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1561 materials found

European Patients’ Academy Expert Training Course

Online course in medicines research and development. Not solely focused on rare diseases.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: online modules, e-learning, Training materials

European Patients’ Academy Expert Training Course https://tess.elixir-europe.org/materials/european-patients-academy-expert-training-course Online course in medicines research and development. Not solely focused on rare diseases. Rare diseases Rare Diseases & Research Patient Advocates rare disease patients representatives
Rheumatic and musculoskeletal diseases online resources from EULAR (European League Against Rheumatism)

Several online courses on rheumatic and musculoskeletal diseases encompassing several rare diseases.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: online modules, e-learning

Rheumatic and musculoskeletal diseases online resources from EULAR (European League Against Rheumatism) https://tess.elixir-europe.org/materials/rheumatic-and-musculoskeletal-diseases-resources Several online courses on rheumatic and musculoskeletal diseases encompassing several rare diseases. Rare diseases Rare Diseases & Research Health Care Professionals health professionals physisians Patient Advocates rare disease patients representatives
Alkaptonuria online course

Royal College of General Practitioners webinar on Alkaptonuria – "Black Bone Disease"

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Alkaptonuria online course https://tess.elixir-europe.org/materials/alkaptonuria-resources Royal College of General Practitioners webinar on Alkaptonuria – "Black Bone Disease" Rare diseases Rare Diseases & Research General Physicians healthcare professionals
Granulomatosis with polyangiitis screencast

Royal College of General Practitioners webinars on Granulomatosis with polyangiitis (GPA)

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Video, e-learning

Granulomatosis with polyangiitis screencast https://tess.elixir-europe.org/materials/granulomatosis-with-polyangiitis-resources Royal College of General Practitioners webinars on Granulomatosis with polyangiitis (GPA) Rare diseases Rare Diseases & Research General Physicians
Integrating to ELIXIR AAI -- instructions for developers

This is a collection of videos, presentations and on-line materials for developers and administrators for integrating a service to ELIXIR AAI, the ELIXIR Compute platform service for user authentication and authorisation.

Scientific topics: Computer science

Keywords: AAI, IAM, Authentication, authorisation

Resource type: Webinar, Presentation, Documentation

Integrating to ELIXIR AAI -- instructions for developers https://tess.elixir-europe.org/materials/integrating-to-elixir-aai-instruction-for-developers This is a collection of videos, presentations and on-line materials for developers and administrators for integrating a service to ELIXIR AAI, the ELIXIR Compute platform service for user authentication and authorisation. Computer science AAI, IAM, Authentication, authorisation software developers, bioinformaticians
Medics4RareDiseases (M4RD) video library

e-learning for medical students and doctors about the fundamentals of rare diseases

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Medics4RareDiseases (M4RD) video library https://tess.elixir-europe.org/materials/medics4rarediseases-m4rd-video-library e-learning for medical students and doctors about the fundamentals of rare diseases Rare diseases Rare Diseases & Research healthcare professionals General Physicians medical students
Integrated DEsign and AnaLysis of clinical trials in small population group (IDeAl) resources

Webinar Series on Integrated DEsign and AnaLysis of small population group trials

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning, Webinar

Integrated DEsign and AnaLysis of clinical trials in small population group (IDeAl) resources https://tess.elixir-europe.org/materials/integrated-design-and-analysis-of-clinical-trials-in-small-population-group-ideal-resources Webinar Series on Integrated DEsign and AnaLysis of small population group trials Rare diseases Rare Diseases & Research
Webinars on rare neurological diseases (ERN-RND)

Rare neurological diseases webinars

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Webinars on rare neurological diseases (ERN-RND) https://tess.elixir-europe.org/materials/ern-rnd-webinars-ec014ea5-fa57-4211-9160-1da47d7ce06f Rare neurological diseases webinars Rare diseases Rare Diseases & Research Neurological Paediatricians healthcare professionals Fellows and Residents health professionals
Webinars on rare neuromuscular diseases (EURO-NMD)

