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45 materials found

Difficulty level: Intermediate 


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
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
PGDH19 - Population Genetics Demographic History: model-based approaches (2019)

Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH19 - Population Genetics Demographic History: model-based approaches (2019) https://tess.elixir-europe.org/materials/pgdh19-population-genetics-demographic-history-model-based-approaches-2019 Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodriguez Vitor Sousa Armando Arredondo Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PDA19 - Proteomics Data Analysis (2019)

Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis.

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

PDA19 - Proteomics Data Analysis (2019) https://tess.elixir-europe.org/materials/pda19-proteomics-data-analysis-2019 Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis. Lennart Martens Harald Barsnes Lieven Clement Proteomics, Biological databases, Mass spectrometry data Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018)

Training material for 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

ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018) https://tess.elixir-europe.org/materials/ader18s-analysis-of-differential-expression-with-rnaseq-second-course-in-2018 Training material for 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
CPANG18 - Computational PANGenomics (2018)

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

CPANG18 - Computational PANGenomics (2018) https://tess.elixir-europe.org/materials/cpang18-computational-pangenomics-2018 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 Jordan Eizenga Genomics Academia/ Research Institution Industry Non-Profit Organisation
PDA18 - Proteomics Data Analysis (2018)

Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis.

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

PDA18 - Proteomics Data Analysis (2018) https://tess.elixir-europe.org/materials/pda18-proteomics-data-analysis-2018 Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis. Lennart Martens Harald Barsnes Lieven Clement Proteomics, Biological databases, Mass spectrometry data Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018)

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

ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018) https://tess.elixir-europe.org/materials/ader18f-analysis-of-differential-expression-with-rnaseq-first-course-in-2018 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
PPB18 - Programming in Python for Biologists (2018)

Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems.

Operations: Data handling, Data retrieval

Keywords: Bioinformatics, Biology, Biological databases

Resource type: Documentation, Exercise, Handout, Scripts

PPB18 - Programming in Python for Biologists (2018) https://tess.elixir-europe.org/materials/ppb18-programming-in-python-for-biologists-2018 Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems. Allegra Via Vincenza Colonna David Philip Judge Bioinformatics, Biology, Biological databases Academia/ Research Institution Industry Non-Profit Organisation Healthcare
3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018)

Training Material focused in 3C-Data Analysis and 3D Chromatin Folding

Keywords: Hi-C

Resource type: Documentation, Exercise, Handout, Scripts

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018) https://tess.elixir-europe.org/materials/3daroc18-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding-2018 Training Material focused in 3C-Data Analysis and 3D Chromatin Folding Marc A. Martí-Renom François Serra David Castillo Hi-C Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018)

Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data.

Keywords: Statistics and probability

Resource type: Documentation, Exercise, Handout, Scripts

ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018) https://tess.elixir-europe.org/materials/abstat18-advanced-biostatistics-for-bioinformatics-tool-users-using-r-2018 Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Lisete Sousa Carina Silva Statistics and probability Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Training material for hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018) https://tess.elixir-europe.org/materials/pgdh18-population-genetics-and-demographic-history-model-based-approaches-2018 Training material for hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodríguez Armando Arredondo Soto Vitor Sousa Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PSLS20 - Practical Statistics for the Life Sciences (2020)

Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences.

Keywords: Statistics, General Linear Models

Resource type: Documentation, Exercise, Handout, Scripts

PSLS20 - Practical Statistics for the Life Sciences (2020) https://tess.elixir-europe.org/materials/psls20-practical-statistics-for-the-life-sciences-2020 Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. Lieven Clement Jeroen Gilis Statistics, General Linear Models Academia/ Research Institution Industry Healthcare Non-Profit Organisation
Implementing GDPR in a Biomedical Research Institute

Slides for the "Data protection, working with sensitive human data in research." session of the "Research Data Management and Stewardship Training" held on 25 June 2019 by ELIXIR-Luxembourg.

Scientific topics: Data management, Data governance

Keywords: GDPR, data protection

Implementing GDPR in a Biomedical Research Institute https://tess.elixir-europe.org/materials/implementing-gdpr-in-a-biomedical-research-institute Slides for the "Data protection, working with sensitive human data in research." session of the "Research Data Management and Stewardship Training" held on 25 June 2019 by ELIXIR-Luxembourg. Regina Becker Data management Data governance GDPR, data protection Researchers data stewards data managers
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 https://tess.elixir-europe.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
Bioinformatics Summer School 2019

This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are...

