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37 materials found

Target audience: policy officer  or bioinformaticians 


Containers & Workflow pipelines workshop

The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...

Keywords: Containers, Nextflow

Resource type: Training materials

Containers & Workflow pipelines workshop http://tess.elixir-uk.org/materials/containers-workflow-pipelines-workshop The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, at the end of the first day, Singularity will be highlighted as well. On the second day (27 May 2021), you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Containers, Nextflow bioinformaticians
Data Management Plans and Policies

PDF with slides of the course: - Data management definitions - RDM and DM policy - DMPs: content and competencies - DMPs for European and National funded projects

Scientific topics: Data management, FAIR data

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, on-line, e-learning

Resource type: PDF, e-learning, slideck/ presentation

Data Management Plans and Policies http://tess.elixir-uk.org/materials/data-management-plans-and-policies PDF with slides of the course: - Data management definitions - RDM and DM policy - DMPs: content and competencies - DMPs for European and National funded projects Data management FAIR data ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, on-line, e-learning project manager Researchers policy officer
FAIR data - Module 4 (share and publish data)

Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données

Scientific topics: Data management, Biology, Bioinformatics

Keywords: data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse

Resource type: Slides

FAIR data - Module 4 (share and publish data) http://tess.elixir-uk.org/materials/fair-data-module-4-share-and-publish-data Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données Hélène Chiapello Thomas Denecker Jean-François Dufayard Gautier Sarah Julien Seiler Data management Biology Bioinformatics data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse Biologists bioinformaticians Biomedical researchers
FAIR data - Module 3 (Metadata)

Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données

Scientific topics: Data management, Biology, Bioinformatics

Operations: Data handling

Keywords: metadata, data annotation, life science standards, data sharing

Resource type: Slides

FAIR data - Module 3 (Metadata) http://tess.elixir-uk.org/materials/fair-data-module-3-metadata Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données Jean-François Dufayard Gautier Sarah Paulette Lieby Data management Biology Bioinformatics metadata, data annotation, life science standards, data sharing Biologists bioinformaticians Biomedical researchers
Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica

PDF with slides of the course in Spanish - Data management definitions - DMP Objectives - DMP Content and structure - Competencies needed - Practical session: DMP content analysis and evaluation

Scientific topics: FAIR data, Data management

Keywords: ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish

Resource type: PDF, e-learning, slideck/ presentation

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica http://tess.elixir-uk.org/materials/elaboracion-de-un-plan-de-gestion-de-datos-dmp-teoria-y-practica PDF with slides of the course in Spanish - Data management definitions - DMP Objectives - DMP Content and structure - Competencies needed - Practical session: DMP content analysis and evaluation FAIR data Data management ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish operational manager IT support data manager project manager policy officer
FAIR data - Module 2 (data life cycle)

La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données

Scientific topics: Bioinformatics, Biology, Data management

Operations: Data handling

Keywords: Data preserving, Data storage

Resource type: Slides

FAIR data - Module 2 (data life cycle) http://tess.elixir-uk.org/materials/fair-data-module-2 La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données Bioinformatics Biology Data management Data preserving, Data storage Biologists bioinformaticians Biomedical researchers
FAIR data - Module 1 (research data)

Research data and their centrality in the research process. This material is mostly in French.

Keywords: metadata, Data Life Cycle, Reproducibility, Data management plan

Resource type: Slides

FAIR data - Module 1 (research data) http://tess.elixir-uk.org/materials/fair-data-module-1 Research data and their centrality in the research process. This material is mostly in French. Gautier Sarah Hélène Chiapello Jean-François Dufayard Julien Seiler Lionel Maurel Paulette Lieby Thomas Denecker metadata, Data Life Cycle, Reproducibility, Data management plan Biologists bioinformaticians Biomedical researchers
Introduction to Nextflow workshop

workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...

