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19 materials found

Target audience: beginner bioinformaticians  or Undergraduate students 


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

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

This training video series includes four short videos on research data management. The titles of the videos are the following:

  1. Introduction to data management for life science researchers
  2. Introduction to data management planning
  3. Introduction to sections of a generic ​data management...

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

MATHEMATICS BOOT CAMP: Introduction to Complex Systems Tools

This intensive course is to provide students with the prerequisites - some conceptual background and sufficient working knowledge of mathematics - necessary to master the mathematically based graduate courses at the Center for Complex Systems & Brain Sciences. By no means it is intended to...

Scientific topics: Mathematics, Computational biology

Keywords: ComputationalBiology, Neuroscience, complex systems, Mathematics

Resource type: Notes, Scripts

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. In our experience, developed at a Master’s course at the...

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

Resource type: course materials

ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

UNIX Fundamentals

This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge.
The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience.
At the end of...

Keywords: Problem based learning, Programming, Unix

Resource type: e-learning

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

Plant and Pathogen Bioinformatics

This package contains presentations and other training material given at the AllBio Plant and Pathogen Bioinformatics training course, held at the European Bioinformatics Institute, Hinxton, United Kingdom, Tuesday, July 8, 2014 - Friday, July 11, 2014. The course was aimed at giving an...

Keywords: Allbio, Bioinformatics, Biological databases, Genome sequence analysis, Pathogenesis, Phytopathogens, Plants

Training Bioinformatics in the Cloud

I present the points of view, the challenges and advantages of developing training materials through the cloud.

Keywords: Advanced bioinformatics training, Cloud computing, Training

Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

Using R with Python

This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...

Keywords: Programming, Python, Python biologists

Searching data using Python

This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...

Keywords: Programming, Python, Python biologists

Pattern Matching

This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...

Keywords: Pattern matching, Programming, Python, Python biologists

Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

Python Programs

This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions. 

Keywords: Programming, Python, Python biologists

Bioinformatics: Gene-protein-structure-function

This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...

Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast

InterPro: An introduction

This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose. 

Keywords: Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis

PRINTS: A protein family database with a difference

A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to...

Keywords: Functional diagnosis, Protein family characterisation, Protein sequence analysis

Parsing data records using Python programming

This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The...

Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing