Linux is the operating system of high performance clusters and supercomputers all over the world. Learning to use Linux is a key part of making use of cutting edge bioinformatics tools. This course provides an extensive introduction to Linux, covering both basic and advanced use.
Keywords: John Innes Centre, JIC
Introduction to Linux: The operating system for bioinformaticshttp://training.scicomp.jic.ac.uk/docs/linux_intro_course_book/index.htmlhttps://tess.elixir-europe.org/materials/introduction-to-linux-the-operating-system-for-bioinformaticsLinux is the operating system of high performance clusters and supercomputers all over the world. Learning to use Linux is a key part of making use of cutting edge bioinformatics tools. This course provides an extensive introduction to Linux, covering both basic and advanced use.The John Innes CentreJohn Innes Centre, JICAny students, postdocs or RAs who have an interest in bioinformatics and who intend to conduct their own analyses on a Linux platform. Those intending to register for the upcoming Introduction to HPC course are very strongly encouraged to attend this short (two morning) course and it should be seen as a prerequisite for later courses to be offered on ChIP-Seq analysis and command line/Galaxy implementations of NGS workflows.
Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.
Scientific topics: Software engineering
Keywords: Python for Biologists, John Innes Centre, JIC
Python for Biologists: Programming for Scientific Computinghttp://training.scicomp.jic.ac.uk/docs/python_for_biologists_book/index.htmlhttps://tess.elixir-europe.org/materials/python-for-biologists-programming-for-scientific-computingPython is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.Tjelvar OlssonMatthew HartleySoftware engineeringPython for Biologists, John Innes Centre, JICFor beginners interested in using Python to solve problems in Biology.
R is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statistical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one...
Scientific topics: Software engineering, Statistics and probability
Keywords: John Innes Centre, JIC
Introduction to R: A software environment for statistical computinghttp://training.scicomp.jic.ac.uk/docs/r_intro_course_book/index.htmlhttps://tess.elixir-europe.org/materials/introduction-to-r-a-software-environment-for-statistical-computingR is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statistical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one package.The John Innes CentreSoftware engineeringStatistics and probabilityJohn Innes Centre, JICAny students, postdocs or RAs who have an interest in bioinformatics and who intend to carry out statistical analysis of their experimental data using R. This two day course is planned to be a very gentle introduction to the very basic concepts of R.
Perl is a powerful programming language that is heavily used in the bioinformatics community. This course will provide a full introduction to the basics of Perl, as well as how to carry out common bioinformatics tasks.
Scientific topics: Software engineering
Keywords: perl, John Innes Centre, JIC
Introduction to Perl: Programming for bioinformaticshttp://training.scicomp.jic.ac.uk/docs/perl_intro_course_book/index.htmlhttps://tess.elixir-europe.org/materials/introduction-to-perlPerl is a powerful programming language that is heavily used in the bioinformatics community. This course will provide a full introduction to the basics of Perl, as well as how to carry out common bioinformatics tasks.Govind ChandraSoftware engineeringperl, John Innes Centre, JICAny students, postdocs or RAs who have an interest in programming and who intend to carry out computational analysis of their experimental data. Perl is often used for preparing input files for more specialized software such as R, and also to post-process the output from R and various other bioinformatics tools. It is a glue language allowing you to build pipelines of analyses of arbitrary complexity. This two day course is planned to be a gentle introduction to the basic concepts of Perl and will also introduce you to the BioPerl library of modules.
Bioimaging is a rich source of data in biology. However, quantifying those data requires a strong understanding of the correct computational techniques. This course provides an introduction to those techniques, with a focus on transforming raw data from microscopes into meaningful information...
Scientific topics: Imaging, Biological imaging
Keywords: John Innes Centre, JIC
Computational Bioimaging: From images to datahttp://training.scicomp.jic.ac.uk/docs/bioimaging_course_book/index.htmlhttps://tess.elixir-europe.org/materials/computational-bioimagingBioimaging is a rich source of data in biology. However, quantifying those data requires a strong understanding of the correct computational techniques. This course provides an introduction to those techniques, with a focus on transforming raw data from microscopes into meaningful information about the systems studied.Matthew HartleyImagingBiological imagingJohn Innes Centre, JICThose interesting in exploring the data contained in their microscopy images, or those planning microscopy as part of their research programme
RNA-Seq provides a method for understanding transcriptional dynamics in biological systems. It has immense power to enhance our understanding of those systems, but carrying out RNA-Seq analysis requires use of multiple related software packages. This hands-on course provides experience in using...
Scientific topics: RNA, RNA-Seq
Keywords: John Innes Centre, JIC
Introduction to RNA-Seq Using Galaxy: Studying the transcriptomehttp://docs.scicomp.jic.ac.uk/galaxy_rnaseq_course_book/index.htmlhttps://tess.elixir-europe.org/materials/introduction-to-rna-seq-using-galaxyRNA-Seq provides a method for understanding transcriptional dynamics in biological systems. It has immense power to enhance our understanding of those systems, but carrying out RNA-Seq analysis requires use of multiple related software packages. This hands-on course provides experience in using these packages as part of an RNA-Seq analysis pipeline. Anmol J. HemromRNARNA-SeqJohn Innes Centre, JICStudents, postdocs or RAs who have an interest in bioinformatics and who intend to conduct RNA-Seq analysis on a Galaxy platform
Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The workbench interface is...
Galaxy for NGS analysis: A web-based platform for data intensive biological researchhttp://training.scicomp.jic.ac.uk/docs/galaxycourse_book/index.htmlhttps://tess.elixir-europe.org/materials/galaxy-for-ngs-analysisGalaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The workbench interface is simple and intuitive, supports collaboration and integrates data and analysis tools together in a single place. Anmol J. HemromWorkflowsHigh-throughput sequencingNucleic acid sequence analysisBioinformaticsJohn Innes Centre, JIC
