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bioinformatics

Course at Breda, The Netherlands: RNA-seq data analysis

The 9th edition of the RNA-seq Data Analysis course will be held on 8-12 April – 2024 in Breda, The Netherlands. This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored.

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Course at Bern, Switzerland: Single-Cell Transcriptomics with R

Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the researchers’ needs. This 3-day course will cover the main technologies as well as the main aspects to consider while designing a scRNAseq experiment. In addition, it will cover the theoretical background of analysis methods with hands-on practical data analysis sessions applied to droplet-based methods.

Application deadline: 06 March 2024

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Course at EMBL-EBI: Summer school in bioinformatics

European Bioinformatics Institute United Kingdom in association with Elixir Estonia are organising summer school in bioinformatics. This course provides an introduction to the use of bioinformatics in biological research, giving you guidance for using bioinformatics in your work whilst also providing hands-on training in tools and resources appropriate to your research.

Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their knowledge and skills further. No previous knowledge of programming is required for this course.

Applications close: 25 February 2024

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Summer school in bioinformatics

 

European Bioinformatics Institute United Kingdom in association with Elixir Estonia are organising summer school in bioinformatics. This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research.

Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management, and reproducibility. To enable specific exploration of resources in their particular field of interest, participants will then be divided into focused groups to work on a project.

Participants will be required to review some pre-recorded material prior to the start of the course.

Information about the summer school

Date: 12 - 16 June 2023

Application deadline: 05 March 2023

Cost: £825.00 inclusive of four nights accommodation and catering, including dinner

Participant limit: Open application with selection 30 places

More info: https://www.ebi.ac.uk/training/events/summer-school-bioinformatics-0/

Group projects:

  • Genome variation across human populations 
  • Interpreting functional information from large scale protein structure data
  • Modelling cell signalling pathways
  • Networks and pathways
  • Reusing FAIR Bioimage data: an AI application

Who is this course for?

Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their knowledge and skills further. No previous knowledge of programming is required for this course; group projects may give you the opportunity to learn basic programming, but participants will be supported in this by their mentors. Depending on your chosen project, an introductory programming tutorial may be given as homework prior to attending the course.

Learning outcomes

  • After this course you should be able to:
  • Discuss applications of bioinformatics in biological research
  • Browse, search, and retrieve biological data from public repositories
  • Use appropriate bioinformatics tools to explore biological data
  • Describe ways that biological data can be stored, organised and integrated

SIB Bioinformatics Awards 2023 are now open to entries

Bioinformaticians of the world, it's your time to shine! The SIB Bioinformatics Awards promote excellence, diversity and innovation in the field of bioinformatics, and are now open to entries until 31 January 2023. 

SIB created the Bioinformatics Awards in 2008 to acknowledge early career bioinformaticians and ground-breaking resources of national and international standing. The international awards honour excellence in bioinformatics and computational biology within three categories:

The awards are assigned by an international jury, revised by the SIB Award Committee and announced during the biennial [BC]2 Basel Computational Biology Conference.

More info available here: https://www.sib.swiss/science-promotion/bioinformatics-awards

Unix Shell Advanced Training courses March 17 and 20

Unix Shell Advanced Courses 17th and 20th of March 2020, 10.15-14.00, Delta #2005

Advanced computing power is hidden away in clouds/cluster/supercomputers that you do not have click and point access. As a general rule these high performance computer resources use Linux operating systems and are accessible only by a shell terminal.

This course is aimed to streamline your skills in Linux and terminal environment. We will teach you how to make your life easier by creating maintainable and flexible bash scripts for your commonly used workflows or SLURM jobs.

Objectives:

  • Learn how to iterate operations over many input files with bash loops and conditions.
  • Learn how to combine complicated command line based workflows into maintainable bash scripts.
  • Add additional useful utility functions and tools to your toolbox.

Expected prior knowledge:
Experience in using the basic commands covered in the Basics course (e.g. cd, ls, mkdir, mv, cp, head, cat, find, less, pwd).

Requirements:
Lecture venue is computer class with linux computers. In case you bring your own Windows laptop, please make sure to install Putty application (https://www.putty.org/) beforehand.

Materials:
https://elixirestonia.github.io/2020-03-17-tartu/

Registration:
Application is open at https://forms.gle/pzWrKDNcxpStEADk8

Time:
March 17, 2020
10:15–14:00

March 20, 2020
10:15–14:00

Venue:
Auditorium 2005 (the Linux classroom)
UT Delta Centre
Narva mnt 18
51009 Tartu
Estonia