Training Courses

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    Disorder in Disorders: Pathogenic mechanisms of Intrinsically Disordered Proteins [open]

    During lectures and practicals, experts of the field will provide students with an overview of Intrinsically Disordered Protein (IDP) biological mechanisms that develop pathogenic phenotypes. They will explore the concepts of folding, unfolding and misfolding, highlighting their differences and similarities. Practical exercises aim at transferring to students basic skills for the study of IDPs using bioinformatic tools to solve complex problems.
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    Software Carpentry Workshop [closed]

    Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. In particular, in this workshop we will cover the Unix Shell, programming in Python and version control with Git.
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    Genome Assembly and Annotation [closed]

    The course will take the participants through all steps of a genome assembly and annotation project, starting with quality control, moving into genome assembly and assembly validation, and ending with structural and functional annotation. Both short and long read technologies will be discussed, as well as supporting technologies. Lectures are mixed with practicals, with a majority of the time spent doing hands-on analyses in the command terminal. Focus is on eukaryotes, although most methods will be applicable to any organism. One day is set aside to discuss the participants own projects, and work with that data, if available.
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    Docker and Reproducibility [closed]

    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.
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    ELIXIR-EXCELERATE Train the Trainer [closed]

    ELIXIR-EXCELERATE, in collaboration with ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
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    Single-Cell RNA Sequencing and Data Analysis [closed]

    Single-Cell Transcriptomics is improving the quality of biological investigations by enhancing the dissection of heterogeneity in complex tissues and cell cultures. This 3-day course aims to provide an overview of a complete Single-Cell RNA sequencing workflow.
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    EMBO Practical Course on "Population Genomics: background and tools" [closed]

    The objective of this EMBO Practical Course is to give an overview of state of the art methods in population genomics combining lecturing from outstanding experienced population geneticists and software developers. After attending the course participants will be aware of up-to-date concepts in population genetics, capable of running analyses using software based on whole genome data sequences and able to deal with basic aspects of any population genomics project. This EMBO Practical Course aims at evolutionary biologists who already have bioinformatics skills. PhD students and Post-Doc researchers will benefit the most out of this course, but applications from all candidates will be evaluated in their context.
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    Data Carpentry Workshop [closed]

    Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
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    Software Carpentry Workshop [closed]

    Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. In particular, in this workshop we will cover the Unix Shell, programming in R and version control with Git.
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    NETTAB18/ELIXIR-IIB Building a FAIR Bioinformatics environment [closed]

    The Eighteenth NETTAB Workshop is organised in collaboration with ELIXIR Nodes of the UK and Italy, as well as the Italian Society of Bioinformatics BITS. The main focus will be on FAIR principles in bioinformatics, a challenging topic that we hope will attract many researchers from all over the world, including but not limited to, Bioinformaticians, Biologists, Computer Scientists, and others working or interested in the above research scope.
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    ELIXIR-EXCELERATE Train the Trainer [closed]

    ELIXIR-EXCELERATE, in collaboration with ELIXIR Sweden and ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
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    ELIXIR-EXCELERATE Train the Trainer [closed]

    ELIXIR-EXCELERATE, in collaboration with ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
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    Docker Advanced Course [closed]

    Docker is an open source software that 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.
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    BITS2018/ELIXIR-IIB Workshop on Docker and Reproducibility [closed]

    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.
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    Population Genomics: background and tools [closed]

    Study methods in population genomics have been profoundly reshaped in the last few years thanks to the growing availability of complete genomic sequences at population level. The rapid and recent growth of data and methods calls for new approaches to become routine in evolutionary genomics laboratories. The objective of this Practical Course is to give an overview of state of the art methods in population genomics combining lecturing from outstanding experienced population geneticists and software developers. All conceptual innovation will be presented in lectures and applied in practice both individually and in group work.
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    ELIXIR-EXCELERATE Train the Trainer [closed]

    ELIXIR-FR in collaboration with ELIXIR-IT and Swiss Institute of Bionformatics (SIB) are pleased to announce a Train the Trainer (TtT) event. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
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    Software Carpentry Workshop [closed]

    Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. In particular, in this workshop we will cover the Unix Shell, programming in Python and version control with Git.
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    ELIXIR-EXCELERATE Train the Trainer [closed]

    ELIXIR-CH in collaboration with ELIXIR-EXCELERATE and ELIXIR Italy are pleased to announce a Train the Trainer (TtT) event. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
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    Linux shell scripting for high-throughput biological data processing on supercomputers [closed]

