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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 

Who should attend

See web page for details 

Requirements

See web page for details 

The workshop will be held in person not online, you will be emailed details once you have registered.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

Whole-genome sequencing (WGS) has been revolutionised by the development of long-read sequencing technologies in the last few years. Driven in no small part by Oxford Nanopore Technologies (https://nanoporetech.com/), we now have the ability to sequence long (kb+) single-molecule DNA fragments. Although these developments are expected to alleviate numerous computational challenges surrounding genome assembly they also bring some interesting bioinformatics challenges to which we have to adapt in order to get the most from this powerful technology.

This exciting new course aims to introduce the principles and practice of long-read genome assembly and analysis using cutting-edge software and best practices tried and tested by our expert bioinformaticians here at Edinburgh Genomics.

Who this course is for

Aside from a basic understanding of molecular biology, attendees must have a working knowledge of how to use the Linux BASH command line - our 1-day "Linux for bioinformatics" course is a suitable background.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

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)

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

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.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS 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, Nathan Medd 

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.

Please register here

Edinburgh Genomics: Data Exploration with Python

One of the strengths of the Python language is the availability of mature, high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. This course is intended for researchers with Python knowledge who need to explore large datasets and quickly visualise patterns and relationships. We will concentrate on how best to use existing libraries with only a small amount of code! There will be opportunities to use your own data throughout.

Instructor
Dr. Martin Jones (Founder, Python for Biologists)

Workshop format
See web page for details 

Who should attend

See web page for details 

Requirements

See web page for details 

The workshop will now be online.

An image is more than a pretty picture.  It contains data that can be extracted and quantified.  During the ten half-day course, students learn about the structure of an image –what a good image is- as well as different techniques to extract data in 2d, over time and in 3D.  The software that we’ll use are all freeware: Fiji, Ilastik, CellProfiler. 

Students get typical images, course notes and access to recording.

Instructors: Matthieu Vermeren

Please give me the name of your PI and the Centre/institute where you are working. Bonus points to those that give their grant number! 

Pre-requisites: You will need to install the following software:
•    Fiji (https://imagej.net/software/fiji/).  
•    Ilastik (https://www.ilastik.org/)
•    CellProfiler and CellProfiler Analyst (https://cellprofiler.org/)


NOTE: You may need to ask IS/administrator for permission. 
NOTE 2: We are using FIJI, which has extra functionalities over ImageJ. Make sure you install Fiji. Fiji needs installing at the root of your C:\ drive, nowhere else. 
 
Course material in form of test files and detailed booklets will be provided.

Location: wherever you have access to a computer and a good internet.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

Edinburgh Genomics: Introduction to Linux for Genomics

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 mperform 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 specially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF).

Instructors:Tim Booth 

Workshop format
The workshop consists of guided tutorials and hands-on exercises. Roughly 3/4 of the workshop will be spent on Linux and 1/4 on command-line tools for genomics and file formats.

Who should attend
Graduates, postgraduates, and PIs, without any previous command-line experience.

Requirements
A general understanding of molecular biology and genomics and elementary skills in computer usage are required. A computer with stable internet connection and small VNC viewer software (download instructions included)