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36 materials found

Target audience: PhD students 


BioExcel Building Blocks (BioBB) Training Material

BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR.

Keywords: molecular dynamics, Docking, Modeling, life sciences

Resource type: Jupyter notebook

Research Data Management Introduction for researchers

Short summary of the previous session
1.Scope of the DM
2.DMP Content and structure
Practical activities
3.Planning the DM of a simple project
4.DMP evaluation

Scientific topics: FAIR data, Data management

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

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

Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome,...

Keywords: Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material

Resource type: Training materials

Ten simple rules for making training materials FAIR

Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. FAIR principles are however not so simple to...

Scientific topics: FAIR data

Operations: Data handling

Keywords: FAIR data, FAIR, ELIXIR-CONVERGE

Resource type: Video

EJP RD MOOC "Diagnosing Rare Diseases: from the Clinic to Research and back"

Topics covered:
- The diagnostic process and the types of genetic tests available for rare diseases
- The differences in rare genetic diseases patient pathways
- Technological advances for diagnostic research
- The role of collaborative studies and data sharing in rare diseases diagnosis
-...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Slides from Data Management Planning Workshop

Slides from Data Management Planning online workshop for Life Science Projects for researchers at UiO 2020-12-11

Scientific topics: Data management

Operations: Deposition, Data retrieval, Data handling

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop

Slides from Data Management Planning online workshop for Life Science Projects for researchers at NTNU 2020-12-01

Scientific topics: Data management

Operations: Deposition, Data retrieval, Data handling

Keywords: Data management plan, data management

Resource type: Slides

Initiation to R programming and descriptive statistics

This course material was designed with the on-site teaching program for PhD students at Institut Pasteur in mind.
It teaches the basics of R programming and descriptive statistics, and is hopefully detailed enough to be usable for self-study, with some rough guidelines given...

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

Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Ås 11 March 2020

Scientific topics: Data management

Operations: Data handling, Data retrieval, Deposition

Keywords: Data management plan, data management

Resource type: Slides

Slides from Data Management Planning Workshop

Slides from Data Management Planning workshop for Life Science Projects in Bergen 04 March 2020

Scientific topics: Data management

Operations: Deposition, Data retrieval, Data handling

Keywords: Data management plan, data management

Resource type: Slides

Ready For BioData Management?

"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.
Under this program, we have organized an intro-level workshop on data management plans, the material for which is available.
We are also organizing an advanced...

Scientific topics: Data management

Keywords: Data managment plan

Resource type: course 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...

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

Operations: Data handling

RRegrs package

This tutorial explains how to use a collection of R regression tools for estimating the optimal model via a fully validated procedure.

Keywords: Regression Models

How to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data

This tutorial explains how to use the AffyQC web tool of ArrayAnalysis.org for quality control and pre-processing of Affymetrix microarray data.

Keywords: Microarray data analysis, Quality control and data pre-processing, Affymetrix microarrays, Systems biology, Pathway and network analyis

How to make a new pathway for WikiPathways using PathVisio

This tutorial explains how to a new pathway for WikiPathways using PathVisio.

Keywords: Systems biology, Pathway analysis, Network analysis, Microarray data analysis, Nanomaterials

Omics descriptors calculation R package

This tutorial explains how to generate a new set of GO descriptors using two novel created R packages.

Keywords: Gene Ontology

Hands-on workshop in Marine Metagenomics

Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway

Scientific topics: Genomics, Metagenomics, Marine biology

Keywords: Marine Metagenomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Pathway module of ArrayAnalysis.org

This tutorial explains how to use the Pathway module of ArrayAnalysis.org for pathway analysis of microarray data.

Keywords: Gene Ontology

Data visualisation with R and ggplot2

This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R...

Keywords: R-programming

Resource type: course materials

Introduction to GitHub for chemists

Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following:

  • Background and motivation
  • What is Git? What is version control? What is GitHub?
  • How can Git and GitHub be useful for you? -...

Keywords: Git, GitHub

Resource type: course materials

Make your academic life easy with ORCID: an introduction

Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure...

Keywords: ORCID

Resource type: Tutorial

Entering and analysing nano safety data

Tutorial that covers various aspects of working with the eNanoMapper database. It discussed searching, adding, and downloading data from an eNanoMapper database.

Keywords: ontologies, enanomapper

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

Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé

This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online.

Keywords: nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé

Resource type: Tutorial

Deep Learning using a Convolutional Neural Network

This course part focuses on a recent machine learning method known as deep learning that emerged as a promising disruptive approach, allowing knowledge discovery from large datasets in an unprecedented effectiveness and efficiency. It is particularly relevant in research areas, which are not...

Scientific topics: Machine learning

Resource type: Video

Introduction to Machine Learning Algorithms

This course offers basics of analysing datasets with machine learning algorithms and data mining techniques in order to understand foundations of learning from large quantities of data.
It starts with general methods for data analysis in order to understand clustering, classification, and...

Scientific topics: Machine learning

Resource type: Video

High-throughput sequencing training materials repository

This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis.
Materials have been annotated following the standards and guidelines proposed at the “Best practices...

Scientific topics: Bioinformatics, Data architecture, analysis and design

Keywords: High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling

EMBO 2015

Link to the GitHub repository containing all the training materials made available for the 2015 EMBO event held at TGAC

Scientific topics: Molecular interactions, pathways and networks, Protein binding sites

Keywords: Bioinformatics, Multiple sequence alignment, Network visualization, Protein protein interaction networks

De Novo

Training Materials from the 2015 De Novo course run by TGAC

Keywords: De novo, De novo genome assembly