GSLS Bioinformatics Training 2014

”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 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.

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.

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.

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 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 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 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.

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 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.

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.

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. 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 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. 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 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. 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.

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.

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.

This session provides an introduction to the tools to access and analyze Transcriptomics 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 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.

• 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.