Scientific topics: Statistics and probability, Omics, RNA-Seq, Proteomics

Operations: Data handling

Bioinformatics Summer School 2019 https://tess.elixir-europe.org/materials/bioinformatics-summer-school-2019 This one-week intensive summer school in bioinformatics will focus on data analysis and high throughput biology, with a special focus on R/Bioconductor and its application to a wide range of topics across bioinformatics and computational biology. The course is intended for researchers who are familiar with omics experimental technologies and their applications in biology, have had some exposure with R, and who want to learn or expand their bioinformatics skills. Martin Morgan Laurent Gatto Janick Mathys Lieven Clement Charlotte Soneson Koen Van den Berge Oliver Crook Statistics and probability Omics RNA-Seq Proteomics PhD students
Adding ontology terms

This tutorial describes how terms can be added to the eNanoMapper ontology.

Keywords: enanomapper, ontologies

Resource type: Tutorial

Adding ontology terms https://tess.elixir-europe.org/materials/adding-ontology-terms-2d31ae63-7f7b-45df-aa37-4b1e14209183 This tutorial describes how terms can be added to the eNanoMapper ontology. enanomapper, ontologies post-docs
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 https://tess.elixir-europe.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
IUPHAR/BPS Guide to Pharmacology online tutorial

Online tutorial for the IUPHAR/BPS Guide to Pharmacology database

Scientific topics: Drug discovery, Pharmacology

Resource type: PDF

IUPHAR/BPS Guide to Pharmacology online tutorial https://tess.elixir-europe.org/materials/iuphar-bps-guide-to-pharmacology-online-tutorial Online tutorial for the IUPHAR/BPS Guide to Pharmacology database Drug discovery Pharmacology
Training on integration of OpenID Connect services to ELIXIR AAI

Materials for hands-on training on connection OpenID Connect relaying party to ELIXIR AAI.

Keywords: AAI, OpenID Connect, Authentication

Training on integration of OpenID Connect services to ELIXIR AAI https://tess.elixir-europe.org/materials/training-on-integration-of-openid-connect-services-to-elixir-aai Materials for hands-on training on connection OpenID Connect relaying party to ELIXIR AAI. AAI, OpenID Connect, Authentication service administrators in organizations that want to make use of ELIXIR AAI
Essential Steps of the FAIRification Process

Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops". This material documents the accumulated practical & teaching...

Keywords: FAIR, data stewardship, metadata, linked data

Resource type: Training materials

Essential Steps of the FAIRification Process https://tess.elixir-europe.org/materials/essential-steps-of-the-fairification-process Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops". This material documents the accumulated practical & teaching experiences from BYODS as well as more high-level FAIR awareness trainings. This document was formerly known as the "Big Book of FAIRification". FAIR, data stewardship, metadata, linked data Researchers Support Staff data librarians software developers, bioinformaticians
Data processing with R tidyverse

R is a powerful language for data science in many disciplines of research with a steep learning curve. The tidyverse group of packages provide a dialect that greatly simplifies: * data importing * cleaning * processing * visualization as well as providing reproducible workflows using...

Keywords: R-programming

Resource type: course materials

Data processing with R tidyverse https://tess.elixir-europe.org/materials/data-processing-with-r-tidyverse R is a powerful language for data science in many disciplines of research with a steep learning curve. The tidyverse group of packages provide a dialect that greatly simplifies: * data importing * cleaning * processing * visualization as well as providing reproducible workflows using pipelines (`%>%`) Adopt Hadley Wickham, Chief Scientist at RStudio, philosophy: take each step of data science and replace many intricacies of R with clear, consistent and easy to learn syntax. RStudio will be the software to use since it eases package management, scripting, plotting and data handling. R-programming Researchers
Learning structural bioinformatics and evolution with a snake puzzle

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding.

Scientific topics: Protein structure analysis, Molecular biology, Evolutionary biology, Bioinformatics

Resource type: course materials

Learning structural bioinformatics and evolution with a snake puzzle https://tess.elixir-europe.org/materials/learning-structural-bioinformatics-and-evolution-with-a-snake-puzzle We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. Protein structure analysis Molecular biology Evolutionary biology Bioinformatics Master students Undergraduate students
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/)

Scientific topics: Plant biology, Functional genomics, Comparative genomics, Evolutionary biology, Phylogenomics, Genotype and phenotype

Operations: Annotation, Visualisation, Comparison

Keywords: plants, Plants bioinformatics, genomics, Visualisation, Annotation

Resource type: Training materials

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics https://tess.elixir-europe.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/) Plant biology Functional genomics Comparative genomics Evolutionary biology Phylogenomics Genotype and phenotype plants, Plants bioinformatics, genomics, Visualisation, Annotation Life Science Researchers plant researchers experimeintal biologist researchers postdoctoral researchers Research Assistants and Research Associates PhD
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 https://tess.elixir-europe.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
Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial

Adding nanomaterial data https://tess.elixir-europe.org/materials/adding-nanomaterial-data This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format. Database management Toxicology nanotoxicology, enanomapper, resource description framework, ontology programmers data entering