Bioinformatics course timetable
April 2017
Wed 19 |
Molecular Phylogenetics
Finished
This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses. Delegates will gain hands-on practice of using a variety of programs freely-available online and commonly used in molecular studies, interspersed with some lectures. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Thu 20 |
Molecular Phylogenetics
Finished
This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses. Delegates will gain hands-on practice of using a variety of programs freely-available online and commonly used in molecular studies, interspersed with some lectures. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Fri 21 |
Molecular Phylogenetics
Finished
This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses. Delegates will gain hands-on practice of using a variety of programs freely-available online and commonly used in molecular studies, interspersed with some lectures. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Mon 24 |
This course provides a refresher on the foundations of statistical analysis. The emphasis is on interpreting the results of a statistical test, and being able to determine the correct test to apply. Practicals are conducted using a series of online apps, and we will not teach a particular statistical analysis package, such as R. For courses that teach R, please see the links under "Related courses" . 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 Interest by linking here. |
Tue 25 |
The course will teach intermediate R object-oriented programming and how to build a fully functional R package. The course page includes slides and handouts; other relevant teaching materials are available here) and the sequences example package used as template in the course can be found 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. |
Wed 26 |
Statistical Analysis using R
Finished
Statistics are an important part of most modern studies and being able to effectively use a statistical package will help you to understand your results. This course provides an introduction to some statistical techniques through the use of the R language. Topics covered include: Chi2 and Fisher tests, descriptive statistics, t-test, analysis of variance and regression. Students will run analyses using statistical and graphical skills taught during the session. The course manual 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. |
Fri 28 |
This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code. In the morning session, we will briefly go over the basic syntax, data structures and control statements. This will be followed by an introduction to writing user-defined functions. We will finish the course by looking into how to incorporate existing python modules and packages into your programs as well as writing you own modules. Course materials can be found here. Note: this one-day course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
May 2017
Tue 2 |
Analysis of small RNA-seq data
Finished
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. |
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. |
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Wed 3 |
Analysis of small RNA-seq data
Finished
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. |
Thu 4 |
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. |
Fri 5 |
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. |
Mon 15 |
This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register 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. |
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Tue 16 |
This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register 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. |
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Wed 17 |
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. |
Thu 18 |
This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:
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. |
Fri 19 |
This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:
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. |
Mon 22 |
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:
This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559. |
Tue 23 |
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:
This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559. |
Wed 24 |
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:
This event is supported by ELIXIR-EXCELERATE, an European Commission grant within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559. |
Thu 25 |
Ensembl REST API workshop
Finished
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. |
Fri 26 |
Ensembl REST API workshop
Finished
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. |
June 2017
Thu 8 |
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. |