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Showing 30 materials out of 117. View all results.
Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle

This material is part of an follow up FAIR data stewardship workshop for the Marie Curie ITN ProEVLifeCycle (The prostate cancer Extracellular Vesicle LifeCycle)

FAIR and data stewardship - November 3th, 2021
Organiser: Dutch Techcentre For Life Sciences, DTL
Setup: Virtual meeting...

Scientific topics: Data management, FAIR data

Operations: Data handling, Analysis

Keywords: Data analysis, Data management planning, Data processing, Data sharing, Data collection, Data preserving, Data reuse

Resource type: Slidedeck

Mantra Research Data Management Training

There are eight online units in this course and one set of offline (downloadable) data handling tutorials that will help you:

Understand the nature of research data in a variety of disciplinary settings
Create a data management plan and apply it from the start to the finish of your research...

WORKSHOP: Refining genome annotations with Apollo

This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.

Workshop description 

Genome annotation is crucial to defining the function of genomic sequences. This...

Keywords: Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This Zenodo record includes training materials associated with the Australian BioCommons webinar ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for...

Scientific topics: Proteomics, Protein modifications

Keywords: Phosphoproteomics

Introductory image processing on biological images using python.

This is an image processing practical for students with an interest in analysing biologically derived images. It is written in the language python and utilises jupyter notebook for annotation and visualisation of the code. The practical is beginner level, although some knowledge of python is...

Resource type: Jupyter notebook, PDF

Open Science MOOC: Module 5, Open Research Software and Open Source

Software and technology underpin modern science. There is an increasing demand for more sophisticated open source software, matched by an increasing willingness for researchers to openly collaborate on new tools. These developments come with a specific ethical, legal and economic challenges that...

Keywords: open source

FAIR Data Stewardship - Data sharing, archiving and publishing

In this workshop we focus on three aspects of FAIR data stewardship: Data sharing, publishing and archiving. Many scientists have an insufficient overview over data services, roles and their responsibilities towards safe data sharing, archiving and publishing. Shedding light on these roles helps...

Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

Resource type: Slides, Training 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 regularly by ELIXIR-Luxembourg.

Scientific topics: Data governance, Data management

Keywords: GDPR, data protection, sensitive data

Introduction to FAIR principles

Slides for the "Introduction to FAIR Principles" session of the "Research Data Manegement and Stewardship Training" held regularly by ELIXIR-Luxembourg.

Keywords: FAIR data

Resource type: Presentation

Data Management Planning

Slides for the Data Management Plannning session of the "Research Data Manegement and Stewardship Training" held regularly by ELIXIR-Luxembourg

Keywords: Data management plan

Resource type: Presentation

Data Stewardship Wizard Workshop (Feb 2020)

Data Stewardship Wizard brings together data stewards and researchers to allow managing data in projects efficiently and in a FAIR manner. Data stewards can easily capture the knowledge including required project data and decisions in knowledge models that are then turned into...

Scientific topics: Data governance, Data management

Keywords: Data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar, Slides

PSLS20 - Practical Statistics for the Life Sciences (2020)

This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data...

Keywords: Statistics, General Linear Models

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the...

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018)

This course is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive...

Keywords: Statistics and probability

Resource type: Documentation, Exercise, Handout, Scripts

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018)

3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are spatially close in the cell nucleus. Overall, these interaction matrices have been used to study how the genome folds within the nucleus, that is one of the most fascinating problems in modern...

Keywords: Hi-C

Resource type: Documentation, Exercise, Handout, Scripts

PPB18 - Programming in Python for Biologists (2018)

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and...

Operations: Data retrieval, Data handling

Keywords: Bioinformatics, Biology, Biological databases

Resource type: Documentation, Exercise, Handout, Scripts

ELB18F - Entry level Bioinformatics (First course in 2018)

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is...

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. We we will also cover some of the initial...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

PDA18 - Proteomics Data Analysis (2018)

Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering peptide and protein identification, quantification,...

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

CPANG18 - Computational PANGenomics (2018)

Reference genomes have become central to bioinformatics approaches, and form the core of standard analyses using contemporary sequencing data. However, the use of linear reference genomes, which provide the sequence of one representative genome for a species, is increasingly becoming a limitation...

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ELBS18 - Entry level Bioinformatics (Second course in 2018)

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is...

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELB19F - Entry level Bioinformatics (First course in 2019)

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is...

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

PDA19 - Proteomics Data Analysis (2019)

Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering peptide and protein identification, quantification,...

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

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

Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the...

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

CPANG19 - Computational PANGenomics (2019)

Reference genomes have become central to bioinformatics approaches, and form the core of standard analyses using contemporary sequencing data. However, the use of linear reference genomes, which provide the sequence of one representative genome for a species, is increasingly becoming a limitation...

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

IBIP19 - Integrative Biological Interpretation using Proteomics (2019)

Quantitative proteomics by mass spectrometry has become an essential tool for multi-omics studies aiming at answering important biological questions in a system-wide perspective. Proteomics data contain rich and deep information that can become challenging to extract, interpret, and interface...

Keywords: Proteomics

Resource type: Documentation, Exercise, Handout, Scripts

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

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