[R-sig-genetics] UK.BioinformaticsForGeneticistsAndBiologists.July3-7

Thu Mar 23 11:46:45 CET 2017

‘Bioinformatics for geneticists and biologists (BIGB02)

Delivered by Dr. Nic Blouin and Dr Ian Misner

http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

This course will run from 3rd – 7th July 2017 at SCENE Field Station, 
Loch Lomond, Glasgow

OVERVIEW
The handling of large datasets has become intractable without some level 
of bioinformatic literacy. Many biologists find that there is a steep 
learning curve to develop the confidence required to explore their 
genomics datasets effectively. This bioinformatics short course includes 
a rich collection of hands-on instruction and lectures specifically 
intended to help novice users become comfortable with a range of tools 
currently used to analyse next-generation data.

INTENDED AUDIENCE
The course is aimed at anyone interested in learning bioinformatics 
tools needed for handling large genomic datasets.

Course content is as follows

Monday 3rd – Classes from 09:00 to 17:00
Module 1: Linux.
Linux is taught on the first day, this takes the entire day. Once you 
get through this portion you will be on your way to completing your own 
NGS analysis. We have created a workbook for this portion of the course. 
This is a step-by-step, or in the case, command-by-command, Linux guide. 
We complete each command as a class and discuss and review issues along 
the way.

Tuesday 4th – Classes from 09:00 to 17:00
Module 2: RNAseq.
We will cover two of the more popular tools in this workshop, The Tuxedo 
package & Trinity. Outcomes; Confidence to design effective RNAseq 
experiments. Knowledge of NGS sequencing platforms and their differing 
applications, ability to analyze Illumina data for quality and 
contamination. Proficiency to implement the Tuxedo package to analyze an 
RNAseq dataset.Create publication ready graphics with cummeRbund and 
EdgeR.

Wednesday 5th – Classes from 09:00 to 17:00
Module 3: Assembly.
Whether you have a reference genome or are working with de novo samples 
there are some basic tools and practices that we cover to help assist 
you in your genome project. In this module we will cover the basic 
metrics you should review when doing assembly as well as best practices 
to consider in your own project. Outcomes; Take raw reads through a 
complete assembly process. Working knowledge of different assembly 
issues/challenges. The effect of assembly settings on assembly outcomes.

Thursday 6th – Classes from 09:00 to 17:00
Module 4: Annotation.
We will use MAKER and Blast2GO and annotate the genome we assembled in 
the assembly module. Outcomes; Understand the differences between 
functional and structural annotations. Train MAKER to improve structural 
annotations. Understand how MAKER improves with more evidence and 
training; visualize structural annotations. Apply functional annotations 
with Blast2GO.

Friday 7th – Classes from 09:00 to 16:00
Module 5: Python.
Why Python? In truth it doesn’t matter what coding language you learn 
but you should learn one. Python has a very straightforward syntax that 
is easy to understand.In this module we will utilise the clearly 
explained training examples from Python for Biologists. Outcomes; 
Understand Python language syntax. Create scripts to answer biological 
problems & parse and analyse BLAST outputs using custom Python code.

Please email any inquiries to oliverhooker at prstatistics.com or visit our 
website www.prstatistics.com

Please feel free to distribute this material anywhere you feel is 
suitable

Upcoming courses - email for details oliverhooker at prstatistics.com

1.	ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R 
#MVSP
3rd – 7th April 2017, Scotland, Prof. Pierre Legendre, Dr. Olivier 
Gauthier
http://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp02/

2.	ADVANCING IN STATISTICAL MODELLING FOR EVOLUTIONARY BIOLOGISTS AND 
ECOLOGISTS USING R #ADVR
17th – 21st April 2017, Scotland, Dr. Luc Bussiere, Dr. Ane Timenes 
Laugen
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr06/

3.	CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR 
EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR
15th - 19th May, Scotland Dr. Aline Quadros
http://www.prstatistics.com/course/coding-data-management-and-shiny-applications-using-rstudio-for-evolutionary-biologists-and-ecologists-cdsr01/

4.	GEOMETRIC MORPHOMETRICS USING R #GMMR
5th – 9th June 2017, Scotland, Prof. Dean Adams, Prof. Michael 
Collyer, Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

5.	MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE
19th – 23rd June, Canada, Prof. Subhash Lele, Dr. Peter Solymos
http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/

6.	TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
26th – 30th June, Canada, Dr. Andrew Parnell
http://www.prstatistics.com/course/time-series-models-foe-ecologists-tsme01/

7.	BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS #BIGB
3rd – 7th July 2017, Scotland, Dr. Nic Blouin, Dr. Ian Misner
http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/

8.	META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES 
#METR01
24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena 
Kulinskaya
http://www.prstatistics.com/course/meta-analysis-in-ecology-evolution-and-environmental-sciences-metr01/

9.	SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE
7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James 
Grecian
http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/

10.	ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/

11.	INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL
16th – 20th October, Scotland, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/

12.	GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR
23rd – 27th October, Wales, Dr. Thibaut Jombart, Zhian Kavar
http://www.prstatistics.com/course/genetic-data-analysis-exploration-using-r-gdar03/

13.	STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY 
BIOLOGISTS USING R #SEMR
23rd – 27th October, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck
http://www.prstatistics.com/course/structural-equation-modelling-for-ecologists-and-evolutionary-biologists-semr01/

14.	LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
6th – 10th November, Wales, Prof. Rodney Dyer
http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg02/

15.	APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
20th - 25th November 2017, Scotland, Prof. Jason Matthiopoulos, Dr. Matt 
Denwood
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/

16.	INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS 
#IRMS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
http://www.prstatistics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/

17.	INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
27th Nov – 1st Dec, Wales, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-python-for-biologists-ipyb04/

18.	DATA VISUALISATION AND MANIPULATION USING PYTHON #DVMP
11th – 15th December 2017, Wales, Dr. Martin Jones
http://www.prstatistics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/

19.	ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, 
Dr. Ane Timenes Laugen,
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/

20.	INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/

21.	ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
??th - ??th February 2018, Wales, Dr Luca Borger, Dr. John Fieberg

22.	AQUATIC TELEMENTRY DATA ANALYSIS USIR R (TBC) #ATDAR
??th - ??th February 2018, Wales,

23.	FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND 
COMPUTATION #FEER
5th – 9th March 2018, Scotland, Dr. Francesco de Bello, Dr. Lars 
Götzenberger, Dr. Carlos Carmona
http://www.prstatistics.com/course/functional-ecology-from-organism-to-ecosystem-theory-and-computation-feer01/

24.	STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be 
confirmed

25.	NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed

26.	MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
Prof David Warton - Date and location to be confirmed

27.	ADVANCED PYTHON FOR BIOLOGISTS #APYB
Dr. Martin Jones - Date and location to be confirmed

28.	PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
Dr. Emmanuel Paradis – Date and location to be confirmed

Oliver Hooker PhD.
PR statistics

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Glasgow
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+44 (0) 7966500340

www.prstatistics.com
www.prstatistics.com/organiser/oliver-hooker/

-- 
Oliver Hooker PhD.
PR statistics

most recent publication - The physiological costs of prey switching 
reinforce foraging specialization - Journal of animal ecology - 
http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12632/full
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