Introduction to Linux workflows for biologists (IBUL03) https://www.prinformatics.com/course/introduction-to-linux-workflows-for- biologists-ibul03/
This course will run from October 1st -5th October 2018 in Glasgow city centre and will be delivered by Dr Martin Jones. Course Overview: Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customize their environment and automate many parts of the bioinformatics workflow. This 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. Monday 1st Module 1: The design of Linux. In the first session we briefly cover the design of Linux: how is it different from Windows/OSX and how is it best used? We’ll then jump straight onto the command line and learn about the layout of the Linux file system and how to navigate it. We’ll describe Linux’s file permission system (which often trips up beginners), how paths work, and how we actually run programs on the command line. We’ll learn a few tricks for using the command line more efficiently, and how to deal with programs that are misbehaving. We’ll finish this session by looking at the built in help system and how to read and interpret manual pages. Module 2: System management. We’ll first look at a few command line tools for monitoring the status of the system and keeping track of what’s happening to processor power, memory, and disk space. We’ll go over the process of installing new software from the built in repositories (which is easy) and from source code downloads (which is trickier). We’ll also introduce some tools for benchmarking software (measuring the time/memory requirements of processing large datasets). Tuesday 2nd Module 3: Manipulating tabular data. Many data types we want to work with in bioinformatics are stored as tabular plain text files, and here we learn all about manipulating tabular data on the command line. We’ll start with simple things like extracting columns, filtering and sorting, searching for text before moving on to more complex tasks like searching for duplicated values, summarizing large files, and combining simple tools into long commands. Module 4: Constructing pipelines. In this session we will look at the various tools Linux has for constructing pipelines out of individual commands. Aliases, shell redirection, pipes, and shell scripting will all be introduced here. We’ll also look at a couple of specific tools to help with running tools on multiple processors, and for monitoring the progress of long running tasks. Wednesday 3rd – Classes from 09:00 to 17:00 Module 5: EMBOSS. EMBOSS is a suite of bioinformatics command-line tools explicitly designed to work in the Linux paradigm. We’ll get an overview of the different sequence data formats that we might expect to work with, and put what we learned about shell scripting to biological use by building a pipeline to compare codon usage across two collections of DNA sequences. Module 6: – Using a Linux server. Often in bioinformatics we’ll be working on a Linux server rather than our own computer— typically because we need access to more computing power, or to specialized tools and datasets. In this session we’ll learn how to connect to a Linux server and how to manage sessions. We’ll also consider the various ways of moving data to and from a server from your own computer, and finish with a discussion of the considerations we have to make when working on a shared computer. Thursday 4th Module 7: Combining methods. In the next two sessions — i.e. one full day — we’ll put everything we have learned together and implement a workflow for next-gen sequence analysis. In this first session we’ll carry out quality control on some paired-end Illumina data and map these reads to a reference genome. We’ll then look at various approaches to automating this pipeline, allowing us to quickly do the same for a second dataset. Module 8: Combining methods. The second part of the next-gen workflow is to call variants to identify SNPs between our two samples and the reference genome. We’ll look at the VCF file format and figure out how to filter SNPs for read coverage and quality. By counting the number of SNPs between each sample and the reference we will try to figure out something about the biology of the two samples. We’ll attempt to automate this analysis in various ways so that we could easily repeat the pipeline for additional samples. Friday 5th Module 9: Customization. Part of the Linux design is that everything can be customized. This can be intimidating at first but, given that bioinformatics work is often fairly repetitive, can be used to good effect. Here we’ll learn about environment variables, custom prompts, soft links, and ssh configuration — a collection of tools with modest capabilities, but which together can make life on the command line much more pleasant. In this last session there will also be time to continue working on the next-gen sequencing pipeline. The afternoon of Friday 19th is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel. Email oliverhoo...