Scientific topics: Workflows

Keywords: Nextflow, DSL2

Resource type: Presentation, course materials

Introduction to Nextflow workshop http://tess.elixir-uk.org/materials/introduction-to-nextflow-workshop workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available [here](https://github.com/vibbits/nextflow-jnj/blob/master/presentation/slidedeck.pdf) Workflows Nextflow, DSL2 bioinformaticians
IFB Shiny training

Shiny package training (in french)

Keywords: R-programming, Reproducible Science

IFB Shiny training http://tess.elixir-uk.org/materials/ifb-shiny-training Shiny package training (in french) Hélène Chiapello Jacques van Helden R-programming, Reproducible Science bioinformaticians statisticians
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics http://tess.elixir-uk.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
DE-Sim examples, tutorials, and documentation

*DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html),...

Scientific topics: Computational biology, Mathematics, Computer science, Simulation experiment

Operations: Visualisation, Modelling and simulation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

DE-Sim examples, tutorials, and documentation http://tess.elixir-uk.org/materials/de-sim-examples-tutorials-and-documentation *DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html), [pandas](https://pandas.pydata.org/), and [SQLAlchemy](https://www.sqlalchemy.org/) to build and simulate complex computational models. Similar to [Simula](http://www.simula67.info/), *DE-Sim* models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time. This website provides examples, tutorials, and documentation for *DE-Sim*. Computational biology Mathematics Computer science Simulation experiment data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science computational scientists Computational biologists bioinformaticians software engineers programmers
Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial

Datanator tutorial http://tess.elixir-uk.org/materials/datanator-tutorial Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. This tutorial provides a brief introduction to the Datanator database and web application. The tutorial illustrates how to search the Datanator database and obtain and refine clouds of data about specific metabolites, RNA, proteins, and reactions of interest. Omics Bioinformatics Systems biology Cell biology Molecular biology genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis mololecular cell biologists systems biologists bioinformaticians Computational biologists modelers
How to use V-pipe (SARS-CoV-2 data)

How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)

Scientific topics: Workflows, Genetic variation, Virology

Operations: Read pre-processing, Alignment, Variant calling

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to use V-pipe (SARS-CoV-2 data) http://tess.elixir-uk.org/materials/how-to-use-v-pipe-sars-cov-2-data How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data) Workflows Genetic variation Virology coronavirus, NGS bioinformatics, Variant-calling bioinformaticians Biologists, Genomicists, Computer Scientists
How to use Common Workflow Language

**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**

Scientific topics: Workflows

Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP

Resource type: Installation instructions, Manual

How to use Common Workflow Language http://tess.elixir-uk.org/materials/how-to-use-common-workflow-language **This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).** Rob Finn Michael Crusoe Workflows commonwl, common workflow language, CWL, Workflows, eLearning, EeLP bioinformaticians life scientists programmers
Helis Academy - FAIRify your data

FAIRify your data: FAIRification & Data modelling using linked data

Keywords: linked data, Wikidata, data management

Resource type: Slides

Helis Academy - FAIRify your data http://tess.elixir-uk.org/materials/helis-academy-fairify-your-data FAIRify your data: FAIRification & Data modelling using linked data linked data, Wikidata, data management bioinformaticians software developers, bioinformaticians Life Science Researchers
OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

OpenRiskNet: Ontology Walkthrough and Workshop http://tess.elixir-uk.org/materials/openrisknet-ontology-walkthrough-and-workshop Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology. Ontology and terminology Toxicology Biologists bioinformaticians Chemists
Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Single cell RNA-seq data analysis using Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
Mascot training course

The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.

Scientific topics: Proteomics

Keywords: Protein identification, Protein Mass Spectrometry

Resource type: Slides, Video, Training materials

Mascot training course http://tess.elixir-uk.org/materials/mascot-training-course The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises. Proteomics Protein identification, Protein Mass Spectrometry Biologists bioinformaticians Biochemists mass spectrometry
Introduction to Persistent Identifiers

Module also available as self-study material in data carpentry style

Scientific topics: Data management

Keywords: system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers

Resource type: course materials

Introduction to Persistent Identifiers http://tess.elixir-uk.org/materials/introduction-to-persistent-identifiers Module also available as self-study material in data carpentry style Data management system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers data stewards data managers bioinformaticians
FAIRification & Data modelling

