All Graduate School of Life Sciences courses

Learn the basics of Twitter by completing 1 short online activity per day, for 10 days and join the global network of researchers who already use it (http://www.nature.com/news/online-collaboration-scientists-and-the-social-network-1.15711)

This is an online course - you will NOT be required to attend a workshop session.

Tasks will cover:

• the basics – how to set up an account, follow people and send tweets
• the conventions (@, #, RT, etc.)
• etiquette and social conventions
• the plethora of ‘apps’ or third party tools to add on
• strategies for tweeting effectively and building a network

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 introduce the R language, and cover basic data manipulation and plotting. We explore more advanced data analysis techniques using the packages dplyr and ggplot. Finally we introduce the concept of reproducible research, and how this may be assisted using 'literate programming'—combining documentation with code.

After the course you should feel confident to start exploring your own dataset, using the materials and references provided.

Sessions

If you book onto this course you must attend all of the sessions as detailed below. Failure to attend a session or cancellation of your place less than 48 hours before the start of the first session will result in an administrative charge of £50.

Please ensure you have permission from your supervisor to attend this course before you make your booking!

Trainers

Dr Michael Grayling, MRC Biostatistics Unit

Dr Simon Frost, Department of Veterinary Medicine

Dr Matt Castle, GSLS

During this one hour presentation I will introduce you to the challenging and diverse topic of regulatory affairs in the pharmaceutical industry and cover some of the aspects we are faced with day to day in the country role. In particular we will look at some of the issues faced with fraudulent and counterfeit medicines and when looking at promotional affairs and product claim development, as these are the two topics for a potential project with Gilead.

About Gilead Sciences Gilead is one of the world's most successful biotech companies with a current market capitalisation of over $150 billion, Gilead Sciences Inc. (www.gilead.com) is a leading research-based biopharmaceutical company which discovers, develops and commercialises innovative medicines in life-threatening diseases. Gilead's primary areas of focus include HIV/AIDS, liver diseases, respiratory diseases, cardiovascular/metabolic diseases, inflammation and oncology

About Alan Collins Alan has 18 years of experience in the pharmaceutical industry and is a Director of Regulatory Affairs at Gilead Sciences. Alan's experience covers the many diverse areas of regulatory affairs, plus pricing and reimbursement, medical affairs, business conduct and auditing - he has never had two working days the same and enjoys the variety and challenge of his role.

An Introduction to R: Software For Statistical Analysis, with Dr Simon R. White, MRC Biostatistics Unit, and Dr Adam P. Wagner, University of Cambridge.

GNU R is (freely) available for all major platforms (Microsoft Windows, Linux, Mac, etc.) and is growing in popularity in academia and beyond for carrying out statistical analysis and data manipulation.

The aim of the course is to introduce participants to the basics of statistical analysis and the open source statistical software GNU R.

Participants will actively use R throughout the course, during which they will be introduced to principles of statistical thinking and interpretation by example, exercises and discussion about a range of problems. The examples will be used to present a variety of statistical concepts and techniques, with no focus on any specific discipline.

Participants Without a Raven Password: If you do not have a Raven's account and would like to attend this course, or have other booking queries, please email Adam Wagner (apw40@medschl.cam.ac.uk).

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This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing data. We will present workflows for the analysis of CHip-Seq and RNA-seq, as well as tools to annotate and visualise results derived from other sequencing experiments (such as DNA resequencing) 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.

A two-day course designed to introduce MATLAB and some basic programming concepts. 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. By the end of this course, attendees should be able to write simple Perl programs and to understand more complex Perl programs written by others. The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside. Further information is available.

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 a gentle and 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 sets out to introduce simple computing tools for molecular biologists. It is intended for users with a reasonable background in molecular biology but little or no experience of using the available computer resources. The course is based around an investigation into the disease aniridia. We have chosen a well researched human topic as it allows us best to demonstrate how information can be obtained both by analysis of raw sequence data and by interrogation of information resources where previously determined facts are organised and stored. Further information for this session is available.

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 the European Nucleotide Archive (ENA) record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation available from the Europian Bioinformatics Institute (EBI). Further information for this session is available here.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see 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.

