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129 events found
  • Ligand-protein docking, and computer-aided drug design

    13 - 15 December 2021

    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-streamed 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. 2021-12-13 09:00:00 UTC 2021-12-15 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • ELIXIR-FR : 4th Workshop Single-Cell 2022 (Roscoff-FRANCE)

    9 - 14 January 2022

    Roscoff, France

    ELIXIR-FR : 4th Workshop Single-Cell 2022 (Roscoff-FRANCE) https://tess.elixir-europe.org/events/elixir-fr-4th-workshop-single-cell-2022-roscoff-france Training : Single-Cell : Transcriptomics, Spatial and Multi-Omics (sincellTE) Deadline pre-registration: 15th September 2021 This one-week class focuses on the large-scale study of heterogeneity across individual cells from the genomic, transcriptomic and epigenomic points of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce comes with novel methodological challenges for the analysis. In this regard, specific bioinformatics and statistical methods have been developed in order to extract robust information. This course is directed towards engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD Student and Post Doc in computational biology or bioinformatics that are interested in the development of methods and pipelines for highly dimensional single-cell data analysis. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, cell phenotyping and additional multi-omics. Requirements : Participants must have prior experience on NGS data analysis  with everyday use of R and good knowledge of Unix command line. Before the training, participants will be asked to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets with provided pedagogic material. It is not necessary to have personal single-cell data to analyse. All information and pre-registration: https://www.france-bioinformatique.fr/formation/single-cell-2022/ 2022-01-09 18:00:00 UTC 2022-01-14 16:00:00 UTC Place Georges Teissier, Roscoff, France Place Georges Teissier Roscoff France 29680 [] [] [] [] [] []
  • Docker (and Singularity) for reproducible and automated data analysis

    10 - 11 January 2022

    Elixir node event
    Docker (and Singularity) for reproducible and automated data analysis https://tess.elixir-europe.org/events/docker-and-singularity-for-reproducible-and-automated-data-analysis Learn the concept of and the difference between Docker & Singularity containers  Write a Docker recipe, build and run a Docker image and containers Pull and push Docker container to / from Docker hub Docker files and layers; Docker cashing Working with volumes Pull Docker containers as a Singularity image 2022-01-10 09:00:00 UTC 2022-01-11 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • Nextflow for reproducible and automated data analysis

    17 - 18 January 2022

    Elixir node event
    Nextflow for reproducible and automated data analysis https://tess.elixir-europe.org/events/nextflow-for-reproducible-and-automated-data-analysis Understand Nextflow's basic concepts: channels, processes, modules, workflows, etc.  Write and run a Nextflow pipeline  Write and modify config files for storing parameters related to computing hardware as well as pipeline dependent parameters 2022-01-17 09:00:00 UTC 2022-01-18 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • Programming Distributed Computing Platforms with COMPSs @ BSC

    25 - 26 January 2022

    Programming Distributed Computing Platforms with COMPSs @ BSC https://tess.elixir-europe.org/events/programming-distributed-computing-platforms-with-compss-bsc-c0947e02-6579-44e3-b688-8abacab9d005 Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course convener: Rosa Badia, Workflows and Distributed Computing Group Manager, Computer Sciences - Workflows and Distributed Computing Department Lecturers:  Rosa M Badia, Workflows and Distributed Computing Group Manager, Computer Sciences - Workflows and Distributed Computing Department, BSC Javier Conejero, Senior Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Jorge Ejarque, Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Daniele Lezzi, Senior Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Francesc Lordan, Postdoctoral Researcher, Computer Sciences - Workflows and Distributed Computing Department, BSC Objectives: The objective of this course is to give an overview of the COMPSs programming model, which is able to exploit the inherent concurrency of sequential applications and execute them in a transparent manner to the application developer in distributed computing platform. This is achieved by annotating part of the code as tasks, and building at execution a task-dependence graph based on the actual data used consumed/produced by the tasks. The COMPSs runtime is able to schedule the tasks in the computing nodes and take into account facts like data locality and the different nature of the computing nodes in case of heterogeneous platforms. Additionally, recently COMPSs has been enhanced with the possibility of coordinating Web Services as part of the applications. COMPSs supports Java, C/C++ and Python as programming languages. Learning Outcomes:  In the course, the COMPSs syntax, programming methodology and an overview of the runtime internals will be given. The attendees will get a first lesson about programming with COMPSs that will enable them to start programming with this framework. A hands-on with simple introductory exercises will be also performed. The students who finish this course will be able to develop simple COMPSs applications and to run them both in a local resource and in a distributed platform (initially in a private cloud). The exercises will be delivered in Python and Java. In case of Python, Jupyter notebooks will be used in some of the exercises. Level: for trainees with some theoretical and practical knowledge. INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Prerequisites: Programming skills in Java and Python  Tentative Agenda: Day 1 (January 25th, 2022) 9:30 - 10:00 - Welcome and round table (30') 10:00 - 10:30 - Session 1: Introduction to COMPSs (30') 10:30 - 11:15 - Session 2: PyCOMPSs: Writing Python applications (45') 11:15 - 11:45 - Coffee break 11:45 - 13:00 - Session 3: Python Hands-on using Jupyter notebooks (1h15') 13:00 - 14:30 - Lunch break 14:30 - 15:00 - Session 4: Machine learning with dislib (30') 15:00 - 16:30 - Session 5: Hands-on with dislib (1h30') Day 2 (January 26th, 2022) 9:30 - 11:00 - Session 6: Java & C++ (1h30') 11:00 - 11:30 - Cofee break 11:30 - 13:00 - Session 7: COMPSs Advanced Features (1h30') 13:00 - 14:30 - Lunch break 14:30 - 16:30 - Session 8: Cluster Hands-on (MareNostrum) (2h) 16:30 - 16:45 - Session 9: COMPSs Installation & Final Notes (15') END of COURSE https://events.prace-ri.eu/event/1233/ 2022-01-25 08:30:00 UTC 2022-01-26 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Managing distributed data with Hecuba and dataClay @ BSC

