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All Bioinformatics courses

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Showing courses 76-100 of 107
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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 bioinformatic analyses. The goal of this course is to demonstrate how to use Galaxy to explore RNA-seq data, for expression profiling, and ChIP-seq data, to assess genomic DNA binding sites. You will learn how to perform analysis in Galaxy, and then how to share, repeat, and reproduce your analyses.

The timetable for this event 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.

Introduction to genome variation analysis using NGS Thu 18 May 2017   09:30 Finished

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

  • an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
  • an overview of available analytical tools and discussion of their limitations; and
  • hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-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 DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Introduction to RNA-seq and ChIP-seq data analysis Wed 25 Oct 2017   09:30 Finished

The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughput sequencing (HTS) assays: ChIP-seq and RNA-seq.

This course starts with a brief introduction to the transition from capillary to high-throughput sequencing (HTS) and discusses quality control issues, which are common among all HTS datasets. Next, we will present the alignment step and how it differs between the two analysis workflows. Finally, we focus on dataset specific downstream analysis, including peak calling and motif analysis for ChIP-seq and quantification of expression, transcriptome assembly and differential expression analysis for RNA-seq.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Introduction to RNA-seq data analysis Wed 27 Mar 2019   09:30 Finished

The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data.

This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.

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 your interest by linking here.

Introduction to Scientific Figure Design Wed 14 Nov 2018   09:30 Finished

This course provides a practical guide to producing figures for use in reports and publications.

It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures.

The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools.

Further information and access to the course materials is here.

The training room is located on the first floor and there is currently no level access.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

This course provides a practical guide to producing figures for use in reports and publications.

It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures.

The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools.

Further information and access 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.

Introduction to Unix shell new Wed 17 Oct 2018   09:30 Finished

This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We will take a problem-solving approach, drawing on types of tasks commonly encountered by Linux users when processing text files.

The training room is located on the first floor and there is currently no level access.

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.

Molecular Phylogenetics Wed 3 Apr 2019   09:00 Finished

This course will provide training for bench-based biologists to use molecular data to construct and interpret phylogenies, and test their hypotheses. Delegates will gain hands-on practice of using a variety of programs freely-available online and commonly used in molecular studies, interspersed with some lectures.

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 by linking here.

Mouse Genome Informatics workshop new Tue 27 Oct 2015   10:00 Finished

Mouse Genome Informatics (MGI) is the international database resource for the laboratory mouse and provides integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

MGI is a free, highly curated resource and offers web and programmatic access to a complete catalogue of mouse genes and genome features, functional annotations, a comprehensive catalogue of mutant and knockout alleles, phenotype and human disease model annotations, gene expression, variation and sequence data.

This workshop will be composed of ~20min overview and ~1 hour hands-on, interactive tutorial.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

MSt in Genomic Medicine - Advanced bioinformatics Mon 20 Mar 2017   09:30 Finished

This module introduces a deeper exploration of bioinformatics analysis of genomic data, providing a greater understanding of the different approaches to mapping and alignment of genome sequence data, programming and scripting, along with approaches for the detection and analysis of genomic changes, gene expression and network analysis.

Network Visualisation and Analysis of Biological Data new Thu 14 Apr 2016   09:30 Finished

This two day course will cover network-based approaches to visualise and analyse complex biological ‘big’ data and model pathway systems. The course will be centred on the use of BioLayout Express3D, a tool developed between scientists at the University of Edinburgh and EBI over the last 10 years.

BioLayout provides rapid and versatile means to explore and integrate very large datasets, providing a stunning interface to visualise the relationships between 10’s of thousands of data points. Originally designed for the analysis of microarray data, it is equally effective in analysing data matrices from other analysis platforms.

Day one of the course will introduce principles of network analysis and their use as a generic medium to understand relationships between entities. We will introduce the basics of network visualisation and navigation within BioLayout and principles of correlation analysis of data matrices. We will then explore how data can be explored and clustered within the tool and how you can use the software to rapidly extract meaning from large and complex datasets.

Day two will focus on pathway modelling. We will explain how to collate information about a given system of interest from the literature, and to turn this information into a logic-based pathway model. We will then explore how these models can be parametrised and imported into BioLayout where simulations can be run that model the dynamics of these systems under different conditions. For more information see: http://www.virtuallyimmune.org/

A draft agenda 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.

