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Introduction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Introduction https://tess.elixir-europe.org/materials/introduction-e309609e-264f-4023-9485-f406549bb597 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Outreach

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Outreach https://tess.elixir-europe.org/materials/outreach Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Challenges and opportunities

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Challenges and opportunities https://tess.elixir-europe.org/materials/challenges-and-opportunities Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Continuous integration with Github Actions

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Continuous integration with Github Actions https://tess.elixir-europe.org/materials/continuous-integration-with-github-actions Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Plant Phenotyping Data managment (MIAPPE)

This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners...

Scientific topics: Data management, Plant biology, Phenomics

Operations: Formatting, Annotation

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

Plant Phenotyping Data managment (MIAPPE) https://tess.elixir-europe.org/materials/plant-phenotyping-data-managment-miappe This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners will know how to use standards and ontologies, how to describe their measurment protocole and practices how to fill a template with their data and how to apply the standards concept in some data managment tools. Data management Plant biology Phenomics Plant Phenotyping, Data-format, data sharing Biologists geneticists plant researchers software engineers database managers
A Tidy Transcriptomics introduction to RNA-Seq analyses

This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.

Scientific topics: RNA-Seq

Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics

Resource type: Tutorial

A Tidy Transcriptomics introduction to RNA-Seq analyses https://tess.elixir-europe.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages. RNA-Seq Differential Expression, Gene Expression, RNA-seq, Transcriptomics Biologists
Plant Bioinformatics Capstone

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply...

Keywords: physical-science-and-engineering, life-sciences, research-methods, basic-science

Plant Bioinformatics Capstone https://tess.elixir-europe.org/materials/plant-bioinformatics-capstone The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse or tap of a finger. In Plant Bioinformatics on Coursera.org, we covered 33 plant-specific online tools from genome browsers to transcriptomic data mining to promoter/network analyses and others, and in this Plant Bioinformatics Capstone we'll use these tools to hypothesize a biological role for a gene of unknown function, summarized in a written lab report. This course is part of a Plant Bioinformatics Specialization on Coursera, which introduces core bioinformatic competencies and resources, such as NCBI's Genbank, Blast, multiple sequence alignments, phylogenetics in Bioinformatic Methods I, followed by protein-protein interactions, structural bioinformatics and RNA-seq analysis in Bioinformatic Methods II, in addition to the plant-specific concepts and tools introduced in Plant Bioinformatics and the Plant Bioinformatics Capstone. This course/capstone was developed with funding from the University of Toronto's Faculty of Arts and Science Open Course Initiative Fund (OCIF) and was implemented by Eddi Esteban, Will Heikoop and Nicholas Provart. Asher Pasha programmed a gene ID randomizer. physical-science-and-engineering, life-sciences, research-methods, basic-science
Eurordis Open Academy

EURORDIS Open Academy encompasses the EURORDIS Summer School, EURORDIS Winter School, EURORDIS Digital School and EURORDIS Leadership School.

Keywords: Rare Diseases & Research

Resource type: course materials

Eurordis Open Academy https://tess.elixir-europe.org/materials/eurordis-online-trainning-modules EURORDIS Open Academy encompasses the EURORDIS Summer School, EURORDIS Winter School, EURORDIS Digital School and EURORDIS Leadership School. Rare Diseases & Research Patient Advocates Life Science Researchers Biomedical researchers
galaxy.sciensano.be

This training is meant specifically for the “Galaxy @Sciensano” that is available at https://galaxy.sciensano.be/ and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the...

