Bioinformatics course timetable
May 2015
Mon 11 |
Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Further information, including some training videos, is also available. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Tue 12 |
Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Further information, including some training videos, is also available. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Wed 13 |
Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Further information, including some training videos, is also available. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Thu 14 |
The aim of this course is to familiarise the participants with the primary analysis of datasets generated through two popular high-throughout sequencing (HTS) assays: ChIP-seq and RNA-seq. This course starts with a brief introduction to the transition from capillary to high-throughput sequencing and discusses quality control issues, which are common among all NGS datasets. Next, we will present the alignment step and how it differs between the two analysis workflows. Finally, we focus on dataset specific downstream analysis, including peak calling and motif analysis for ChIP-seq and quantification of expression, transcriptome assembly and differential expression analysis for RNA-seq. The timetable for this event 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 Interest by linking here. |
Fri 15 |
The aim of this course is to familiarise the participants with the primary analysis of datasets generated through two popular high-throughout sequencing (HTS) assays: ChIP-seq and RNA-seq. This course starts with a brief introduction to the transition from capillary to high-throughput sequencing and discusses quality control issues, which are common among all NGS datasets. Next, we will present the alignment step and how it differs between the two analysis workflows. Finally, we focus on dataset specific downstream analysis, including peak calling and motif analysis for ChIP-seq and quantification of expression, transcriptome assembly and differential expression analysis for RNA-seq. The timetable for this event 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 Interest by linking here. |
Mon 18 |
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 from scratch and to customize more complex code to fit their needs. The timetable for this event is available here. The Course Web Site providing links to the course materials is 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 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. Further information is available here. 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. |
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Tue 19 |
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 from scratch and to customize more complex code to fit their needs. The timetable for this event is available here. The Course Web Site providing links to the course materials is 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 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. Further information is available here. 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. |
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Wed 20 |
Introduction to Metabolomics
Finished
The aim of this course is to provide an overview of the applications, laboratory equipment and online bioinformatic portals for metabolomics research. The timetable for this event 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. |
Thu 21 |
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. Further information is available here. The Course Web Site providing links to the course materials is here. 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. |
Fri 22 |
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. Further information is available here. The Course Web Site providing links to the course materials is here. 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. |
Wed 27 |
This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Morning Timetable
Afternoon Timetable
Further information and access to the course materials is available. 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. |
Thu 28 |
Genome Annotation with Artemis
Finished
This one day workshop aims to give an introduction to Artemis and ACT (Artemis Comparison Tool). Both tools enable the visualization, analysis and comparison of genome data. They are freely available for all operating systems and can be downloaded here. This is a hands-on course with short talks introducing the tools. The course is taught by members of the Pathogen and Parasite Genomic Teams from the Wellcome Trust Sanger Institute. Further information is available 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 29 |
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
June 2015
Mon 1 |
This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment. During this course you will learn about:
The course timetable is available here. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Tue 2 |
This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment. During this course you will learn about:
The course timetable is available here. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Wed 3 |
This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in bam format. We will also describe the various resources available through Bioconductor to annotate and visualize HTS data, which can be applied to any type of sequencing experiment. During this course you will learn about:
The course timetable is available 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 5 |
This event provides an introduction to the EMBL-European Bioinformatics Institute (EMBL-EBI) resources. During the workshop we will introduce ways to navigate the EMBL-EBI website, search EMBL-EBI database resources and explore our bioinformatics tools, including sequence searching and alignment tools. It will also highlight additional resources such as Train Online. Also note: If you wish to learn any specific information about particular EMBL-EBI resources, then we will be running a series of separate short introductions later in the year, which will be bookable separately (see Related Courses below). Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Mon 8 |
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 from scratch and to customize more complex code to fit their needs. Further information is available here. The Course Web Site providing links to the course materials is here. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Tue 9 |
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 from scratch and to customize more complex code to fit their needs. Further information is available here. The Course Web Site providing links to the course materials is here. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Wed 10 |
This session provides an introduction to Network Analysis using Cytoscape and PSICQUIC [from the European Bioinformatics Institute (EBI)]. It is aimed at biologists and computer scientists wanting to learn the basics of network analysis. Further information for this session is available 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 session provides an introduction to Network Analysis using Cytoscape and PSICQUIC [from the European Bioinformatics Institute (EBI)]. It is aimed at biologists and computer scientists wanting to learn the basics of network analysis. Further information for this session is available here. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
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Thu 11 |
Galaxy (http://galaxyproject.org/) is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share bioinformatic analyses. The goal of this course is to demonstrate how to use Galaxy to explore RNA-seq data, for expression profiling, and ChIP-seq data, to assess genomic DNA binding sites. You will learn how to perform analysis in Galaxy, and then how to share, repeat, and reproduce your analyses. The timetable for this event 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 12 |
Galaxy (http://galaxyproject.org/) is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share bioinformatic analyses. The goal of this course is to demonstrate how to use Galaxy to explore RNA-seq data, for expression profiling, and ChIP-seq data, to assess genomic DNA binding sites. You will learn how to perform analysis in Galaxy, and then how to share, repeat, and reproduce your analyses. The timetable for this event 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. |