Bioinformatics 2017

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information.

This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.

Materials for this event are available here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This course focuses on methods for the analysis of small non-coding RNA data obtained from high-throughput sequencing (HTS) applications (small RNA-seq). During the course, approaches to the investigation of all classes of small non-coding RNAs will be presented, in all organisms.

Day 1 will focus on the analysis of microRNAs and day 2 will cover the analysis of other types of small RNAs, including Piwi-interacting (piRNA), small interfering (siRNA), small nucleolar (snoRNA) and tRNA-derived (tsRNA).

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented.

The course website providing links to the course materials is here.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This course provides an introduction to the R programming language and software environment for statistical computing and graphics. A variety of examples with a biological theme will be presented.

The course website providing links to the course materials is here.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

• an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
• an overview of available analytical tools and discussion of their limitations; and
• hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

• an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
• an overview of available analytical tools and discussion of their limitations; and
• hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This three day workshop will bring together representatives of the ELIXIR Galaxy Working Group, as well as trainers and developers working on the Galaxy project from Europe and beyond, to:

• Build on an existing collection of Galaxy training materials. During the workshop we will collate additional materials, including topics relevant to the ELIXIR use-cases, and ensure that, for each workflow, a minimum set of training materials is available, including slides, practical exercises, Docker containers, and Galaxy tours.
• Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop materials will be curated to ensure they are properly described, according to the ELIXIR/GOBLET guidelines, and BioSchemas compliant.
• Extend the existing “curated” dataset collection and assign DOI to individual datasets.
• Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments.
• Explore the feasibility of developing a toolkit to facilitate plug in of different datasets in existing training material/workflows through a templating approach.

This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

This three day workshop will bring together representatives of the ELIXIR Galaxy Working Group, as well as trainers and developers working on the Galaxy project from Europe and beyond, to:

• Build on an existing collection of Galaxy training materials. During the workshop we will collate additional materials, including topics relevant to the ELIXIR use-cases, and ensure that, for each workflow, a minimum set of training materials is available, including slides, practical exercises, Docker containers, and Galaxy tours.
• Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop materials will be curated to ensure they are properly described, according to the ELIXIR/GOBLET guidelines, and BioSchemas compliant.
• Extend the existing “curated” dataset collection and assign DOI to individual datasets.
• Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments.
• Explore the feasibility of developing a toolkit to facilitate plug in of different datasets in existing training material/workflows through a templating approach.

This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

This three day workshop will bring together representatives of the ELIXIR Galaxy Working Group, as well as trainers and developers working on the Galaxy project from Europe and beyond, to:

• Build on an existing collection of Galaxy training materials. During the workshop we will collate additional materials, including topics relevant to the ELIXIR use-cases, and ensure that, for each workflow, a minimum set of training materials is available, including slides, practical exercises, Docker containers, and Galaxy tours.
• Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop materials will be curated to ensure they are properly described, according to the ELIXIR/GOBLET guidelines, and BioSchemas compliant.
• Extend the existing “curated” dataset collection and assign DOI to individual datasets.
• Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments.
• Explore the feasibility of developing a toolkit to facilitate plug in of different datasets in existing training material/workflows through a templating approach.

This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.

This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers using the REST API to query the core, variation, compara and functional genomics (regulation) databases.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.

This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers using the REST API to query the core, variation, compara and functional genomics (regulation) databases.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

The workshop will cover the basics of de novo genome assembly using a small genome example. This includes project planning steps, selecting fragment sizes, initial assembly of reads into fully covered contigs, and then assembling those contigs into larger scaffolds that may include gaps. The end result will be a set of contigs and scaffolds with sufficient average length to perform further analysis on, including genome annotation (link to that nomination). This workshop will use tools and methods targeted at small genomes. The basics of assembly and scaffolding presented here will be useful for building larger genomes, but the specific tools and much of the project planning will be different.

This workshop will also introduce genome annotation in the context of small genomes. We’ll begin with genome annotation concepts, and then introduce resources and tools for automatically annotating small genomes. The workshop will finish with a review of options for further automatic and manual tuning of the annotation, and for maintaining it as new assemblies or information becomes available.

This session will include an introduction to the Galaxy platform.

This event is co-organized with EMBL-ABR and the Genomics Virtual Lab. Course materials can be found here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs.

Course materials are available here.

Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs.

Course materials are available here.

Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Working with Python: functions and modules.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

This course will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications.

It will also include exploratory analysis of methylation, looking at different methods of quantitation, and a variety of ways of looking more widely at the distribution of methylation over the genome. Finally the course will look at statistical methods to predict differential methylation.

The course will be comprised of a mixture of theoretical lectures and practicals covering a range of different software packages.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.