@prinformatics.com with any questions Check out our sister sites, www.PRstatistics.com (Ecology and Life Sciences) www.PRinformatics.com (Bioinformatics and data science) www.PSstatsistics.com (Behaviour and cognition) Upcoming courses 1. April 9th – 13th 2018 NETWORK ANAYLSIS FOR ECOLOGISTS USING R (NTWA02 Glasgow, Scotland, Dr. Marco Scotti www.prstatistics.com/course/network-analysis-ecologists-ntwa02/ 2. April 16th – 20th 2018 INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R (IPSY01) Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre http://www.psstatistics.com/course/introduction-to-statistics-using-r-for- psychologists-ipsy01/ 3. April 23rd – 27th 2018 MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE (VGNR01) Glasgow, Scotland, Dr. Peter Solymos, Dr. Guillaume Blanchet www.prstatistics.com/course/multivariate-analysis-of-ecological-communities- in-r-with-the-vegan-package-vgnr01/ 4. April 30th – 4th May 2018 QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND COMMUNITIES (QGER01) Glasgow, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick www.prstatistics.com/course/quantitative-geographic-ecology-using-r- modelling-genomes-niches-and-communities-qger01/ 5. May 7th – 11th 2018 ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R (MVSP02) CANADA (QUEBEC), Prof. Pierre Legendre, Dr. Guillaume Blanchet www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate- ecological-data-theory-and-practice-mvsp03/ 6. May 14th - 18th 2018 INTRODUCTION TO MIXED (HIERARCHICAL) MODELS FOR BIOLOGISTS (IMBR01) CANADA (QUEBEC), Prof Subhash Lele www.prstatistics.com/course/introduction-to-mixed-hierarchical-models-for- biologists-using-r-imbr01/ 7. May 21st - 25th 2018 INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB05) SCENE, Scotland, Dr. Martin Jones http://www.prinformatics.com/course/introduction-to-python-for-biologists- ipyb05/ 8. May 21st - 25th 2018 INTRODUCTION TO REMOTE SENISNG AND GIS FOR ECOLOGICAL APPLICATIONS (IRMS01) Glasgow, Scotland, Prof. Duccio Rocchini, Dr. Luca Delucchi www.prinformatics.com/course/introduction-to-remote-sensing-and-gis-for- ecological-applications-irms01/ 9. May 28th – 31st 2018 STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04) CANADA (QUEBEC) Dr. Andrew Parnell, Dr. Andrew Jackson www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/ 10. May 28th – June 1st 2018 ADVANCED PYTHON FOR BIOLOGISTS (APYB02) SCENE, Scotland, Dr. Martin Jones www.prinformatics.com/course/advanced-python-biologists-apyb02/ 11. June 12th - 15th 2018 SPECIES DISTRIBUTION MODELLING (DBMR01) Myuna Bay sport and recreation, Australia, Prof. Jane Elith, Dr. Gurutzeta Guillera www.prstatistics.com/course/species-distribution-models-using-r-sdmr01/ 12. June 18th – 22nd 2018 STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS USING R (SEMR02) Myuna Bay sport and recreation, Australia, Dr. Jon Lefcheck www.prstatistics.com/course/structural-equation-modelling-for-ecologists- and-evolutionary-biologists-semr02/ 13. June 25th – 29th 2018 SPECIES DISTRIBUTION/OCCUPANCY MODELLING USING R (OCCU01) Glasgow, Scotland, Dr. Darryl McKenzie www.prstatistics.com/course/species-distributionoccupancy-modelling-using-r- occu01/ 14. July 2nd - 5th 2018 SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R (SNAR01) Glasgow, Scotland, Prof James Curley http://www.psstatistics.com/course/social-network-analysis-for-behavioral- scientists-snar01/ 15. July 8th – 12th 2018 MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R (MBMV02) Glasgow, Scotland, Prof David Warton www.prstatistics.com/course/model-base-multivariate-analysis-of-abundance- data-using-r-mbmv02/ 16. July 16th – 20th 2018 PRECISION MEDICINE BIOINFORMATICS: FROM RAW GENOME AND TRANSCRIPTOME DATA TO CLINICAL INTERPRETATION (PMBI01) Glasgow, Scotland, Dr Malachi Griffith, Dr. Obi Griffith www.prinformatics.com/course/precision-medicine-bioinformatics-from-raw- genome-and-transcriptome-data-to-clinical-interpretation-pmbi01/ 17. July 23rd – 27th 2018 EUKARYOTIC METABARCODING (EUKB01) Glasgow, Scotland, Dr. Owen Wangensteen http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/ 18. October 8th – 12th 2018 INTRODUCTION TO SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (ISAE01) Glasgow, Scotland, Prof. Subhash Lele https://www.prstatistics.com/course/introduction-to-spatial-analysis-of- ecological-data-using-r-isae01/ 19. October 15th – 19th 2018 APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (ABME Glasgow, Scotland, Dr. Matt Denwood, Emma Howard http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists- epidemiologists-abme04/ 20. October 29th – November 2nd 2018 PHYLOGENETIC COMPARATIVE METHODS FOR STUDYING DIVERSIFICATION AND PHENOTYPIC EVOLUTION (PCME01) Glasgow, Scotland, Prof. Subhash Lele Dr. Antigoni Kaliontzopoulou https://www.prstatistics.com/course/phylogenetic-comparative-methods-for- studying-diversification-and-phenotypic-evolution-pcme01/ 21. November 26th – 30th 2018 FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND COMPUTATION (FEER Glasgow, 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/ 22. February 2018 TBC MOVEMENT ECOLOGY (MOVE02) Margam Discovery Centre, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr Jonathan Potts www.prstatistics.com/course/movement-ecology-move01/
