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  • Genome assembly using Galaxy

    2 - 3 August 2017

    Australia

    Genome assembly using Galaxy https://tess.elixir-europe.org/events/genome-assembly-using-galaxy 2017-08-02 09:00:00 UTC 2017-08-03 12:30:00 UTC QFAB Bioinformatics Room 3.141, Queensland Bioscience Precinct, The University of Queensland, Australia Room 3.141, Queensland Bioscience Precinct, The University of Queensland Brisbane Australia Bioinformatics University of Queensland [] [] workshops_and_courses [] Genome AssemblyGalaxy
  • Introduction to long-read genome assembly

    22 March 2018

    Carlton, Australia

    Introduction to long-read genome assembly https://tess.elixir-europe.org/events/introduction-to-long-read-genome-assembly 2018-03-22 13:30:00 UTC 2018-03-22 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 [] Genome Assembly
  • 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
  • Introduction to long-read genome assembly

    5 April 2019

    Melbourne, Australia

    Introduction to long-read genome assembly https://tess.elixir-europe.org/events/introduction-to-long-read-genome-assembly-c43a1031-7b9c-4893-8b28-7844d2bc1741 2019-04-05 09:00:00 UTC 2019-04-05 17:00:00 UTC Melbourne Bioinformatics 187 Grattan St, 187, Grattan Street, Melbourne, Australia 187 Grattan St, 187, Grattan Street Melbourne Australia Bioinformatics University of Melbourne [] [] [] [] bioinformaticsGalaxyGenome Assembly
  • 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
  • Introduction to Python for Biologists

    12 - 16 August 2019

    Liverpool, United Kingdom

    Introduction to Python for Biologists https://tess.elixir-europe.org/events/introduction-to-python-for-biologists-965f36b3-e040-43cd-bb06-f4e5e3cc588e Registration fee: £500 Places: 15 (first come, first served) Application deadline: 14th June 2019 DESCRIPTION Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way. The instructor of the workshop is the Founder of Python for Biologists, Dr. Martin Jones. Format The workshop will take place over 5 days. Each day will consist of 2 half-day sessions, each consisting of a ~1 hour lecture followed by 2 hours of practical exercises. It is important that attendees attend each session as they will use examples and exercises that build on the materials from previous sessions. For more information and a detailed syllabus please see the following link: https://pythonforbiologists.com/introduction-to-python-for-biologists Who should attend This workshop is aimed at all researchers and technical workers with a background in biology who want to learn programming. The syllabus has been planned with complete beginners in mind. Requirements Attendees will require a level of biological and bioinformatics background so they can appreciate the examples and exercises (i.e. they should know what a protein accession number, BLAST report, and FASTA sequence is). Attendees will require the ability to us a text editor (e.g. nano, vim, or gedit). No previous programming knowledge is required. Attendees will use their own laptops during the workshop. Instructions for any software to be installed will be sent out prior to the course. If you are not sure if this course is suitable for you please do not hesitate to contact Dr Martin Jones (martin@pythonforbiologists.com) Please fill in the following form (https://forms.gle/mkjiASxS7sKBxeGo7) if you would like to register for the Introduction to Python for Biologists workshop. Applicants will be asked to pay a registration fee of £500. After the application deadline (14th of June) or when all places are fill applicants will be asked to pay for the workshop. Once your fee is paid your place on the course will be confirmed. 2019-08-12 09:00:00 UTC 2019-08-16 17:00:00 UTC Centre for Genomic Research, University of Liverpool (https://www.liverpool.ac.uk/genomic-research/) 126 Mount Pleasant, 126, Mount Pleasant, Liverpool, United Kingdom 126 Mount Pleasant, 126, Mount Pleasant Liverpool Merseyside United Kingdom L3 5SR University of Liverpool [] [] 15 workshops_and_courses [] pythonbioinformaticsprogrammingintrobeginner
  • Nextflow 2019

    17 - 20 September 2019

    Barcelona, Spain

    Elixir node event
    Nextflow 2019 https://tess.elixir-europe.org/events/nextflow-2019 **Create. Deploy. Share.** Nextflow is a popular workflow management solution that allows scientists and engineers to create data-driven applications which can be effortlessly scaled across clusters and clouds. It simplifies the writing of complex distributed computational workflows in a portable and replicable manner. Nextflow allows the seamless parallelization and deployment of any existing application with minimal development and maintenance overhead, irrespective of the original programming language. Containerisation technologies and inbuilt executors for the most popular cluster systems (SLURM, PBS, UGE, LSF, etc) and cloud infrastructure (AWS Batch & Google Cloud Platform) ensures unrivalled deployment. The built-in support for code repositories provides code sharing for the collaborations that matter most and enable your applications to touch the world. But most of all, the active community of that has formed around Nextflow provides inspirational, best-in-class technical examples from global leaders in workflow deployment as well as lasting relationships in a growing community. __Nextflow Training - 17th and 18th September 2019__ The week kicks off with a two-day intensive workshop intended for Nextflow beginners and intermediate users. In these practical sessions, participants learn about Nextflow technology starting from basic through to advanced concepts, with the expectation they will acquire the proficiency to develop and deploy their own workflows. The workshop will be provided across 14 topics including processes, operators, executors, containers and best practices. A GitHub repository will be provided with all the necessary material and software as well as AWS cloud instances for running the deployments in the relevant practical sessions. The audience is expected to have at least some prior basic command line experience. __Nextflow Camp - 19th and 20th September 2019__ Nextflow Camp brings together the Nextflow community of developers and users to discuss the state of Nextflow technology, the latest developments and tackle the open questions in a collaborative manner. Each day is split between talks from Nextflow experts and tutorial breakout sessions where participants get a flavour for the possibilities for their own applications. We hope to see you in Barcelona in September! 2019-09-17 09:00:00 UTC 2019-09-20 18:00:00 UTC Paolo Di Tommaso PRBB Parc de Recerca Biomèdica de Barcelona, 88, Carrer del Doctor Aiguader, Barcelona, Spain PRBB Parc de Recerca Biomèdica de Barcelona, 88, Carrer del Doctor Aiguader Barcelona Barcelona Spain 08003 Centre for Genomic Regulation training@crg.eu AWS Bioinformaticians 50 meetings_and_conferencesworkshops_and_courses first_come_first_served NextflowWorkflowsContainersCloud ComputingHPC
  • Advances in Computational Biology Conference 2019