An understanding protein structure is vital for the elucidation of its function. Information gleaned from the three dimensional structures of proteins is used to understand the biochemical and functional roles of such molecules in life and for the design and discovery of drug molecules for a variety of diseases and illnesses such as cancer, influenza and tuberculosis.

The Protein Data Bank (PDB) is the central publicly accessible repository of all experimentally derived macromolecular structures. Containing over 80,000 structures of proteins and nucleic acids the PDB is an essential scientific resource.

The PDB is managed by a consortium of international organizations collectively known as the worldwide Protein Data Bank (wwPDB). The Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB along with the RCSB Protein Data Bank in the USA and Protein Data Bank Japan(PDBj) in Japan.

In addition to serving as a deposition site for data deposited to the PDB, the PDBe also provides services for the search and analysis of the collective wealth of data contained within the PDB. Further information is available here.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see 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.

Annotators from the Pathogen Genomics Group at the Wellcome Trust Sanger Institute give a comprehensive introduction to the latest Genome Analysis software (Artemis and ACT). 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.

• 'Bioinformatics: Genomics in Medicine ' has been approved by the Federation of the Royal Colleges of Physicians of the United Kingdom for 6 category 1 (external) CPD credits.

This course, devised by Life Technologies in conjunction with internationally regarded experts, offers a unique learning opportunity for healthcare professionals who are looking to gain knowledge and practical guidance in genomics and pharmacogenomics. No laboratory work will be involved. The course will be comprised of lectures, demonstrations and discussion activities and will focus on how modern DNA sequencing technologies are impacting clinical medicine. Further information is available here.

Booking for this event:

Raven password holders may book a provisional place on this course for themselves. It would be helpful, and save time if they would also follow the procedures for people without a Raven password, specified as follows.

To apply for a place on this course, please fill in your details here

A place will be reserved for you and you will be contacted as soon as your application has been reviewed.

Successful applicants will be provided with details of how to make payment of the course fee of £200 within 2 working days. Your reservation will be confirmed on receipt of the course fee.

This course aims to introduce researchers to software and techniques for the analysis of RNA data. More 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 cover, at a basic level, building phylogenetic trees based on molecular sequence data. This will include the general context and uses of tree-building, choosing models of DNA and protein evolution, tree-building methods including distance, parsimony, maximum likelihood and Bayesian MCMC, and confidence in results. Examples will be worked through using MEGA. Further information 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.

”To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.” - R.A. Fisher

Modern genomics technologies are able to deliver an unprecedented amount of data rapidly. However, without due care and attention early in the experimental process, such data are meaningless if they cannot adequately answer the intended research question. This course is aimed at those planning high-throughput genomics experiments and highlights the kinds of questions they should be asking themselves. We we also review key statistical concepts that underpin the design process and are referred to throughout further Bioinformatics training courses.

Timetable

• 12:30 - 13:30 - Introductory Statistics (Lecture) - Mark Dunning
• 13:30 - 14:15 - Exploratory data analysis (Discussion) - Mark Dunning
• 14:30 - 15:30 - Experimental Design (Lecture) - Roslin Russell
• 15:30 - 17:00 - Experimental Design (Discussion) Roslin Russell, Mark Dunning

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 Mass spectrometry Proteomics at the European Bioinformatics Institute (EBI). Further information for this session is available.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see 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 course covers state-of-the-art tools and methods for system biology using biological data of different types. The participants will learn about the basis of modelling large-scale datasets as logic networks, as well as a more detailed approach using deterministic and stochastic modelling. At the end of the course the basis of three dimensional modelling of protein-protein interaction will be covered.

The course timetable 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.

This session provides an introduction to the IntAct and Reactome database systems. Also to the analysis tools for molecular interaction data available from the European Bioinformatics Institute (EBI). Further information for this session is available here.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see 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 course provides an introduction to the construction of high quality Multiple Sequence Alignments (MSAs) and the computation of phylogenetic trees from those alignments. 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 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 BS-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 BS-seq data under the guidance of the lecturers and teaching assistants.

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.

• 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.