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  • 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
  • Microscopy Image Analysis Course

    19 - 20 September 2019

    Heidelberg, Germany

    Microscopy Image Analysis Course https://tess.elixir-europe.org/events/microscopy-image-analysis-course Educators: Karl Rohr, Thomas Wollmann, Manuel Gunkel (HD-HuB), Qi Gao, Leonid Kostrykin Date: 19.-20.9.2019 Location: Heidelberg University IPMB (Institute of Pharmacy and Molecular Biotechnology) Im Neuenheimer Feld 364 Contents: The course gives an introduction into the field of microscopy image analysis for cell biology and the use of software tools for automated processing of image data. Basic methods for computer-based analysis of microscopy images are introduced such as image preprocessing, segmentation, feature extraction, classification, colocalization, and tracking. Concepts of software platforms with focus on ImageJ and their use for analyzing cell microscopy image data are also taught. Workflow systems for automating image analysis pipelines are also considered (e.g., KNIME, Galaxy). The course consists of lectures and practical sessions. Participants should bring their laptops for the practical sessions. The target group are researchers with a background in biology or medicine that need to analyze their data and have little or no experience in automated image analysis. Learning goals: - Introduction into cell microscopy image analysis - Application of software tools for automated analysis of image data Prerequisites: Basic knowledge in using software tools for image analysis is helpful but not mandatory Keywords: Computer-based image analysis, image preprocessing, segmentation, feature extraction, classification, colocalization, tracking Tools: Image J Course fee: Participants will be charged with a course fee of 40 Euros (to cover the lunch and infrastructure related cost). The invoice details will be shared via email. Registration: Please register directly on the HD-HuB website: https://www.hd-hub.de/course-dates/3-all/47-microscopy-image-analysis-course In the "Comments" section of the registration form, please provide some information about yourself and your motivation to attend the training (e.g. Position, Field of study/Background, Topic of work, Knowledge of image analysis methods/tools). Registration closes on August 11, 2019. The capacity is limited to 20 participants and applicants will be selected after registration closed. You will be notified of the outcome by e-mail on August 23, 2019. 2019-09-19 09:00:00 UTC 2019-09-20 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] [] [] []
  • Initiation to Linux command line

    25 September 2019

    Ghent, Belgium

    Elixir node event
    Initiation to Linux command line https://tess.elixir-europe.org/events/initiation-to-linux-command-line After this training you will: feel comfortable using Linux command line use bash to execute commands in Linux and know your way around the file system 2019-09-25 09:00:00 UTC 2019-09-25 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • First Steps with UNIX in Life Sciences

    25 September 2019

    Lausanne, Switzerland

    Elixir node event
    First Steps with UNIX in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-unix-in-life-sciences-4430cc52-cd66-4a18-89c1-dc7e7fbe1bc1 Overview With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis. 2019-09-25 09:00:00 UTC 2019-09-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Galaxy Training: Using Galaxy for RNA-seq

    8 October 2019

    Ghent, Belgium

    Elixir node event
    Galaxy Training: Using Galaxy for RNA-seq https://tess.elixir-europe.org/events/galaxy-training-using-galaxy-for-rna-seq This practical aims to familiarize you with the Galaxy user interface & execute a complete analysis of RNA-seq data. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. In this tutorial we will introduce you to bare basics of Galaxy: Getting data from external databases such as UCSC Performing simple data manipulation Understanding Galaxy’s History system Creating and running a workflow The RNA-seq data analysis part comprises: Filtering and quality control of reads Mapping of reads to reference genomes Examples of downstream data-analysis possibilities (variant calling, differential expression, etc.)  This workshop is organised by ELIXIR Belgium. 2019-10-08 09:00:00 UTC 2019-10-08 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • First steps with R in Life Sciences

    8 - 9 October 2019

    Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-31722d33-fefc-4aaa-a004-cd69bbab054e The course is now full with a long waiting list. Application is still open but you will be directly put in the waiting list. There will be other sessions next year. Thank you for your understanding. 2019-10-08 09:00:00 UTC 2019-10-09 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Software Carpentry Workshop

    16 - 18 October 2019

    Heidelberg, Germany

    Software Carpentry Workshop https://tess.elixir-europe.org/events/software-carpentry-workshop-ab3af408-aa91-49ed-bab2-5db1f2e6d15d Educators: Malvika Sharan, Georg Zeller, Mike Smith, Thomas Schwarzl, Frank Thommen (HD-HuB), Holger Dinkel Date: 16-10-2019 - 18-10-2019 09:00-18:00 Location: ATC Computer Training Lab, EMBL Heidelberg Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2019-10-16 09:00:00 UTC 2019-10-18 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • SPHN Data Privacy and IT Security Training

