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).

This course will focus on the structure of good scientific writing, first at the micro-level of sentences and paragraphs and then at the macro-level of abstracts and entire papers. Writing exercises will form an important part of the day. We will look at into the practical process of writing, the nature of scientific publishing and the importance of editing. The day will finish with a group editing session in which the students apply the ideas they've learnt to editing each other's work. For this students will write a 300-word abstract about their mini-dissertation in advance. The course instructors are Mark Buchanan and Justin Mullins, two highly experienced scientific writers/editors.

Because pre-course work is required, bookings must be made by 9 Jan 2015 and cancellations cannot be accepted thereafter.

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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 will cover all aspects of The analysis of DNA Methylation using Sequencing. It will cover the primary analysis, mapping and Quality Control (QC) of BS-Seq data and will talk about common pitfalls and complications. It will then cover exploratory analysis of Methylation looking at different methods of Quantitation' and a variety of ways of looking more widely at the distribution of Methylation over the genome. Finally the course will look at statistical methods to predict differential Methylation.
• The course will be comprised of a mixture of theoretical lectures and practicals covering a range of different software packages.
• By the end of the course students should be able to perform an analysis of Methylation Data all the way from raw sequencing to the selection of interesting targets.
• Further information, including a Timetable, will soon be 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 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 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 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.

An introduction on how to search EBI databases using sequence search tools. The workshop will introduce tools such as BLAST, FASTA and PSI-BLAST; explain how they function and the ways to make effective use of them to locate different types of biological data and information. 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.

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.

This workshop will introduce open-source tools for creating, representing and analysing molecular interaction data. Practical sessions will explore the EMBL-EBI IntAct database and use Cytoscape visualise protein interactions. 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 workshop will introduce open-source tools for creating, representing and analysing molecular interaction data. Practical sessions will explore the Reactome pathway database, showing participants how to navigate molecular reactions and the pathways they form. 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 introduction the European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI). The workshop will introduce ways to navigate the website, search EBI database resources and access useful information and metadata. It will also highlight additional resources such as Train Online. 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 by linking here.

This session provides an introduction to the tools to access and analyze Metabolomics data available from the European Bioinformatics Institute (EBI). Further information for this session is available here.

The 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 session provides an introduction to Network Analysis at 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.

In this session we will introduce the major protein databases available from the EBI. The use of the UniProtKB database will be especially considered. 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 introduction to the chemical biology resources available from the EBI. The workshop will cover ontology and bio-activity data, structure representation and tools for protein-ligand investigation. 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.