We currently have three courses scheduled for the first half of 2014, click on the links below, or scroll down for more information.
- Ensembl (1st – 2nd April)
- Bioconductor (12th – 16th May)
- Command Line Bioinformatics and High Throughput Sequencing Analysis – TBA
See the foot of the page for general information such as pricing and how to book.
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. This two-day course, run by Denise Carvalho-Silva and Thomas Juettemann from the European Bioinformatics Institute (EBI) will introduce attendees to the Ensembl genome browser and a number of associated tools for dealing with genomic scale data. Amongst other things the course can cover:
- Introduction to Ensembl: origin, goals and organization of the Ensembl project.
- Worked example: guided tour of the most important pages of the Ensembl website.
- Data mining with BioMart: retrieving genomic information using a web interface (no programming required).
- Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions.
- Variation: SNPs, CNVs, VEP, phenotypes.
- Regulation: ENCODE data hub, and annotation of regulatory elements based on ChIP-Seq, DNase1-Seq, FAIRE-Seq and TFBS.
This course is run in conjunction with Colin Gillespie of the School of Mathematics and Statistics, and teaches the fundamentals of the R statistical programming language and the Bioconductor suite of bioinformatics analysis tools. Course participants will learn how to use R for data manipulation and visualisation, and how to use Bioconductor to analyse biological data. The final day will provide an opportunity for participants to bring along their own data and get some expert help on how to tackle their own specific analysis.
More information about the course is available here: http://www.ncl.ac.uk/maths/rcourse/bioconductor.html
4th – 6th February 2014
Many powerful bioinformatics applications do not come packaged with an easy-to-use graphical user interface. Since many people are unfamiliar and uncomfortable with the command-line interface that is necessary to get such applications to work, they are unable to unlock the full potential of the valuable data they are generating. The aim of this course is to enable scientists with no prior exposure to a command-line interface to get up and running with this kind of work, and provide them with the fundamentals to use any command-line application. We will start from the basics (not assuming any prior knowledge), and will move through popular bioinformatics tools such as BLAST. The second and third days of the course will focus on tools for the analysis of high-throughput (or “next generation”) sequencing data.
Linux Basics – What is Linux? What is it good for? An introduction to many basic command-line tools that we’ll build upon in the rest of the course.
BLAST – Have you ever found yourself filling in the BLAST form on the NCBI website over and over? Wondering that there must surely be a better way? There is – command-line BLAST lets you run all of those searches with a single command, and gives you far more flexibility and power than the web app ever will.
Multiple Sequence Alignments – A natural extension from the pairwise alignments of BLAST – how are all those sequences you’ve identified in your search related to one another? In this session we’ll cover tools such as ClustalW and MUSCLE.
HMMER – More powerful sequence similarity searches and domain finding with Hidden Markov Models.
Introduction to NGS technologies, file formats such as SAM, BAM and BED, common tools such as SAMtools and BEDTools and de novo High Throughput Sequence Assembly using Velvet.
High Throughput Sequence Alignment (mapping to a reference genome) using tools such as Bowtie.
Tools for RNA-Seq Analysis (‘Tuxedo’ pipeline: TopHat, Bowtie, Cufflinks)
RNA-Seq cont. (possibility for other analysis tools at attendees request).
Spaces can be reserved for the High Throughput Sequence Analysis and Ensembl courses for internal Newcastle University staff by clicking on the links in the table below, spaces on all other courses and for external people can be reserved by emailing Simon Cockell. The Bioconductor course is booked via the school of Mathematics and Statistics. All courses are subject to a fee.
Costs for Newcastle University Faculty of Medical Sciences attendees are subsidised, except for the Bioconductor course (which is run in conjunction with the school of Mathematics and Statistics).
|Booking links (Cost)|
|Course||Length||Newcastle University – FMS||Newcastle University – Other||External – Academic/NHS/Charity||External – Commercial|
currently full, email us for dates of subsequent courses
|3 days||Book (£100)||Book (£300)||Book (£360)||Book (£450)|
|Ensembl||2 days||Book (£75)||Book (£75)||Book (£75)||Book (£150)|
|Bioconductor||5 days||Book (£560)||Book (£560)||Book (£640)||Book (£800)|
Cancellations up to 14 days before the course start date will incur a 30 per cent cancellation fee. For later cancellations, or non attendance, the full course fee will be charged. (edit)