Rare neuromuscular diseases webinars

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Webinars on rare neuromuscular diseases (EURO-NMD) https://tess.elixir-europe.org/materials/ern-rnd-webinars Rare neuromuscular diseases webinars Rare diseases Rare Diseases & Research healthcare professionals Neurologists health professionals
RD-Connect Webinars

Three informative webinars for those researchers involved in ERNs

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

RD-Connect Webinars https://tess.elixir-europe.org/materials/euro-nmd-and-rd-connect-webinars Three informative webinars for those researchers involved in ERNs Rare diseases Rare Diseases & Research
Transplantchild Webinars (ERN TransplantChild)

E-learning webinars on various pediatric transplantation items

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Transplantchild Webinars (ERN TransplantChild) https://tess.elixir-europe.org/materials/transplantchild-webinars-ern-transplantchild E-learning webinars on various pediatric transplantation items Rare diseases Rare Diseases & Research
European training programme in pharmacovigilance and pharmacoepidemiology (EU2P)

Innovative web-based education & training offer in Pharmacovigilance and Pharmacoepidemiology

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

European training programme in pharmacovigilance and pharmacoepidemiology (EU2P) https://tess.elixir-europe.org/materials/european-training-programme-in-pharmacovigilance-and-pharmacoepidemiology-eu2p Innovative web-based education & training offer in Pharmacovigilance and Pharmacoepidemiology Rare diseases Rare Diseases & Research
Research Data Management online courses

eLearning course about the importance of good research data management (RDM)

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Research Data Management online courses https://tess.elixir-europe.org/materials/research-data-management-online-courses eLearning course about the importance of good research data management (RDM) Rare diseases Rare Diseases & Research PhD Students Researchers Support Staff
Genomics in Healthcare

Online course available on FutureLearn and developed by St George’s, University of London on genomic technologies.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomics in Healthcare https://tess.elixir-europe.org/materials/genomics-in-healthcare Online course available on FutureLearn and developed by St George’s, University of London on genomic technologies. Rare diseases Rare Diseases & Research healthcare professionals Scientists
Patient-Centered Outcomes Research Institute (PCORI) Training : A Program for Rare Disease Patient Advocates

Tools and templates on the subject of "patient and research"

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: educational materials, e-learning

Patient-Centered Outcomes Research Institute (PCORI) Training : A Program for Rare Disease Patient Advocates https://tess.elixir-europe.org/materials/patient-centered-outcomes-research-institute-pcor-training-a-program-for-rare-disease-patient-advocates Tools and templates on the subject of "patient and research" Rare diseases Rare Diseases & Research Patient Advocates rare disease patients representatives
Findacure's e-learning resources on rare diseases

Findacure’s e-learning portal is a central hub of information and training for rare disease advocates and patient groups. It contains educational materials, including written guides, animated videos, presentations and webinars, to help the establishment and growth of rare disease patient groups.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, Video, Presentation, Training materials, e-learning

Findacure's e-learning resources on rare diseases https://tess.elixir-europe.org/materials/findacure-s-e-learning-video-library Findacure’s e-learning portal is a central hub of information and training for rare disease advocates and patient groups. It contains educational materials, including written guides, animated videos, presentations and webinars, to help the establishment and growth of rare disease patient groups. Rare diseases Rare Diseases & Research Patient Advocates rare disease patients representatives
Bioinformatics - Food Detective: a Practical Guide

This Practical Guide introduces the idea of computers as tools to help understand aspects of biology. In particular, it looks at how DNA sequences can be used to identify specific organisms, why this is important in the food industry, and how this can be used to help de- tect food fraud. Analyses...

