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Edinburgh Genomics: Introduction to Python for Biologists

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.

 Instructor:

Tim Booth

Course Developer:
Dr. Martin Jones (Founder, Python for Biologists)

Workshop format
Five days. See web page for details 

Event Website

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The ability to identify organisms from traces of genetic material in environmental samples has reshaped the way we see life on earth. Especially for microorganisms, where traditional identification is hard or near impossible, metagenomic techniques have granted us unprecedented insight into the microbiome of animals and the environment more broadly.

Instructors

Urmi Trivedi, Heleen De Weerd

Workshop format

This live online workshop consists of presentations and hands-on tutorials.

Who should attend

Graduates, postgraduates, and PIs, who are using, or planning to use, metagenomic technology in their research and want to learn how to process and analyse the data produced.

Requirements

A general understanding of molecular biology and genomics. A working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop.

Event website

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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. Finally, we will learn how to visualise your data to generate publication-ready plots using the package ggplot2.

Instructors

• Frances Turner (Bioinformatician)
• Heleen De Weerd (Bioinformatician)

Workshop format

The workshop consists of presentations and hands-on tutorials.

Who should attend

Undergraduates, Graduates, postgraduates, and PIs, who are using, or planning to use, the statistical software R to manipulate and analyse biological data in their research. This is an introductory level course: no prior experience of R (or any other programming language) is necessary before starting the workshop.

Event website

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Single cell RNA-Seq offers many advantages over bulk RNA-Seq, but the richer data produced requires a more complex analysis. In this course we will learn about the advantages of single cell sequencing, and when it may be an appropriate choice, how to perform common types of data analysis, and to spot and deal with potential problems.  We will analyse 10X genomics data with the R package Seurat.

Who this course is for

Graduates, postgraduates, and PIs, who are using, or planning to use, RNA-seq technology in their research and want to learn how to process and analyse RNA-seq data.

Requirements

• A general understanding of molecular biology and genomics.
• A working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop.
• A working knowledge of R at the level of Edinburgh Genomics R for Biologists workshop.
  (If you are unsure of how these relate to your coding skills please check the above course pages and look at topics covered)

Event website

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Edinburgh Genomics: Advanced Python for Biologists

Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work. This workshop is aimed at people who already have a basic knowledge of Python. We will look at the parts of the language which are particularly useful in scientific programming. The workshop will use examples 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.

Instructors: Dr. Martin Jones (Founder, Python for Biologists)

Workshop format: Each session consists of a lecture followed by practical exercises. Each session uses examples and exercises that build on material from the previous one, so it’s important to attend all sessions. Description of the sessions can be found on the pdf you receive when signing up.

Who should attend: This workshop is aimed at researchers & technical workers with a background in biology and knowledge of Python.

Requirements

Students should have enough biological/bioinformatics background to appreciate the examples and exercise problems (i.e. they should know what a protein accession number, BLAST report, and FASTA sequence is). Students should be familiar with the use of lists, loops, functions & conditions.

Event website

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Edinburgh Genomics: RNA Library Preparation Lab Course 

In this course you will learn how to produce directional mRNA sequencing libraries using the NEBNext UltraExpress® RNA Library Prep Kit from NEB, which provides a robust, 1 day work-flow for library production from total RNA. You will get to work on both a high-quality training sample and have the opportunity to bring your own RNA sample for library preparation and sequencing. This course assumes you have a basic level of laboratory experience in a molecular biology lab, although experienced demonstrators will always be on hand to guide you. If you have limited lab experience, please indicate this on the registration form and we will try to accommodate you.

Who should attend: This workshop is aimed at researchers & technical workers with a background in biology who intend to use their skills in a molecular biology lab.

Requirements

That you attend all parts of the course.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS online COURSE

Edinburgh Genomics: RNA-seq Data Analysis 

RNA sequencing (RNA-seq) has become 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 to correctly interpret RNA-seq results, as well as knowledge of 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.

Instructors: Urmi Trivedi, Frances Turner

Workshop format

The workshop consists of presentations and hands-on tutorials.

Who should attend

Graduates, postgraduates, and PIs, who are using, or planning to use, RNA-seq technology in their research and want to learn how to process and analyse RNA-seq data.

Requirements

A general understanding of molecular biology and genomics. Experience of command-line computing and a working knowledge of R at the level of Edinburgh Genomics introductory courses.

Event website