Scientific topics: Microbiology, Sequencing, Genomics, Public health and epidemiology, Bioinformatics

Resource type: Video, Tutorial

galaxy.sciensano.be https://tess.elixir-europe.org/materials/galaxy-sciensano-training This training is meant specifically for the “Galaxy @Sciensano” that is available at https://galaxy.sciensano.be/ and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the basics of next-generation sequencing data analysis, but also more specialized topics of interest in public health (e.g. AMR detection, cgMLST analysis etc., SNP-based outbreak analysis etc.). The training consists specifically out of a series of training videos that are publicly available on YouTube. Microbiology Sequencing Genomics Public health and epidemiology Bioinformatics Microbiologists Public Health Professionals Life Science Researchers
Educational webinars on rare endocrine conditions (ENDO-ERN)

Various webinar on rare endocrine conditions

Keywords: Rare Diseases & Research

Resource type: Webinar

Educational webinars on rare endocrine conditions (ENDO-ERN) https://tess.elixir-europe.org/materials/endo-ern-educational-webinars Various webinar on rare endocrine conditions Rare Diseases & Research Clinical Scientists Biomedical researchers healthcare professionals
Educational webinars on rare and complex epilepsies (EpiCARE ERN)

Free online seminars on Thursdays related to rare epilepsies

Keywords: Rare Diseases & Research

Resource type: Webinar

Educational webinars on rare and complex epilepsies (EpiCARE ERN) https://tess.elixir-europe.org/materials/epicare-ern-educational-webinars Free online seminars on Thursdays related to rare epilepsies Rare Diseases & Research Health Care Professionals health professionals Biomedical researchers
Postgraduate Curriculum in Rare Kidney Diseases developed by ERKNet

ERKNet Postgraduate Curriculum in Rare Kidney Diseases / ESPN – IPNA Curriculum in Pediatric Nephrology

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar

Postgraduate Curriculum in Rare Kidney Diseases developed by ERKNet https://tess.elixir-europe.org/materials/erknet-education-and-training ERKNet Postgraduate Curriculum in Rare Kidney Diseases / ESPN – IPNA Curriculum in Pediatric Nephrology Rare diseases Rare Diseases & Research
Webinars from the European Reference Network in Rare Hematological Diseases (EuroBloodNet)

The aim of these educational activities is to promote the interest on very innovative topics in order to stress among health professionals the cutting-edge advances in the field of Rare Hematological Diseases. One or 2 webinars per month, each of them lasting 45 minutes.

Keywords: Rare Diseases & Research

Resource type: Webinar

Webinars from the European Reference Network in Rare Hematological Diseases (EuroBloodNet) https://tess.elixir-europe.org/materials/ern-eurobloodnet-thursdays-webinars The aim of these educational activities is to promote the interest on very innovative topics in order to stress among health professionals the cutting-edge advances in the field of Rare Hematological Diseases. One or 2 webinars per month, each of them lasting 45 minutes. Rare Diseases & Research Health Care Professionals health professionals Patient Advocates rare disease patients representatives
Rare and complex urogenital diseases and condition webinars (eUROGEN ERN)

Monthly webinar programme on rare congenital uro-recto-genital anomalies.

Keywords: Rare Diseases & Research

Resource type: Webinar

Rare and complex urogenital diseases and condition webinars (eUROGEN ERN) https://tess.elixir-europe.org/materials/eurogen-education-and-training-webinars Monthly webinar programme on rare congenital uro-recto-genital anomalies. Rare Diseases & Research healthcare professionals health professionals
Education and Training webinars on genetic tumor risk syndromes (ERN GENTURIS)

Target audience for the webinars are clinicians, genetic counsellors, clinical scientists and other genetics health professionals. The presentation itself lasts approximately 20-30 minutes, and viewers have the opportunity to send questions on the subject area which will be addressed in a...