Scientific topics: Sequence analysis, DNA barcoding

Keywords: Basic bioinformatics, Bioinformatics schools, Dna barcoding, Food fraud, Sequence analysis, Sequence database searching, Species identification, Training material

Bioinformatics - Food Detective: a Practical Guide https://tess.elixir-europe.org/materials/bioinformatics-food-detective-a-practical-guide This Practical Guide introduces the idea of computers as tools to help understand aspects of biology. In particular, it looks at how DNA sequences can be used to identify specific organisms, why this is important in the food industry, and how this can be used to help de- tect food fraud. Analyses are run online using sequence data from the 4273pi project website: 4273pi.org. This Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how to identify different spe- cies based on their specific DNA sequences – their ‘barcodes’. On reading the Guide and completing the exercises, you will be able to: i) explain what is meant by DNA barcoding; ii) search biological sequence databases using the online program BLAST; iii) judge the reliability of database-search results in terms of their statistical significance; and iv) evaluate the biological implications of search results with reference to food safety. Sequence analysis DNA barcoding Basic bioinformatics, Bioinformatics schools, Dna barcoding, Food fraud, Sequence analysis, Sequence database searching, Species identification, Training material 2020-06-23
BioSimulations tutorial and help

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...

Scientific topics: Simulation experiment, Systems biology, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE

Resource type: Documentation

BioSimulations tutorial and help https://tess.elixir-europe.org/materials/biosimulations-help BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface. Simulation experiment Systems biology Computational biology SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE Life Science Researchers Computational biologists modelers
Initiation to R programming and descriptive statistics

On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France).

Keywords: R-programming, Descriptive statistics, Statistics, Bioinformatics

Initiation to R programming and descriptive statistics https://tess.elixir-europe.org/materials/initiation-to-r-programming-and-descriptive-statistics On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France). Blaise Li Étienne Kornobis Sébastien Mella Vincent Guillemot R-programming, Descriptive statistics, Statistics, Bioinformatics PhD students Post-Doctoral Fellows Biologists
BcForms tutorial

BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models...

Scientific topics: Systems biology, Protein modifications, Proteomics

Operations: Validation

Keywords: BiologicalMacromolecules, protein complex, macromolecular complex, crosslink, modification

Resource type: Jupyter notebook

BcForms tutorial https://tess.elixir-europe.org/materials/bcforms-tutorial BcForms is a toolkit for concretely describing the molecular structure (atoms and bonds) of macromolecular complexes, including non-canonical monomeric forms, circular topologies, and crosslinks. BcForms was developed to help describe the semantic meaning of whole-cell computational models . BcForms includes a grammar for describing forms of macromolecular complexes composed of DNA, RNA, protein, and small molecular subunits and crosslinks between the subunits. The DNA, RNA, and protein subunits can be described using BpForms and the small molecule subunits can be described using SMILES. BcForms also includes four software tools for verifying descriptions of complexes and calculating physical properties of complexes such as their molecular structure, formula, molecular weight, and charge: this website, a JSON REST API, a command line interface, and a Python API. This tutorial provides an introduction to BcForms. Systems biology Protein modifications Proteomics BiologicalMacromolecules, protein complex, macromolecular complex, crosslink, modification genomics researchers computational biologists bioinformaticians systems biologists
BpForms tutorial

BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of...

Scientific topics: Systems biology, Protein modifications, Proteomics, Transcriptomics, Epigenomics

Operations: Validation

Keywords: RNA modification, protein modification, DNA repair, DNA damage, crosslink, nick

Resource type: Jupyter notebook

BpForms tutorial https://tess.elixir-europe.org/materials/bpforms-tutorial BpForms is a toolkit for unambiguously describing the molecular structure (atoms and bonds) of DNA, RNA, and proteins, including non-canonical monomeric forms (subunits which compose polymers), crosslinks, nicks, and circular topologies. By concretely describing the molecular structure of biopolymers, BpForms aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. This tutorial provides an introduction to BpForms. Systems biology Protein modifications Proteomics Transcriptomics Epigenomics RNA modification, protein modification, DNA repair, DNA damage, crosslink, nick genomics researchers computational biologists bioinformaticians systems biologists
ObjTables Python tutorials

ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of...

