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SeqMonk is a graphical program for the visualisation and analysis of large mapped datasets such as ChIP-Seq, RNA-Seq, and BS-Seq. 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.

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.

This course is aimed at those new to programming and provides an introduction to programming using Perl.

During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures.

The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside.

The course website 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 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.

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.

This workshop introduces the area of sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases. This session will include tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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 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 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.

• This course will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

• It is aimed at researchers who are applying or planning to apply image analysis in their research

• On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based around Fiji, an extensible open source software package.

• On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.

• On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.

• A draft agenda can be found here.

• This event is sponsored by the Systems Microscopy NoE.

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.

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 their own bioinformatic analyses. This introductory course will cover Galaxy's basic functionality, simple data manipulation and visualization. This event is mostly targeted at first time users. Further information is available from the course website.

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

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.

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

• Introduction
• Data Visualisation Theory
• Coffee
• Data Representation Practical
• Ethics talk

Afternoon Timetable

• Design theory talk
• Ethics practical
• GIMP Tutorial
• GIMP Practical
• Coffee
• Inkscape Tutorial
• Inkscape Practical
• Final practical

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.

This course provides an introduction to next generation sequencing (NGS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply NGS technologies and bioinformatics methods in their 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 or register Interest by linking here.

• Nowomics - Access to the latest data and papers relevant to your research
• Nowomics is a new website to help biologists stay up to date with the latest data and papers relevant to their research. Try it here.
• Nowomics tracks new papers and many types of data in online repositories. You ‘follow’ the genes and processes you work on to see a Twitter-like news feed of new papers, annotation, interactions, curated comments and more.
• For each gene you can also include information from orthologues and related genes directly in your news feed.
• Data are currently included for human, mouse, rat, fly and plant.
• This short workshop will show you how to use the Beta version of Nowomics to find the latest information for genes & keywords, how to set up your personalised news feed and configure email alerts. We’ll also demonstrate new portals to help researchers working on Drosophila or Arabidopsis find the latest and most popular papers.

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

This practical-based course will deal with all aspects of the prediction of protein structure, concentrating on the prediction of secondary structure, fold recognition and comparative modelling of structures. Computational aspects of protein structure determination, validation and analysis will be covered. The course will be a mixture of talks and guided practicals. 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.

The course will present intermediate to advanced R programming using the object-oriented programming paradigm. It will cover how to document code and data to produce a fully functional R package. 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 register Interest by linking here.

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

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 workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team.

• You will learn why each step is essential to the variant calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. Special attention will be given to the newest functionalities in GATK3, including joint discovery in cohorts and RNAseq analysis.

• The workshop will last two days, with a day and a half of lectures (including many opportunities for Q&A) and one half day of hands-on training.

• On the first day, we will explain the rationale, theory and real-life applications of our Best Practices for Variant Discovery in high-throughput sequencing data.

• On the second day, in the morning we will cover additional topics such as the differences between whole genome vs. exome analysis, sequence data QC metrics, and how to apply GATK to non-model organisms. In the afternoon, we will hold a hands-on session in which attendees will learn to interact with the GATK tools and apply them effectively.

• The lecture-based component of the workshop is aimed at a mixed audience of people who are new to GATK seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. The hands-on component is aimed mainly at beginners who have basic familiarity with the command line environment.

• A draft agenda can be found here.

• This event is sponsored by eLife.

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 covers state-of-the-art tools and methods for NGS RNA-seq and exome variant data analysis, which are of major relevance in today's genomic and gene expression studies.

It is oriented to experimental researchers, post-doctoral and PhD students who want to learn about the state-of-the-art of genomic variant and transcriptomics data analysis methodologies and carry out their own analysis.

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.