Next Generation Sequencing data analysis Tue 17 Mar 2015   09:00 Finished

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 DNA-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 DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply NGS technologies and bioinformatics methods in their research.

The timetable for this event 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.

  • 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.

Ontologies and ontology-based data analysis Wed 21 Nov 2018   10:00 Finished

Ontologies have long provided a core foundation in the organization of biomedical entities, their attributes, and their relationships. With over 500 biomedical ontologies currently available there are a number of new and exciting opportunities emerging in using ontologies for large scale data sharing and data analysis.

This tutorial will help you understand what ontologies are and how they are being used in computational biology and bioinformatics. It will include hands-on examples and exercises and an introduction to Onto2Vec and OPA2Vec, two methods that can be used to learn semantic similarity measures in a data- and application-driven way.

The training room is located on the first floor and there is currently no level access.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. The consortium was founded in 2014 by GSK, EMBL-EBI and the Wellcome Sanger Institute, and later welcomed three new partners, Biogen, Takeda, and Celgene. Underpinning this partnership is the Open Targets Platform, an open source, user-friendly web interface to investigate causal links between genes, pathways and diseases. These links are computed, scored and ranked using biological evidence integrated from many public data sources, including the NHGRI-EBI GWAS Catalog, Genomics England, PheWAS, ClinVar, Expression Atlas, UniProt, and ChEMBL to name a few.

In addition to data integration, Open Targets also generates new data using human cellular models (e.g. organoids, iPSCs) and genome editing (CRISPR/Cas9) to identify drug targets in oncology, immunology and neurodegenerative diseases. This will be publicly available in the public domain and integrated into the Open Targets Platform.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA.

Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication.

The course involves of a mixture of talks and hands-on exercises.

Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview.

Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch.

Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues.

There will be opportunities for attendees to get advice on analysis of their own sequence families.

Further information, including some training videos, is also available.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Protein Structure Analysis new Thu 24 May 2018   09:30 Finished

This course covers data resources and analytical approaches for the discovery and interpretation of biomacromolecular structures.

Day 1 focuses on public repositories of structural data (Protein Data Bank and Electron Microscopy Data Bank) and resources for protein analysis and classification (Pfam, InterPro and HMMER).

Day 2 covers how to find information about the structure and function of your protein sequence using CATH, principles of modern state-of-the-art protein modelling with Phyre2 and methods for predicting the effects of mutations on protein structure and function using the SAAP family of tools.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Protein Structure Analysis new Thu 20 Jun 2019   10:00 [Places]

This course covers analytical approaches for the interpretation of biomacromolecular structures including how to find information about the structure and function of your protein sequence using CATH, principles of modern state-of-the-art protein modelling with Phyre2 and methods for predicting the effects of mutations on protein structure and function using the SAAP family of tools. In addition, we will look at mapping genetic variants onto structures as well as visualisation and basic analysis of protein structures.

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 by linking here.

The course will teach intermediate R object-oriented programming and how to build a fully functional R package.

Relevant teaching materials are available here and the sequences example package used as template in the course 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 your interest by linking here.

Software Carpentry: Instructor training Mon 19 Sep 2016   09:30 Finished

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.

Statistical Analysis using R Fri 12 Jul 2019   09:30 [Full]

Statistics are an important part of most modern studies and being able to effectively use a statistical package will help you to understand your results.

This course provides an introduction to some statistical techniques through the use of the R language. Topics covered include: Chi2 and Fisher tests, descriptive statistics, t-test, analysis of variance and regression.

Students will run analyses using statistical and graphical skills taught during the session.

The course manual can be found here.

This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).

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 by linking here.

Statistics for Biologists in R Thu 19 Sep 2019   09:30 [Places]

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 using the R software package.

In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. 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.

This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1).

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 your interest by linking here.

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

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 your interest by linking here.

Train the Trainer for Image Analysts Thu 30 May 2019   09:30 Finished

This course aims to provide trainers with guidance and tips for developing and delivering training in image analysis, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic).

The first part of the course will give participants principles of training theory and best practises for developing and delivering their future training content; the second part will be a hackathon to kick start the development of a common set of training materials in image analysis.

This event is organized in collaboration with the Image Analysis Focused Interest Group and is supported by the Royal Microscopical Society.

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.

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