Scientific topics: Data submission, annotation, and curation, Data quality management, Data integration and warehousing, Data management

Operations: Validation

Keywords: spreadsheet, schema, table, workbook, worksheet, XLSX, Excel, standard, reuse, compose, integrate, quality control

Resource type: Jupyter notebook

ObjTables Python tutorials https://tess.elixir-europe.org/materials/objtables-python-tutorials ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a markup format for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. ObjTables is ideal for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. The tutorials provide a brief introduction to the ObjTables format for schemas for spreadsheets, the ObjTables markup syntax for spreadsheets, and the ObjTables Python package for parsing, validating, querying, editing, comparing, merging, splitting, revisioning, migrating, and analyzing spreadsheets. Data submission, annotation, and curation Data quality management Data integration and warehousing Data management spreadsheet, schema, table, workbook, worksheet, XLSX, Excel, standard, reuse, compose, integrate, quality control Researchers Scientists Data scientists computational scientists
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 https://tess.elixir-europe.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
BiocCheck-a-thon check in

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

BiocCheck-a-thon check in https://tess.elixir-europe.org/materials/bioccheck-a-thon-check-in 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.
Annotating data using ontologies

This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems.

Scientific topics: Ontology and terminology, Data integration and warehousing, Data management

Keywords: Ontologies, Annotation, Data integration

Resource type: Video

Annotating data using ontologies https://tess.elixir-europe.org/materials/annotating-data-using-ontologies This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems. Ontology and terminology Data integration and warehousing Data management Ontologies, Annotation, Data integration
Solutions for overcoming cohort data integration challenges using ontology: an introduction

Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups.

Scientific topics: Data management, Data integration and warehousing, Ontology and terminology

Keywords: Ontologies, Data integration, Annotation

Resource type: Video

Solutions for overcoming cohort data integration challenges using ontology: an introduction https://tess.elixir-europe.org/materials/solutions-for-overcoming-cohort-data-integration-challenges-using-ontology-an-introduction Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups. Data management Data integration and warehousing Ontology and terminology Ontologies, Data integration, Annotation
Data harmonization and enrichment using EMBL-EBI ontology tools

This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data. The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators...

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

Keywords: CINECA, data harmonization, Annotation, Ontologies

Resource type: Video

Data harmonization and enrichment using EMBL-EBI ontology tools https://tess.elixir-europe.org/materials/data-harmonization-and-enrichment-using-embl-ebi-ontology-tools This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data. The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators access the tools through their respective websites. REST APIs are available for software developers who want to build systems based on these services. Ontology and terminology Data submission, annotation, and curation Data management CINECA, data harmonization, Annotation, Ontologies biocurators software developers, bioinformaticians
IBIP19 - Integrative Biological Interpretation using Proteomics (2019)

Training Material aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments.

Keywords: Proteomics

Resource type: Documentation, Exercise, Handout, Scripts

IBIP19 - Integrative Biological Interpretation using Proteomics (2019) https://tess.elixir-europe.org/materials/ibip19-integrative-biological-interpretation-using-proteomics-2019 Training Material aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. David Bouyssié Veit Schwämmle Marc Vaudel Proteomics Academia/ Research Institution Industry Non-Profit Organisation Healthcare
CPANG19 - Computational PANGenomics (2019)

Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

CPANG19 - Computational PANGenomics (2019) https://tess.elixir-europe.org/materials/cpang19-computational-pangenomics-2019 Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Erik Garrison Mikko Rautiainen Genomics Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019)

Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq.

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019) https://tess.elixir-europe.org/materials/ader19f-analysis-of-differential-expression-with-rnaseq-first-course-in-2019 Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq. Daniel Sobral Daniel Faria Daniel Neves RNA-Seq, Genomics, RNA Academia/ Research Institution Industry Non-Profit Organisation Healthcare