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Bioinformatics for geneticists and biologists

Oliver Hooker, March 31, 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@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@prstatistics.com

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  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

3/1 128 Brunswick Street Glasgow G1 1TF

+44 (0) 7966500340

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

-- Oliver Hooker PhD. PR statistics

2017 publications - 2) Ecosystem size predicts eco-morphological variability in post-glacial diversification. Ecology and Evolution. In press. 1) The physiological costs of prey switching reinforce foraging specialization. Journal of animal ecology.

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3/1, 128 Brunswick Street Glasgow G1 1TF

+44 (0) 7966500340