    Biological big data increasingly require supercomputers for their processing and analysis. Running high-throughput (HTP) bioinformatics data pipelines on supercomputing machines requires advanced Linux shell command line and scripting skills. In this two-day course, we will introduce the Linux shell and we will show how to navigate and work with files and directories, how to combine commands to do new things, how to perform the same actions on many different files, how to filter and selectively extract data from tables, and how to find objects in files. Moreover, we will show how to connect to a remote supercomputer and how to utilise a supercomputing environment to analyse big amount of biological data.
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    Curation workshop on molecular and causal interactions [closed]

    The curation workshop on molecular and causal interactions is organized by the University of Rome Tor Vergata under the ELIXIR Italy training program and the ELIXIR-EXCELERATE project. The workshop will bring together the main European protagonists in the landscape of manually curated molecular and causal interactions databases.
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    Elixir-IIB/NETTAB Tutorial on Biological Networks: data analysis, visualization and medical application [closed]

    Participants in the course will be introduced to protein-protein interactions, biochemical reactions and causal interactions field. During the course the participants will be exposed to the literature curation principles and methods. In addition, there will be a session dedicated to common standards and ontologies adopted to describe data retrieved from the literature in a formalized manner. A large number of molecular interaction resources and methodologies to analyze them will be introduced during hand-on sessions.
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    ELIXIR-EXCELERATE Train the Trainer [closed]

    ELIXIR-IIB, in cooperation with the ELIXIR-EXCELERATE Train-The-Trainer programme, will hold a Train the Trainer (TtT) event in connection with a course on "Best Practices for RNA-Seq analysis". The course is meant to offer guidance, ideas and tips for training / teaching design, development and delivery based on research-driven educational principles. Examples and discussions will also focus on the challenges presented by academic teaching.
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    Training Course on Best practices for RNA-Seq data analysis [closed]

    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. Some strategies are illustrated for detecting genes, which are differentially expressed across different biological conditions, alternative splicing products, 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.
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    Training course on Python for Life Scientists [closed]

    Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organising data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. The course will be highly interactive and the students will continuously put theory into practice while learning.
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    Training course on Machine Learning for Biologists [closed]

    The aim of the course is to provide a practical introduction to the analysis of "omics" data. Topics will range from data visualization/exploration to univariate/multivariate analysis and machine learning. Practical examples and applications will be illustrated by using R and Python.
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    Training Course on RNA-Seq data analysis [closed]

    The course will provide students with theoretical and practical knowledge on how to perform bioinformatic analyses of RNA-Seq data, mainly aimed at the identification of genes differentially expressed across different conditions.
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    Training Course on Galaxy for Bioinformatics tool developers [closed]

    Galaxy is an open source, web-based platform for data intensive biomedical analysis. The aim of this course is to make participants familiarize with the Galaxy platform and prepare them to work independently, using best practices guidelines for building, maintaining and installing Galaxy tools. The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the practices for the most successful Galaxy tool development. During this 2 days course participants will learn a modern approach to create, configure and install their own tools into a Galaxy server.
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    Workshop + Summer School in Advanced Computational Metagenomics [closed]

    Two connected events on Advanced Computational Metagenomics - a 2-day workshop followed by a three-day intensive practical school - will take place on 19-23 June 2017 in Bari, Italy. Both the workshop and the school will focus on the computational aspects of metagenomics analysis including reference databases, software and data retrieval and submission. The investigation of microbial communities will be discussed with an overview on real projects cases, both in ecological, clinical and nutrition fields. During the practical sessions students will experience how to analyze meta-barcoding and shotgun data from Next Generation Sequencing and to perform statistical inference on them.
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    EMBO Practical Course on "Population Genomics: background and tools" [closed]

    The objective of this EMBO Practical Course is to give an overview of state of the art methods in population genomics combining lecturing from outstanding experienced population geneticists and software developers. After attending the course participants will be aware of up-to-date concepts in population genetics, capable of running analyses using software based on whole genome data sequences and able to deal with basic aspects of any population genomics project. This EMBO Practical Course aims at evolutionary biologists who already have bioinformatics skills. PhD students and Post-Doc researchers will benefit the most out of this course, but applications from all candidates will be evaluated in their context.
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    Workshop on "Computational approaches to the study of protein interactions and rational drug design" [closed]

    This workshop is aimed at students in master degree courses, PhD students and post-doctoral researchers who are working or planning to work in the field of protein interactions from a molecular and structural point of view. In this workshop, participants will familiarise with docking approaches to the study of protein-protein interactions (PPIs) and protein-small molecule interactions. Irreversible binders design using molecular docking and computational methods to rational drug design will be also described, as well as the functional role of the intrinsically disordered proteins.