    25 October 2019

    Lausanne, Switzerland

    Elixir node event
    SPHN Data Privacy and IT Security Training https://tess.elixir-europe.org/events/sphn-data-privacy-and-it-security-training-45f9b664-6a6d-4fd1-bcad-c2201297c947 Overview Within the Swiss Personalized Health Network (SPHN) and related national initiatives researchers use patient data (i.e., confidential human data) in their research projects. 2019-10-25 09:00:00 UTC 2019-10-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Data Management Plan

    31 October - 1 November 2019

    Lausanne, Switzerland

    Elixir node event
    Data Management Plan https://tess.elixir-europe.org/events/data-management-plan-812edd6d-94f8-445e-9830-257ec0790d90 Overview Recent studies have shown that worldwide, between 51% and 89% of published life sciences research is not reproducible, with consequent losses estimated at around $100 billions/year in biomedical research (Chalmers et al., 2009; Freedman et 2019-10-31 09:00:00 UTC 2019-11-01 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Machine Learning in R

    6 - 7 November 2019

    Heidelberg, Germany

    Machine Learning in R https://tess.elixir-europe.org/events/machine-learning-in-r Date Nov 6 - Nov 7 2019 Location EMBL Heidelberg Tutors and helpers - Dr. Malvika Sharan - Prof Bernd Bischl - Martin Binder - Giuseppe Casalicchio Affiliation: Ludwig-Maximilians-University Munich Course Information This two-day course, on the implementation of Machine Learning in R, using mlr package will be delivered as practical sessions on programming and data analysis. The main goal of mlr is to provide a unified interface for machine learning tasks as classification, regression, cluster analysis and survival analysis in R. Sessions will be driven by many practical exercises and case studies. Before this workshop, participants are expected to review the official material introducing the principle of Machine Learning (see the prerequisite). Course Content This 2-day course will cover hands-on sessions using `mlr` and other relevant packages. Daily schedule - 09:30-12:30 3h morning, 90 min Theory + 90 min Practical - 12:30-13:30 1h Lunchbreak - 13:30-16:30 3h afternoon, 90 min Theory + 90 min Practical - 16:30-17:00 Time for general questions Day 1 Introduction to the concepts and Practical with mlr - Performance Evaluation and Resampling (Metrics, CV, ROC) - Introduction to Boosting Day 2 Introduction to the concepts and Practical with mlr - Tuning and Nested Cross-Validation - Regularization and Feature Selection Prerequisite The course is aimed at advanced R programmers, preferably with some knowledge of statistics and data modeling (See prerequisite materials from Day-1, 2, & 4). In this course, our learners will learn more about machine learning and its application and implementation through the hands-on sessions and use cases. Optional: Discussion-Based Session On The Principle of Machine Learning Anna Kreshuk (EMBL Group Leader) will lead a one-day discussion-based session on 14 October 2019 to address your questions on the prerequisite materials on the principle of Machine Learning. This will also allow you to connect with other participants of this workshop informally, and discuss the materials in smaller groups. Please register for this workshop separately: https://bio-it.embl.de/events/machine-learning-discussion-workshop-2019/. Registration Please register on this page: https://bio-it.embl.de/events/machine-learning-in-r-2019/ Please note that the maximum capacity of this course is 40 participants and registration is required to secure a place. If you have any questions, please contact Malvika Sharan. In your registration, please mention your EMBL group name, or institute's name (e.g. DKFZ, Uni-HD) if you are registering as an external participant. Costs 60,00 EUR Keywords: Machine Learning, R 2019-11-06 09:00:00 UTC 2019-11-07 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Bioinformatics and Software Developers Community Event: Containerization & Reproducible Workflows

    7 November 2019

    Ghent, Belgium

    Elixir node event
    Bioinformatics and Software Developers Community Event: Containerization & Reproducible Workflows https://tess.elixir-europe.org/events/bioinformatics-and-software-developers-community-event-containerization-reproducible-workflows Get insights from your peers Isolate your computer environment or newly developed software tools using Docker Containers Use Nextflow as your workflow pipeline 2019-11-07 09:00:00 UTC 2019-11-07 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • Translational Medicine Explained course

    11 - 15 November 2019

    Barcelona, Spain

    Elixir node event
    Translational Medicine Explained course https://tess.elixir-europe.org/events/translational-medicine-explained-course Interested in discovering the landscape of Translational Medicine? Want to learn about the job profiles of scientists in Industry? Then join the 2019 Winter school “Translational Medicine Explained (TMex)” which will be held in the beautiful Palau Macaya in Barcelona from… The post Translational Medicine Explained course appeared first on Dutch Techcentre for Life Sciences. 2019-11-11 09:00:00 UTC 2019-11-15 00:00:00 UTC Barcelona, Spain, Barcelona, Spain Barcelona, Spain Barcelona Spain [] [] [] workshops_and_courses [] []
  • 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
  • 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
  • Advanced R Shiny