Wikidata fairification

Keywords: FAIR, linked data, ontologies, metadata

Resource type: Slides

FAIRification & Data modelling http://tess.elixir-uk.org/materials/fairification-data-modelling Wikidata fairification FAIR, linked data, ontologies, metadata Life Science Researchers bioinformaticians
Helis Academy - Persistent identifiers and their use cases

Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source

Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management

Resource type: Slides

Helis Academy - Persistent identifiers and their use cases http://tess.elixir-uk.org/materials/persistent-identifiers-and-their-use-cases Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source Referencing data and code, Findability of data and code, Identifying data and code, data management data stewards Life Science Researchers bioinformaticians
Single cell RNA-seq data analysis with R

This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r-26ec3ec0-8f43-47db-9788-7f8f63eb447b This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE project. Note: You can find all the course material including the R code and data files in the course [GitHub](https://github.com/NBISweden/excelerate-scRNAseq) repository, and the lecture videos are available as a [YouTube playlist](https://www.youtube.com/playlist?list=PLjiXAZO27elC_xnk7gVNM85I2IQl5BEJN). Eija Korpelainen @eija, ekorpelainen@gmail.com RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
CWL User Guide

This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0.

Keywords: CWL, commonwl, Workflows

Resource type: Tutorial

CWL User Guide http://tess.elixir-uk.org/materials/cwl-user-guide This guide will introduce you to writing tool wrappers and workflows using the Common Workflow Language (CWL). This guide describes the current stable specification, version 1.0. CWL, commonwl, Workflows bioinformaticians tool authors
Implementation of Data Management Plans & Data Stewardship in practice

Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece.

Scientific topics: Data submission, annotation, and curation, Data management

Keywords: data management, data stewardship, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Implementation of Data Management Plans & Data Stewardship in practice http://tess.elixir-uk.org/materials/implementation-of-data-management-plans-data-stewardship-in-practice Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece. Celia van Gelder Roland Krause Mateusz Kuzak Brane Leskosek Marko Vidak Robert Pergl Marek Suchanek Jan Slifka Vojtech Knaisl Data submission, annotation, and curation Data management data management, data stewardship, eLearning, EeLP bioinformaticians data stewards
Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials

Single cell RNA-seq data analysis with R http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
Programming in the Life Sciences

This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.

Scientific topics: Pharmacology, Drug discovery

Programming in the Life Sciences http://tess.elixir-uk.org/materials/programming-in-the-life-sciences This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API. Pharmacology Drug discovery bioinformaticians
Introductory image processing on biological images using python.

A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.

Resource type: Jupyter notebook, PDF

Introductory image processing on biological images using python. http://tess.elixir-uk.org/materials/introductory-image-processing-on-biological-images-using-python A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples. Anatole Chessel Volker Baecker Bioimage Analysts Image Analysts Computer Vision scientists bioinformaticians computational scientists Biophysicists Biologists Microscopists Python for Biologists PhD students
Introduction to Biopython

This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.

Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists

Introduction to Biopython http://tess.elixir-uk.org/materials/introduction-to-biopython This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs. Bioinformatics, Biopython, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists bioinformaticians 2013-11-04 2017-10-09
Bioinformatics approaches to Identify causative sequence variants in farm animals

ALLBIO and DEANN Training course: 12-16 May 2014, SLU, Uppsala, Sweden The training is mainly intended for researchers that want or already use techniques like genome-wide SNP genotyping, candidate gene sequencing, transcriptome sequencing and other bioinformatics tools in their work to...

Keywords: Allbio, Farm animals, Qtl, Rnaseq, Transcription factors

Bioinformatics approaches to Identify causative sequence variants in farm animals http://tess.elixir-uk.org/materials/bioinformatics-approaches-to-identify-causative-sequence-variants-in-farm-animals ALLBIO and DEANN Training course: 12-16 May 2014, SLU, Uppsala, Sweden The training is mainly intended for researchers that want or already use techniques like genome-wide SNP genotyping, candidate gene sequencing, transcriptome sequencing and other bioinformatics tools in their work to elucidate the specific contributions of genetic and other factors in shaping the phenotypic variability in farm animals. Allbio, Farm animals, Qtl, Rnaseq, Transcription factors Biologists bioinformaticians geneticists 2014-11-17 2017-10-09