interest DockerReproducibilityContainercomputer-science
  • 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
  • Docker Advanced Course

    26 - 27 September 2018

    Milano, Italy

    Docker Advanced Course https://tess.elixir-europe.org/events/docker-advanced-course Docker is used to run “containers” that are essentially lightweight virtual machines. Containers are isolated from each other and use their own set of tools and libraries; they can communicate through well-defined channels. This allows to easily deploy programs since all requisites of a program are stored inside the containers. This course will provide the basic notions and tool to allow a developer to “dockerize” her programs, and to manage a set of containers, hence greatly improving the installation process. 2018-09-26 09:00:00 UTC 2018-09-27 18:00:00 UTC Gianluca Della Vedova (Department of Computer Science, University of Milano-Bicocca, IT), Loredana Le Pera (ELIXIR-IIB Training Coordinator Deputy, IBIOM-CNR, IT), Allegra Via (ELIXIR-IIB Training Coordinator, IBPM-CNR, IT) Via Bicocca degli Arcimboldi, 8, Lab. 715, U7 Building, Milano, Italy Via Bicocca degli Arcimboldi, 8, Lab. 715, U7 Building Milano Città Metropolitana di Milano Italy 20126 Computer science Bioinformatics University of Milano-Bicocca, Italy gianluca.dellavedova@unimib.it [] DevelopersDevOps in any field 20 workshops_and_courses first_come_first_servedregistration_of_interest DockerContainersVirtual machine
  • Containerised Bioinformatics: Docker and other tools for reproducible analysis

    29 October 2018

    Melbourne, Australia

    Containerised Bioinformatics: Docker and other tools for reproducible analysis https://tess.elixir-europe.org/events/containerised-bioinformatics-docker-and-other-tools-for-reproducible-analysis-8ea6f943-f007-425b-8c78-2216438b214a 2018-10-29 01:30:00 UTC 2018-10-29 04:30:00 UTC Melbourne Bioinformatics Melbourne Bioinformatics Boardroom, 187 Grattan St, Carlton, Melbourne, Australia Melbourne Bioinformatics Boardroom, 187 Grattan St, Carlton Melbourne Australia 3053 Bioinformatics Melbourne BioinformaticsUniversity of Melbourne [] [] [] [] bioinformaticsDocker
  • Workshop on Research Objects (RO2018)

    29 October 2018

    Amsterdam, Netherlands

    Workshop on Research Objects (RO2018) https://tess.elixir-europe.org/events/workshop-on-research-objects-ro2018 In this workshop we will explore recent advancements in Research Objects and publishing of research data. **Deadlines**: * 2018-07-01 Abstracts due * 2018-07-15 Research articles and software/data articles due A travel bursary is available for accepted speakers, sponsored by [BioExcel](http://bioexcel.eu) (H2020-675728) ## Research Objects Scholarly Communication has evolved significantly in recent years, with an increasing focus on **Open Research**, [FAIR](https://doi.org/10.1038/sdata.2016.18)data sharing and community-developed open source methods. A question remains on how to publish, archive and explore digital research outputs. A number of initiatives have begun to explore how to package and describe research outputs, data, methods, workflows, provenance and structured metadata, reusing existing Web standards and formats. Such efforts aim to address the challenges of structuring multi-part research outcomes with their context, handling distributed and living content and porting and safely exchange what we collectively can call **Research Objects** between platforms and between researchers. In the workshop **RO2018**, part of [IEEE eScience 2018](https://www.escience2018.com) in Amsterdam, we will explore recent advancements in Research Objects and publishing of research data with peer-reviewed presentations, invited talks, short demos, lightning talks and break-out sessions to further build relationships across scientific domains and RO practitioners. ## Call for Papers RO2018 welcomes submissions of academic abstracts (1-2 pages), data/software articles (3-6 pages) and short research articles (4-8 pages) on cross-cutting case studies or specific research on topics including, but not limited to: FAIR metrics; platforms, infrastructure and tools; lifecycles; access control and secure exchange; examples of exploitation and application; executable containers; metadata, packaging and formats; credit, attribution and peer review; dealing with scale and distribution; driving adoption within current scholarly communications and alignments with community efforts; and domain-specific and cross-domain Research Objects. Further details on submitting: [http://www.researchobject.org/ro2018/submitting-to-ro2018/](http://www.researchobject.org/ro2018/submitting-to-ro2018/) ## Timeline 2018-07-01 Abstracts due 2018-07-15 Research articles and software/data articles due 2018-08-31 Notification of acceptance 2018-08-31 IEEE eScience 2018 early-bird registration deadline 2018-10-29 RO2018 workshop at IEEE eScience 2018 2018-10-29 09:00:00 UTC 2018-10-29 17:00:00 UTC The University of Manchester, researchobject.org, IEEE Mövenpick Hotel Amsterdam City Centre, 11, Piet Heinkade, Amsterdam, Netherlands Mövenpick Hotel Amsterdam City Centre, 11, Piet Heinkade Amsterdam Amsterdam Netherlands Workflows Software engineering Ontology and terminology Informatics Data submission, annotation and curation Data identity and mapping Data integration and warehousing Data architecture, analysis and design Data management Computer science [] For any questions, email the Workshop Organizers at ro2018@easychair.org BioExcel [] workshops_and_courses [] digital archivesdata repositorylinked dataWorkflows
  • Containerised Bioinformatics: Docker and other tools for reproducible analysis