    28 - 29 November 2019

    Barcelona, Spain

    Elixir node event
    Advances in Computational Biology Conference 2019 https://tess.elixir-europe.org/events/advances-in-computational-biology-conference-2019 The first **Advances in Computational Biology conference – _Fostering collaboration among women scientists_** will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing with applications to biology from both the public and private sectors. One of the main purposes of the conference is to **visualize and promote the research done by women scientists** and for this reason, all presenters will be women, although the conference is open to everyone. We want to create a space to foster collaborations between scientists, providing an excellent opportunity to share ideas and build research networks. Topics included: - **Learning from Biological Sequences**: population genomics, evolutionary genomics, systems biology, transcriptomics, sequence analysis - **When Computational Biology meets Medicine**: biomedical applications, mutational landscapes, clinical genomics - **Machines Speeding up Research**: high performance computing, machine learning in the life sciences, imaging data analysis, dynamic simulations and algorithm development Key dates: - Open registration: May 6th, 2019 - Abstract submission opens: May 6th, 2019 - **Abstract submission deadline: July 1st, 2019** - Early bird registration deadline: September 15th, 2019 - Registration deadline: November 1st, 2019 - AdvCompBio Conference: November 28th - 29th, 2019 The programme will include poster and oral presentations, as well as keynotes from leading scientists in the computational biology and high-performance computing fields. The keynote speakers of the conference are: **Christine Orengo**, group leader of Orengo Group at University College London, **Natasa Przulj**, group leader of the Life Sciences – Integrative Computational Network Biology at the Barcelona Supercomputing Center and **Marie-Christine Sawley**, director of the Exascale Lab at Intel. The confirmed chairs of the conference are: **Alison Kennedy**, director of the STFC Hartree Centre, **Janet Kelso**, group leader of the Minerva Research Group for Bioinformatics at the Max Planck Institute for Evolutionary Anthropology, and **Nuria Lopez-Bigas**, leader of the Biomedical Genomics Research Group at the Institute for Research in Biomedicine Barcelona. Furthermore, the participants will have the opportunity to interact personally with female leaders in the fields of IT, academic research and politics that support the conference. The conference is organised by the Bioinfo4Women programme from the Barcelona Supercomputing Center (BSC-CNS) with the collaboration of IMIM-UPF Research Programme on Biomedical Informatics (GRIB), the Spanish National Bioinformatics Institute (INB/ELIXIR-ES) and the Universitat Politècnica de Catalunya (UPC). It is an affiliate conference of the International Society for Computational Biology (ISCB). 2019-11-28 09:00:00 UTC 2019-11-29 17:00:00 UTC La Pedrera, 92, Passeig de Gràcia, Barcelona, Spain La Pedrera, 92, Passeig de Gràcia Barcelona Barcelona Spain Imaging Machine learning Computational biology Computer science Biomedical science Sequence analysis Transcriptomics Evolutionary biology Population genomics Omics Systems biology Bioinformatics [] [] ResearchersPhD studentsPostdoctoral studentsComputer scienceComputational biologistsbioinformaticians meetings_and_conferences [] HPCBioinformaticsComputational BiologyArtificial IntelligenceGenomicsTranscriptomicsSystems biologyPopulation GenomicsEvolutinary genomicsSequence Analysisbiomedical applicationsmutational landscapesclinical genomicsImagingdynamic simulationsalgorithmsmachine learning
  • Genome assembly using Galaxy

    14 July 2020

    Saint Lucia, Australia

    Genome assembly using Galaxy https://tess.elixir-europe.org/events/genome-assembly-using-galaxy-bfd44b56-d4a3-4863-a62b-e7656374a9a9 2020-07-14 09:00:00 UTC 2020-07-14 17:00:00 UTC QCIF The University of Queensland, Saint Lucia, Australia The University of Queensland Saint Lucia Queensland Australia 4072 University of Queensland Mark Crowe - mark.crowe@qcif.edu.au [] Postgraduate studentsPostdoctoral researchers [] [] Genome AssemblyDe novo genome assemblyGalaxyBioinformatics
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