Bioinformatics 2017

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

The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets.

This course provides an introduction to the main features of SeqMonk and will run through the analysis of a couple of different datasets to show what sort of analysis options it provides.

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 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 is aimed at researchers who want to learn core skills and best practices for scientific computing. It will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

The course covers the core skills needed to be productive in a small research team:

• Unix command line (and how to automate repetitive tasks);
• Python or R (and how to grow a program in a modular, testable way); and
• version control with Git (and how to track and share work efficiently).

Further information is available here.

Applicants for this course are requested to complete a pre-course survey. This will be used to tailor the course content to the audience research interests and background.

This event is organized in collaboration with Software Carpentry.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book 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 workshop will give an introduction to the Reactome pathway database website and analysis tools, using short presentations and practical hands-on exercises. The session will also explain where to learn more, get help, and how to become involved in adding more pathway information to Reactome.

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 by linking here.

This workshop is an introduction to EMBL-EBI and the life science data resources it provides. Participants will be shown how to navigate the website and search for appropriate database resources and tools, whilst also highlighting resources such as Train online (our e-learning portal) and the literature resources at Europe PMC.

The timetable for this event can be found here.

This workshop will not focus on a set of specific resources; for more focused workshops please see the others within this series (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 by linking here.

This workshop will give an introduction to the functional genomics resources provided by EMBL-EBI and hands-on practical experience of searching and accessing appropriate data and information. The session will also cover data submission to ArrayExpress using Annotare.

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 by linking here.

Galaxy 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 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.