    30 May 2019

    Melbourne, Australia

    Containerised Bioinformatics: Docker and other tools for reproducible analysis https://tess.elixir-europe.org/events/containerised-bioinformatics-docker-and-other-tools-for-reproducible-analysis-0b64e419-834f-43dd-8605-6ed093fc6caa 2019-05-30 09:00:00 UTC 2019-05-30 17:00:00 UTC Melbourne Bioinformatics 187 Grattan St, 187, Grattan Street, Melbourne, Australia 187 Grattan St, 187, Grattan Street Melbourne Melbourne City Australia 3053 Bioinformatics University of Melbourne [] [] [] [] bioinformaticsDocker
  • Docker and Reproducibility

    13 - 14 June 2019

    Torino, Italy

    Docker and Reproducibility https://tess.elixir-europe.org/events/docker-and-reproducibility Docker is a container framework for Linux that allows a developer to make easier the creation, deployment and execution of applications by using containers. During the workshop the participant will learn the core concepts of Docker and how to easily embed bioinformatic pipelines/workflows into a docker container. By the end of this course, the participants will learn: - the basic concepts of Docker; - to assess the advantages of a containerized software development & deployment; - to use Docker engine features necessary for running containerized applications; - how to use the Docker File and Docker Hub to create a Docker image; - the various networking mechanisms available in Docker. 2019-06-13 09:00:00 UTC 2019-06-14 18:00:00 UTC ELIXIR-IIB, CNR, University of Turin University of Turin, Molecular Biotechnology Center, Torino, Italy University of Turin, Molecular Biotechnology Center Torino Città Metropolitana di Torino Italy 10126 Bioinformatics Computer science University of Turin elixir.ita.training@gmail.com [] bioinformaticiansBiologists, Genomicists, Computer ScientistsPhD and graduate students, young researchers and PIs in the life science and computational biology field 15 workshops_and_courses first_come_first_served DockerContainersReproducibilitycomputer-science
  • ELIXIR Norway: Hands-on bioinformatics NeLS workshop

    26 November 2019

    Tromsø, Norway

    Elixir node event
    ELIXIR Norway: Hands-on bioinformatics NeLS workshop https://tess.elixir-europe.org/events/elixir-norway-hands-on-bioinformatics-nels-workshop We are pleased to announce the second hands-on bioinformatics NeLS workshop organised in Tromsø by [ELIXIR Norway](https://www.elixir-norway.org/). The topic is on how you can use the Norwegian e-Infrastructure for Life Sciences - [NeLS](nels.bioinfo.no) to store and share data, and to run analyses via customisable analysis workflows in Galaxy. More specifically, we will go through how you can store data in NeLS and upload it directly into Galaxy. We will also construct and run a complete sequence analysis workflow for taxonomic profiling on a metagenomic sample. There are no requirements for programming skills or experience using the command line, as Galaxy provides a web interface for running analysis. 2019-11-26 09:00:00 UTC 2019-11-26 15:00:00 UTC ELIXIR Norway University of Tromsø, Medisin og helsefagbygget (MH øst): Datarom (U7.110), Tromsø, Norway University of Tromsø, Medisin og helsefagbygget (MH øst): Datarom (U7.110) Tromsø Tromsø Norway 9019 Bioinformatics University of Tromsø ELIXIR Norway life scientistsdata managers 20 workshops_and_courses by_invitation bioinformaticsNeLSGalaxyEeLPeLearning
  • Introductory Linux Tutorial for Life Sciences 4

    10 - 12 December 2019

    Elixir node event
    Introductory Linux Tutorial for Life Sciences 4 https://tess.elixir-europe.org/events/introductory-linux-tutorial-for-life-sciences-4 NBIS (the Swedish node of ELIXIR) and ELIXIR Slovenia are offering an "Introduction to Linux" course targeted at life scientists who want to extend their skills and knowledge. Big data (usually in the form of large text files) are generated nowadays in many fields of science. Trying to handle this data with applications like Word or Excel is difficult or impossible, while using the Linux command line can improve data processing efficiency. Unix/Linux provides an excellent computing environment for several disciplines (such as bioinformatics, physics, engineering) and the command line interpreter (shell) serves as an interface to many big-data processing programs. The course provides a basic introduction to Unix/Linux commands and covers how Unix/Linux commands can be used to manage and inspect your data and results, and how to generate and run pipelines and workflows using basic shell scripting. Finally, we will show you how the command line is used for access to supercomputers for boosting your scientific research. Participants will be able to attend the course either by traveling to Stockholm or to Umeå in Sweden, to Ljubljana in Slovenia, or by connecting remotely via the ELIXIR Slovenia eLearning Platform (EeLP). The number of remote students is limited to 30. The number of students per classroom is limited to 15 for Stockholm and Umeå, and 20 for Ljubljana. Additional participants will be placed on a waiting list and contacted as soon as space becomes available. The course will be broadcast from Sweden. ***The registration deadline has been extended until Friday, November 22.*** 2019-12-10 09:00:00 UTC 2019-12-12 17:00:00 UTC ELIXIR Sweden (NBIS) and ELIXIR Slovenia Bioinformatics Computer science NBISUniversity of Ljubljana, Faculty of Medicine [] Life Science ResearchersbioinformaticiansBiophysicistsengineers [] [] life sciences LinuxUnixEeLPeLearningCommand line

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