Hey Seq-ers!
Wanted to let you all know we at Edinburgh Genomics have a range of bioinformatics courses running this summer. From beginner level through to specific bioinformatics analysis, and both online and in-person, we have a course to suit a wide range of aspiring data scientists. See the list below or check out our website for more details including how to book!
Happy Coding!
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Introduction to Python for Biologists- in-person
Date: 18-22 July 2022
Location:
James Clerk Maxwell Building
The University of Edinburgh
The King's Buildings
Edinburgh EH9 3FL
Scotland, United Kingdom
Description:
Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way.
Instructors: Tim Booth (Developer, Programmer, Edinburgh Genomics), Nathan Medd (Training Manager, Edinburgh Genomics)
Registration fee:
£510 - University of Edinburgh Staff/Students
£535 - Other university Staff/Students
£560 - Industrial employees
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R for Biologists - in-person
Date: 8-10 August 2022 (9am - 5pm)
Location: Murchison House
10 Max Born Cres
Kings Buildings
Edinburgh EH9 3BF
Description: The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to biological data science. This online workshop is taught by experienced Edinburgh Genomics’ trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types and structures. We then move on to using functions, introducing a selection of packages for biological data science. We then focus on data handling and tidying datasets using the 'tidyverse' family of packages. Finally we use mock RNA-seq data to learn how to visualise your data to generate publication ready plots using the package ggplot2.
Instructors: Nathan Medd (Training and Outreach Manager, Edinburgh Genomics)
Registration fee:
£350 - University of Edinburgh staff/students
£375 - Other university or registered charity staff/students
£400 - Industrial researchers
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Introduction to Linux for Genomics - online
Date: 15-16 August 2022, (1pm - 5pm)
Description: Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command-line enables one to view, filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to perform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were especially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF).
This exciting new course aims to introduce the principles and practice using long-read data analysis with focus on Oxford Nanopore data. We will present the cutting edge software and best practices tried and tested by our expert bioinformaticians here at Edinburgh Genomics.
Instructors: Tim Booth (Developer, Programmer, Edinburgh Genomics), Nathan Medd (Training Manager, Edinburgh Genomics)
Registration fee:
£100 - University of Edinburgh staff/students
£125 - Other university or registered charity staff/students
£150 - Industrial researchers
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Introduction to RNA-seq Data Analysis - in-person
Date: 22-24 August 2022 (9am - 5pm)
Location: Murchison House
10 Max Born Crescent
The King's Buildings
Edinburgh EH9 3BF
Scotland, United Kingdom
Description: RNA sequencing (RNA-seq) is the method of choice for transcriptome profiling. Nevertheless, it is a non-trivial task to transform the vast amount of data obtained with high-throughput sequencers into useful information. Thus, RNA-seq data analysis is still a major bottleneck for most researchers in this field. The ability of correctly interpreting RNA-seq results, as well as knowledge on the intrinsic properties of these data, are essential to avoid incorrect experimental designs and the application of inappropriate analysis methodologies.
The aim of this workshop is to familiarise researchers with RNA-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs will be used.
Tutors: Frances Turner (Bioinformatician, Edinburgh Genomics), Urmi Trivedi (Bioinformatician, Edinburgh Genomics) Nathan Medd (Training Manager, Edinburgh Genomics)
Registration fee: £410/£435/£460 (UoE/Other Uni/Industry)
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Advanced Python for Biologists - in-person
Date: 29 August - 2 September 2022 (9am - 5pm)
Location: Murchison House
10 Max Born Crescent
The King's Buildings
Edinburgh EH9 3BF
Scotland, United Kingdom
Description: Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at people who already have a basic knowledge of Python and are interested in using the language to tackle larger problems. In it, we will look in detail at the parts of the language which are particularly useful in scientific programming, and at the tools Python offers for making development faster and easier. The workshop will use examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to (1) take advantage of the advanced language features in their own programs and (2) use appropriate tools when developing software programs.
Instructor: Martin Jones (Founder of Pythonforbiologists.com)
Registration fee: £510/£535/£560 (UoE/Other Uni/Industry)
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Variant Analysis - online
Date: 12-15 September 2022, (9.30am - 3.30pm)
This course aims to provide an introduction to the principles of short variant discovery (both germline and somatic) from short-read data. We will look at a complete workflow, from data QC to functional interpretation of variant calls. The practical sessions will focus on running the GATK pipeline from the Broad Institute (https://gatk.broadinstitute.org/hc/en-us).
Tutors: Frances Turner (Bioinformatician, Edinburgh Genomics), Urmi Trivedi (Bioinformatician, Edinburgh Genomics)
Registration fee:£380/£405/£430 (UoE/Other Uni/Industry)
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