    3 December 2019

    Lausanne, Switzerland

    Elixir node event
    Advanced R Shiny https://tess.elixir-europe.org/events/advanced-r-shiny-a89ad51d-0f85-4fbb-9dc3-fc055b677e84 More information coming up 2019-12-03 09:00:00 UTC 2019-12-03 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First steps with Git for reproducible research (date to be confirmed)

    5 December 2019

    Lausanne, Switzerland

    Elixir node event
    First steps with Git for reproducible research (date to be confirmed) https://tess.elixir-europe.org/events/first-steps-with-git-for-reproducible-research More information soon 2019-12-05 09:00:00 UTC 2019-12-05 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • High Performance Computing (HPC) in Life Sciences: Vital-IT Infrastructure Training

    12 December 2019

    Lausanne, Switzerland

    Elixir node event
    High Performance Computing (HPC) in Life Sciences: Vital-IT Infrastructure Training https://tess.elixir-europe.org/events/high-performance-computing-hpc-in-life-sciences-vital-it-infrastructure-training-7a057fe4-5717-4c6a-a567-ba2cb95bb755 Overview Several scientific applications require computing and/or storage resources that go beyond the processing power of a single multi-core machine. 2019-12-12 09:00:00 UTC 2019-12-12 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research

    29 January 2020

    Hinxton, United Kingdom

    FAIRplus Innovation and SME Forum: Implementing FAIR data principles in industrial life science research https://tess.elixir-europe.org/events/fairplus-innovation-and-sme-forum The agenda includes: Introduction to FAIRplus Guidelines for making data FAIR Flastalks from SMEs Hands-on session on FAIRification   Who should attend: Biotech companies owning data potentially in need of FAIRification  Technology companies who are planning to provide FAIRification services  Academic groups interested in FAIRification for their data collections       2020-01-29 09:00:00 UTC 2020-01-29 00:00:00 UTC Wellcome Genome Campus, Hinxton, United Kingdom Wellcome Genome Campus Hinxton United Kingdom [] [] [] [] [] []
  • ELIXIR Scientific Advisory Board meeting 2020

    11 - 12 February 2020

    Hinxton, United Kingdom

    ELIXIR Scientific Advisory Board meeting 2020 https://tess.elixir-europe.org/events/elixir-scientific-advisory-board-meeting-2020 The ELIXIR Scientific Advisory Board will hold their annual meeting from 11-12 February 2020 at the Wellcome Genome Campus in Hinxton, UK. Details of agenda and registration will be made available to participants. Contacts For all logistical inquiries, please contact: Melissa Balzano (melissa.balzano@elixir-europe.org)  Tel: +44 (0)1223 494305 For all documentation inquiries, please contact: Joana Wingender (joana.wingender@elixir-europe.org)  Tel: +44 (0)1223 492670 2020-02-11 09:00:00 UTC 2020-02-12 17:00:00 UTC Wellcome Genome Campus, Hinxton, United Kingdom Wellcome Genome Campus Hinxton United Kingdom [] [] [] meetings_and_conferences [] []
  • First steps with Git for reproducible research

    27 February 2020

    Lausanne, Switzerland

    Elixir node event
    First steps with Git for reproducible research https://tess.elixir-europe.org/events/first-steps-with-git-for-reproducible-research-date-to-be-confirmed More information soon 2020-02-27 09:00:00 UTC 2020-02-27 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • 13th ELIXIR Board meeting (Hinxton)

    22 - 23 April 2020

    Hinxton, United Kingdom

    13th ELIXIR Board meeting (Hinxton) https://tess.elixir-europe.org/events/thirteenth-elixir-board-meeting-hinxton The thirteenth ELIXIR Board will take place at the Wellcome Genome Campus in Hinxton, UK From 29 - 30 April 2020. This meeting is only open to the ELIXIR Board and Observers. Agenda items and meeting documentation will be made available to Board members in due time.  Any inquiries regarding ELIXIR Board meetings should be sent to info@elixir-europe.org. 2020-04-22 09:00:00 UTC 2020-04-23 00:00:00 UTC Wellcome Genome Campus, Hinxton, United Kingdom Wellcome Genome Campus Hinxton United Kingdom CB10 1SD [] [] [] meetings_and_conferences [] []
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