Bioinformatics Courses @ Edinburgh Genomics this summer/autumn.
TRAIN edgenomics-training
Dear All
We are pleased to say bookings for a range of Edinburgh Genomics online courses, running this Summer/Autumn, are now open! Details below and on our
website.
Any questions about up coming courses check our
FAQ page or get in contact with our
training team.
Kind Regards
Nathan Medd
(Training Manager - Edinburgh Genomics)
----------------------------------------------------------------------------------------------------
RNA-seq Data Analysis 27-29 August (9.30am - 3.30pm) - Last few spaces remaining!
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: Urmi Trivedi (Bioinformatician, Edinburgh Genomics), Frances Turner (Bioinformatician, Edinburgh Genomics), and Nathan Medd (Training Manager, Edinburgh Genomics)
Registration fee: £250/£263/£325 (UoE staff or student/Other University staff or student/Industry staff)
R for Biologists 13-17 September (1-5pm)
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 learn how to visualise your data to generate publication ready plots using the package ggplot2.
Intructors: Nathan Medd (Training Manager), Donald Dunbar (Head of Bioinformatics)
Registration fee:£250/£263/£325 (UoE staff or student/Other University staff or student/Industry staff)
----------------------------------------------------------------------------------------------------
Introduction to Metagenomic Data Analysis, 21-23 September (10am - 3pm)
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. In this course you will be introduced to methods used for assembly from metagenomics samples. Attendees will use tools to assemble
metagenome assembled genomes (MAGs) from short read and long read data. We will discuss the different approaches and tools available for these assemblies and the benefits and limitations of each options.
Tutors: Urmi Trivedi (Bioinformatician, Edinburgh Genomics) Nathan Medd (Training Manager, Edinburgh Genomics)
Registration fee: £250/£263/£325
(UoE staff or student/Other University staff or student/Industry staff)
----------------------------------------------------------------------------------------------------
Variant Analysis, 27-30 September (9am - 3pm)
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: £250/£263/£325
(UoE staff or student/Other University staff or student/Industry staff)
----------------------------------------------------------------------------------------------------
Long-read Bioinformatics, 11-13 October (10am-3pm)
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 (mb+) single-molecule DNA fragments. Although these developments are expected to alleviate numerous computational challenges surrounding genome analysis 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 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.
Instructor: Urmi Trivedi - Bioinformatician, Edinburgh Genomics
Registration fee: £150/£158/£195 (UoE staff or student/Other University staff or student/Industry staff)
----------------------------------------------------------------------------------------------------
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 specially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM,
VCF).
Instructors: Tim Booth and Nathan Medd (Edinburgh Genomics Bioinformatics team)
Registration fee: £75/£79/£95 (UoE staff or student/Other University staff or student/Industry staff)
-- ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ========================================================The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
TRAIN edgenomics-training
Dear All
We have some great online courses scheduled for the next couple of months: check out our website for more info and for new courses as they're released.
Also, please do forward to any budding bioinformaticians you may know!
Kind Regards
Nathan
Introduction to Python for Biologists 22-29 March (09.30 - 16.30)
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.
Tutor: Tim Booth (Edinburgh Genomics)
Registration fee: £450/£473/£585
(UoE staff or student/Other University staff or student/Industry staff)
Where: Online
----------------------------------------------------------------------------------------------------
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 learn how to visualise your data to generate publication ready plots using the package ggplot2.
Tutor: Nathan Medd (Training Manager)
Registration fee:£250/£263/£325
(UoE staff or student/Other University staff or student/Industry staff)
Where: Online
----------------------------------------------------------------------------------------------------
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: Urmi Trivedi (Bioinformatician, Edinburgh Genomics), Frances Turner (Bioinformatician, Edinburgh Genomics), and Nathan Medd (Training Manager, Edinburgh Genomics)
Registration fee: £250/£263/£325 (UoE staff or student/Other University staff or student/Industry staff)
-- Training and Outreach Manager - Edinburgh Genomics ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at:
http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ========================================================