    27 January 2022

    Managing distributed data with Hecuba and dataClay @ BSC https://tess.elixir-europe.org/events/managing-distributed-data-with-hecuba-and-dataclay-bsc-b47a99b3-4cfe-4b3b-bb06-b529efc290ff Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course conveners: Department and Research group: Computer Science - Workflows and Distributed Computing Yolanda Becerra, Data-driven Scientific Computing research line, Senior researcher Anna Queralt, Distributed Object Management research line, Senior researcher Course Lecturers: Department and Research group: Computer Sciences - Workflows and Distributed Computing Alex Barceló, Distributed object Management research line, Researcher Yolanda Becerra, Data-driven Scientific Computing research line, Senior researcher Daniel Gasull, Distributed object Management research line, Research engineer Juanjo Costa, Computer Architecture Department at UPC Anna Queralt, Distributed object Management research line, Senior researcher Objectives: The objective of this course is to give an overview of BSC storage solutions, Hecuba and dataClay. These two platforms allow to easily store and manipulate distributed data from object-oriented applications, enabling programmers to handle object persistence using the same classes they use in their programs, thus avoiding time consuming transformations between persistent and non-persistent data models. Also, Hecuba and dataClay enable programmers to transparently manage distributed data, without worrying about its location. This is achieved by adding a minimal set of annotations in the classes. Both Hecuba and dataClay can work independently or integrated with the COMPSs programming model and runtime to facilitate parallelization of applications that handle persistent data, thus providing a comprehensive mechanism that enables the efficient usage of persistent storage solutions from distributed programming environments. Both platforms offer a common interface to the application developer that facilitates using one solution or the other depending on the needs, without changing the application code. Also, both of them have additional features that allow the programmer to take advantage of their particularities. Learning Outcomes:   In the course, the Hecuba and dataClay syntax, programming methodology and an overview of their internals will be given. Also, an overview of COMPSs at user level will be provided in order to take advantage of the distribution of data with both platforms. The attendees will get a first lesson about programming with the common storage interface that will enable them to start programming with both frameworks. A hands-on with simple introductory exercises will be also performed for each platform, with and without COMPSs to distribute the computation. The students who finish this course will be able to develop simple Hecuba and dataClay applications and to run them both in a local resource and in a distributed platform (initially in a private cloud) Prerequisites: Basic programming skills in Python and Java. Previous attendance to PATC course on programming distributed systems with COMPSs is recommended. Tentative Agenda:   Day 1 (Jan 27) Session 1 / 9:30 – 13:00 9:30-10:00 Round table. Presentation and background of participants 10:00-11:00 Motivation, introduction and syntax of BSC storage platforms 11:00-11:30 Coffee break 11:30-12:15 Hands-on with storage API 12:15-13:00 COMPSs overview and how to parallelize a sequential application 13:00-14:30 Lunch break Session 2/ 14:30 – 18:00 14:30-16:00 Hecuba specifics and hands-on 16:00-16:30 Break 16:30-18:00 dataClay specifics and hands-on       https://events.prace-ri.eu/event/1234/ 2022-01-27 09:00:00 UTC 2022-01-27 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] PATC: Introduction into the Big Data Analytics @ BSC

    7 - 11 February 2022

    [ONLINE] PATC: Introduction into the Big Data Analytics @ BSC https://tess.elixir-europe.org/events/online-patc-introduction-into-the-big-data-analytics-bsc All the PATC courses at BSC are free of charge. Course Convener:  Maria-Ribera Sancho Course Lecturers: To be determined Objectives: The course brings together key information technologies used in manipulating, storing, and analysing data including: the basic tools for statistical analysis techniques for parallel processing tools for access to unstructured data storage solutions Learning outcomes: Students will be introduced to systems that can accept, store, and analyse large volumes of unstructured data. The learned skills can be used in data intensive application areas. Level: For trainees with some theoretical and practical knowledge   Agenda: To be determined https://events.prace-ri.eu/event/1245/ 2022-02-07 08:30:00 UTC 2022-02-11 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • Data analysis for Metabolomics

    7 - 8 February 2022

    Wageningen Campus, Wageningen Campus

    Elixir node event
    Data analysis for Metabolomics https://tess.elixir-europe.org/events/data-analysis-for-metabolomics Metabolomics experiments based on mass spectrometry (MS) or nuclear magnetic resonance (NMR) produce large and complex data sets. This course will introduce approaches to process and analyse data and design high-quality experiments. Through hands-on workshops and lectures highlighting the different… The post Data analysis for Metabolomics appeared first on Dutch Techcentre for Life Sciences. 2022-02-07 09:00:00 UTC 2022-02-08 00:00:00 UTC Wageningen Campus, Wageningen Campus, Wageningen Campus Wageningen Campus Wageningen Campus Wageningen Campus [] [] [] workshops_and_courses [] []
  • Single-cell RNA-seq analysis using Galaxy

    7 - 12 March 2022

    Single-cell RNA-seq analysis using Galaxy https://tess.elixir-europe.org/events/single-cell-rna-seq-analysis-using-galaxy 2022-03-07 09:00:00 UTC 2022-03-12 00:00:00 UTC [] Dayane Araújo, Wendi Bacon [] [] [] [] []

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