Keywords: Rare Diseases & Research

Resource type: Webinar

Education and Training webinars on genetic tumor risk syndromes (ERN GENTURIS) https://tess.elixir-europe.org/materials/genturis-education-and-training-webinars Target audience for the webinars are clinicians, genetic counsellors, clinical scientists and other genetics health professionals. The presentation itself lasts approximately 20-30 minutes, and viewers have the opportunity to send questions on the subject area which will be addressed in a question & answer session afterwards. Rare Diseases & Research Clinicians Clinical Scientists health professionals geneticists
Educational videos on rare and low prevalence complex diseases of the heart (ERN GUARD-Heart)

Educational videos for experts

Keywords: Rare Diseases & Research

Resource type: Video

Educational videos on rare and low prevalence complex diseases of the heart (ERN GUARD-Heart) https://tess.elixir-europe.org/materials/ern-guard-heart-educational-videos Educational videos for experts Rare Diseases & Research health professionals Health Care Professionals
Webinars on Hereditary metabolic diseases (MetabERN)

To share information and documentation with stakeholders involved in the field of hereditary metabolic disorders.

Keywords: Rare Diseases & Research

Resource type: Webinar

Webinars on Hereditary metabolic diseases (MetabERN) https://tess.elixir-europe.org/materials/metabern-library-teaching-and-training-programmes To share information and documentation with stakeholders involved in the field of hereditary metabolic disorders. Rare Diseases & Research Health Care Professionals health professionals
Educational webinars on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET)

ERN ReCONNET proposes free online training and education.

Keywords: Rare Diseases & Research

Resource type: Webinar, Video

Educational webinars on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET) https://tess.elixir-europe.org/materials/ern-reconnet-educational-webinars ERN ReCONNET proposes free online training and education. Rare Diseases & Research Health Care Professionals health professionals
Webinars and Pills of knowledge Videos on rare vascular diseases (VASCERN)

Short single video lessons (of approximately 3-5 minutes long) and webinars.

Keywords: Rare Diseases & Research

Webinars and Pills of knowledge Videos on rare vascular diseases (VASCERN) https://tess.elixir-europe.org/materials/vascern-webinars-and-pills-of-knowledge-videos Short single video lessons (of approximately 3-5 minutes long) and webinars. Rare Diseases & Research medical students Health Care Professionals health professionals
MGnify quick tour

This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets.

Scientific topics: Metagenomics

Keywords: Metagenomics, Sequence analysis, MGnify, Microbiology

Resource type: Tutorial

MGnify quick tour https://tess.elixir-europe.org/materials/mgnify-quick-tour This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets. Ola Tarkowska Lorna Richardson Metagenomics Metagenomics, Sequence analysis, MGnify, Microbiology Life Scientists
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 https://tess.elixir-europe.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
Jaqpot Hackathon - Training materials

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, attendees learned how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file. Jaqpot is a computational platform for in silico...

Keywords: nanoinformatics, toxicity prediction, e-tools, Modeling, data FAIRness

Jaqpot Hackathon - Training materials https://tess.elixir-europe.org/materials/jaqpot-hackathon-training-materials Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, attendees learned how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file. Jaqpot is a computational platform for in silico modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot. Attached you find the following presentations: 1. Intro to NanoCommons by Martin Himly, PLUS 2. Electronic Lab Notebooks by Iseult Lynch, UoB 3. NanoCommons Knowledgebase by Dieter Maier, Biomax 4. Jaqpot Suite by Philip Doganis, NTUA Lee Walker, UKCEH Christine Balmer, UKCEH Irini Liampa, NTUA Pantelis Karatzas, NTUA Beatriz Alfaro Serrano, BNN Harry Sarimveis, NTUA nanoinformatics, toxicity prediction, e-tools, Modeling, data FAIRness
The Genomics Era: the Future of Genetics in Medicine

This free online course is available on FutureLearn and developed by the St George's University of London and St George's University Hospitals NHS Foundation Trust. It provides healthcare professionals with a basic grounding in genomic medicine. It will introduce you to new genomic technologies,...

