[BBC] New Workshops @ Edinburgh Genomics

[TRAIN edgenomics-training]

Dear All


Start your new term with a boost to your bioinformatics skills! Here at Edinburgh Genomics we have a range of new courses running this autumn, from introductory to advanced level at a range of locations. Check them out below or visit our website (https://genomics.ed.ac.uk/services/training) for more information.


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Bioinformatics Workflows with Snakemake - 30 September - 01 October 2019 *NEW*<http://genomics.ed.ac.uk/services/bioinformatics-workflows-snakemake>

Are you running data analysis workflows? Want to step up to the next level of organisation and efficiency?

Save yourself time, increase replicability, and master your analysis with Snakemake.

The Snakemake workflow system provides effective solutions to organise your tasks, document and share your methods, make effective use of compute resources, and handle unexpected errors in processing.

Edinburgh Genomics are offering a two-day course that will have you confident in using Snakemake to tackle complex workflow problems and in your day-to-day research.

Tutors: Tim Booth, Analyst - Developer, Edinburgh Genomics; Hywel Dunn-Davis, Analyst - Developer, Edinburgh Genomics

Registration fee: £400 (including lunches and refreshments)

Where: Ashworth Building, The Kings Buildings, Edinburgh.

Register here <https://www.surveymonkey.co.uk/r/X8GFP99>


Bioinformatics for Genomics - 28 October - 01 November 2019 <https://genomics.ed.ac.uk/services/bioinformatics-genomics-0> <https://genomics.ed.ac.uk/services/bioinformatics-genomics-0> *Little France Campus*
<https://genomics.ed.ac.uk/services/introduction-python-biologists-0><https://genomics.ed.ac.uk/services/introduction-python-biologists-0>

This is a week-long workshop that combines our popular ‘Linux for Genomics’, ‘R for Genomics’, and ‘Introduction to RNA-seq Data Analysis’, taught by Edinburgh Genomics’ Bioinformaticians. By the end of the five days, you will be: comfortable on the Linux command line; able to view, filter and manipulate large text files; able to write pipelines to perform certain bioinformatics tasks; familiar with and able to use the basics of R; confident using several data QC and processing tools; able to generate gene counts and differential expression statistics; and prepared to put it all together with visualization, interpretation, and gene set analysis.

Tutors: Urmi Trivedi, Bioinformatician, Edinburgh Genomics; Frances Turner, Bioinformatician, Edinburgh Genomics; Tim Booth, Analyst - Developer, Edinburgh Genomics; Nathan Medd, Training and Outreach Manager, Edinburgh Genomics

Registration fee: £750 (including lunches and refreshments)

Where: Chancellors Building, The little France (BioQuarter) Campus, Edinburgh.

Register here<https://www.surveymonkey.co.uk/r/PRXMJL2>


<http://genomics.ed.ac.uk/services/bioinformatics-workflows-snakemake>

Introduction to Linux and Workflows for Biologists, 04 - 08 November 2019 <https://genomics.ed.ac.uk/services/introduction-linux-and-workflows-biologists>

This week-long course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data.

Tutor: Martin Jones (Founder of Python for Biologists)

Registration fee: £550 (includes coffee/tea, but no lunch)

Where: Ashworth Building, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3FL

Register here <https://www.surveymonkey.co.uk/r/VZQY9HZ>


Introduction to R for Genomics, 14 - 15 November 2019 <https://genomics.ed.ac.uk/services/r-genomics>

The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to genomic data science. This two day workshop is taught by experienced Edinburgh Genomics’ bioinformaticians and 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. We then move on to using functions, including those specific to genomic science. We look at how to handle various genomic data files and where to find relevant tools via online resources. Finally we use mock RNA-seq data to learn how to visualize your data to generate publication ready plots using the package ggplot2.

Tutors: Nathan Medd, Training and Outreach Manager, Edinburgh Genomics; Hywel Dunn-Davis, Analyst - Developer, Edinburgh Genomics

Registration fee: £400 (includes coffee/tea, but no lunch)

Where: Microlabs, The Chancellors Buildings, Little France Campus (BioQuarter), Edinburgh.

Register here <https://www.surveymonkey.co.uk/r/83FGGXV>


Introduction to RNA-seq Data Analysis 18-20 November 2019 <https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis> *NEW THREE-DAY FORMAT*<https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis>
<https://genomics.ed.ac.uk/services/introduction-python-biologists-0>

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; Nathan Medd, Training and Outreach Manager, Edinburgh Genomics (demonstrator)

Registration fee: £500 (including lunches and refreshments)

Register here<https://www.surveymonkey.co.uk/r/9PGK7KX>


Introduction to Linux for Genomics<https://genomics.ed.ac.uk/services/introduction-linux-genomics> 04 December 2019


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).


Tutors: Tim Booth, Bioinformatician, Edinburgh Genomics; Nathan Medd, Training and Outreach Manager, Edinburgh Genomics

Registration fee: £225 (including lunches and refreshments)

Where: Microlab 2, The Chancellors Building, The University of Edinburgh, Little France Campus, Edinburgh, Scotland, UK


Register here<https://www.surveymonkey.co.uk/r/95GCMM8>



Advanced Python for Biologists <https://genomics.ed.ac.uk/services/advanced-python-biologists> 09-13 December 2019
<https://genomics.ed.ac.uk/services/introduction-python-biologists-0>


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.


Tutors: Martin Jones (Founder of Pythonforbiologists.com)

Registration fee: £550 (including lunches and refreshments)

Where: James Clerk Maxwell Building, Kings Buildings, University of Edinburgh, Edinburgh

Register here<https://www.surveymonkey.co.uk/r/2DKXBWM>


Can't see the course you need to progress your skills? Tell us what your training needs are by completing this short survey<https://www.surveymonkey.co.uk/r/7M6QB2D>.

Kind Regards

Nathan Medd

Training and Outreach Manager - Edinburgh Genomics



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