All-provider course timetable

Microsoft Excel is the chosen spreadsheet package as it is a popular choice, both on Apple Mac and PC. This is an instructor-led course for absolute beginners. There is a self-paced Excel Beginners course for those who prefer to learn at their own pace.

This workshop will focus on the core steps involved in calling germline short variants, somatic short variants, and copy number alterations with the Broad’s Genome Analysis Toolkit (GATK), using “Best Practices” developed by the GATK methods development team. A team of methods developers and instructors from the Data Sciences Platform at Broad will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are 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. If you are an experienced GATK user, you will gain a deeper understanding of how the GATK works under-the-hood and how to improve your results further, especially with respect to the latest innovations.

• Day 1: Introductory and Overview. The first day of the workshop gives a high-level overview of various topics in the morning, and in the afternoon we show how these concepts apply to a case study. The case study is tailored based on the audience, as represented by their answers in our pre-workshop survey.

• Day 2: Germline Short Variant Discovery. Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.

• Day 3: Somatic Variant Discovery. Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.

• Day 4: Pipelining. Over the first three days, you would have learned a lot about different pipelines and tools that you can use in GATK. Today we will be learning all about how those pipelines are written in a language called WDL. In the afternoon we cover other useful topics to working on the cloud, including Docker and BigQuery.

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

The hands-on GATK tutorials in this workshop will be conducted on Terra, a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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 intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

1. Use R confidently for statistics and data analysis
2. Be able to analyse datasets using standard statistical techniques
3. Know which tests are and are not appropriate

R is a free, software environment for statistical and data analysis, with many useful features that promote and facilitate reproducible research.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to generalised linear model analysis. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

In 1906, Melvil Dewey wrote that ‘what we call books have no exclusive rights in a library. The name “library” has lost its etymologic meaning and means not a collection of books, but the central agency for disseminating information, innocent recreation or, best of all, inspiration among the people.’ Most libraries contain mostly books. But most libraries have other things in them too. Some of these things – films, musical recordings, maps, sheet music – have standard cataloguing practices. But what about flashcards, skeletons, jigsaws, bookstands, postage stamps, DVD players, and the many other odds and ends we collate, curate and circulate. Should they be catalogued? Perhaps. Can they be catalogued? Certainly. This course provides an introduction to the theory and practice of cataloguing ‘realia.’ Examples will be provided for group cataloguing activities, but feel free to bring along your own unusual library materials too.

This participative, discussion based workshop will provide an opportunity to reflect on how students with mental health difficulties can be supported in postgraduate study. It will cover best practice in supporting students and update on services available to all involved.

Whether you are considering collaborating on dynamic projects with small business; want to work better with an industrial partner or you are considering commercialising your research, this programme will develop the people management skills and self-awareness that help you to manage the Human Factor challenges.

Workshop content includes:

• Build a successful organisational culture
• How to be productive and manage workload
• Develop business analysis and influencing skills
• Understand professional interpersonal relations
• Improve your resilience when managing change
• Manage stress and make good decisions

Giving presentations is an essential skill for a researcher, be it in your deparment, at a major conference, or in your next job interview! You know your subject but sometimes issues of performance and clarity stop you being your best. Perhaps you can't project your voice, perhaps you are terrified of the Q&A, perhaps you feel your slides let you down, or perhaps you just don't know what to do to get better.

This is a highly interactive workshop that requires you to throw yourself into the activities. Everyone will be involved as we apply some of the material from the online Presentation and Performance toolkit and try it out in a safe and supportive environment.

The workshop is especially designed for those who feel less confident with the performance aspects of giving presentations. If you are comfortable standing up and talking in front of others then we recommend starting with the online materials.