Keywords: Rare Diseases & Research

Resource type: e-learning

The Genomics Era: the Future of Genetics in Medicine https://tess.elixir-europe.org/materials/the-genomics-era-the-future-of-genetics-in-medicine This free online course is available on FutureLearn and developed by the St George's University of London and St George's University Hospitals NHS Foundation Trust. It provides healthcare professionals with a basic grounding in genomic medicine. It will introduce you to new genomic technologies, which are revolutionizing medicine and will, in time, provide the mainstay of patient diagnosis, treatment and disease prevention. Rare Diseases & Research healthcare professionals
Whole Genome Sequencing: Decoding the Language of Life and Health

This course is available on FutureLearn and developed by Health Education England (NHS). The course has been designed for healthcare professionals and science/medical students who have limited or no understanding of the who genome sequencing process and its many varied uses. Non-specialists who...

Keywords: Rare Diseases & Research

Resource type: e-learning

Whole Genome Sequencing: Decoding the Language of Life and Health https://tess.elixir-europe.org/materials/whole-genome-sequencing-decoding-the-language-of-life-and-health This course is available on FutureLearn and developed by Health Education England (NHS). The course has been designed for healthcare professionals and science/medical students who have limited or no understanding of the who genome sequencing process and its many varied uses. Non-specialists who want to learn more about sequencing and genomic medicine are also very welcome. Rare Diseases & Research Health Care Professionals health professionals medical students science students
Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing

This course is available on FutureLearn and developed by St George's University of London. This postgraduate-level course will help you understand these new and established genetic technologies, and their application to clinical practice.

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing https://tess.elixir-europe.org/materials/genomic-technologies-in-clinical-diagnostics-next-generation-sequencing This course is available on FutureLearn and developed by St George's University of London. This postgraduate-level course will help you understand these new and established genetic technologies, and their application to clinical practice. Rare Diseases & Research postgrad Scientists Healthcare
Genomic Technologies in Clinical Diagnostics: Molecular Techniques

This course is available on FutureLearn and developed by St George’s, University of London. This postgraduate-level course, in combination with Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing Technologies, will help you understand these new and established genetic...

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomic Technologies in Clinical Diagnostics: Molecular Techniques https://tess.elixir-europe.org/materials/genomic-technologies-in-clinical-diagnostics-molecular-techniques This course is available on FutureLearn and developed by St George’s, University of London. This postgraduate-level course, in combination with Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing Technologies, will help you understand these new and established genetic technologies, and their application to clinical practice. This course focuses on molecular techniques. Rare Diseases & Research Scientists healthcare professionals
Metagenomics Bioinformatics

Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis.

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Tutorial

Metagenomics Bioinformatics https://tess.elixir-europe.org/materials/metagenomics-bioinformatics Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis. Alex Mitchell Varsha Kale Rob Finn Guillermo Rangel Pineros Rebecca Campos Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
EBI Metagenomics: analysing and exploring metagenomics data

EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets...

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Webinar

EBI Metagenomics: analysing and exploring metagenomics data https://tess.elixir-europe.org/materials/ebi-metagenomics-analysing-and-exploring-metagenomics-data EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive. Alex Mitchell Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
Analysing and visualising microbiome-derived datasets using the MGnify Web API

MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available...

Analysing and visualising microbiome-derived datasets using the MGnify Web API https://tess.elixir-europe.org/materials/analysing-and-visualising-microbiome-derived-datasets-using-the-mgnify-web-api MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets drawn from the European Nucleotide Archive (ENA).
Genetics education for primary care resources from the Gen-Equip project

Gen-Equip project is a project combining education, primary care and genetics. Its aim is to enable health professionals who are working in primary care to update their knowledge and skills in genetics. The aims is the long-term outcome of improvement in care of patients with genetic conditions...

Keywords: Rare Diseases & Research

Resource type: Documentation, Video, Training materials, online modules

Genetics education for primary care resources from the Gen-Equip project https://tess.elixir-europe.org/materials/genetics-education-for-primary-care-resources Gen-Equip project is a project combining education, primary care and genetics. Its aim is to enable health professionals who are working in primary care to update their knowledge and skills in genetics. The aims is the long-term outcome of improvement in care of patients with genetic conditions or concerns. They offer genetics education free of charge to those who want continuing medical or professional education in genetics. Rare Diseases & Research Primary care doctors health professionals