Bioinformatics course timetable
May 2016
Wed 11 |
EXCELERATE: Train the Trainer
Finished
This course aims to provide trainers with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic). This event is organized as part of the Horizon 2020 ELIXIR-EXCELERATE project. 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. |
Thu 12 |
In this course we will introduce web-based, open source tools to analyse and interpret high-throughput biological data. The main focus will be g:Profiler - a toolset for finding most significant functional groups for a given gene or protein list; MEM - a query engine allowing to mine hundreds of public gene expression datasets to find most co-expressed genes based on a query gene; and ClustVis - a web tool for visualizing clustering of multivariate data using Principal Component Analysis (PCA) plot and heatmap. MEM and g:Profiler are ELIXIR-Estonia node services. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Mon 16 |
ElixirUK: Data Carpentry
Finished
In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. Data Carpentry workshops are designed to teach basic concepts, skills and tools for working more effectively with data. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. During this course you will learn about:
This event is organized in collaboration with Data Carpentry and is sponsored by the HORIZON 2020 TWINNING Project TrainMalta. Materials for this 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 by linking here. |
Tue 17 |
ElixirUK: Data Carpentry
Finished
In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. Data Carpentry workshops are designed to teach basic concepts, skills and tools for working more effectively with data. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. During this course you will learn about:
This event is organized in collaboration with Data Carpentry and is sponsored by the HORIZON 2020 TWINNING Project TrainMalta. Materials for this 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 by linking here. |
Modern genomics technologies are able to produce large volumes of data that often leave researchers feeling overwhelmed and unsure of how to begin the process of biological interpretation. In this course, we explain the common file formats generated by sequencing technologies and how they can be manipulated and explored by non bioinformaticians. The main tools that we will use are the Integrative Genomics Viewer (IGV) and University of Santa Cruz (UCSC) genome browser. This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute. The materials for the course were developed in collaboration with Dr. Thomas Carroll from the MRC CSC. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book by linking here. |
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Thu 19 |
Image Analysis for Biologists
Finished
This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines. On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package. On day 2, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager). The 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. |
Fri 20 |
Image Analysis for Biologists
Finished
This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines. On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based on Fiji, an extensible open source software package. On day 2, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager). The 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. |
June 2016
Mon 6 |
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. The course website 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. |
Tue 7 |
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. The course website 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. |
Wed 8 |
This course will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications. It will also include 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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Thu 9 |
Using the Ensembl Genome Browser
Finished
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. There may be some tools and topics that do not apply to non-vertebrates; if you have any questions about this, please email the Ensembl Outreach Project Leader, Emily Perry. 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. |
Fri 10 |
Using the Ensembl Genome Browser
Finished
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. There may be some tools and topics that do not apply to non-vertebrates; if you have any questions about this, please email the Ensembl Outreach Project Leader, Emily Perry. 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. |
Mon 13 |
Variant Analysis with GATK
Finished
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations 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. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery. The workshop is composed of one day of lectures (including many opportunities for Q&A) and one day of handson training. On the first day, we explain the rationale, theory and application of our Best Practices for Variant Discovery in high-throughput sequencing data. On the second day, we walk attendees through handson exercises that teach how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to various use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK, dealing with problems, and using thirdparty tools such as Samtools, IGV and RStudio. 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 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. |
Tue 14 |
Variant Analysis with GATK
Finished
This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations 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. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery. The workshop is composed of one day of lectures (including many opportunities for Q&A) and one day of handson training. On the first day, we explain the rationale, theory and application of our Best Practices for Variant Discovery in high-throughput sequencing data. On the second day, we walk attendees through handson exercises that teach how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to various use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK, dealing with problems, and using thirdparty tools such as Samtools, IGV and RStudio. 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 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. |
Thu 16 |
This course provides a 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. 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. |
Fri 17 |
This course provides a 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. 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. |
Mon 20 |
The goal of metabolomics is to identify and quantify the complete biochemical composition of a biological sample. With the increase in genomic, transcriptomic and proteomic information there is a growing need to understand the metabolic phenotype that these genes and proteins ultimately control. The aim of this course is to provide an overview of metabolomics and its applications in life sciences, clinical and environmental settings. Over 2 days we will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways. The course content will predominantly be based on analysing samples from model plant species such as Arabidopsis thaliana but the procedures are transferable to all other organisms, including clinical and environmental settings. 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 by linking here. |
CRUK: Basic Unix
Finished
The Unix shell has existed since the early days of computers, and yet is still the preferred way to run many popular Bioinformatics tools. This course aims to take the novice and turn them into a beginning Linux user. We will describe the Linux environment so they can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute. 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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Tue 21 |
The goal of metabolomics is to identify and quantify the complete biochemical composition of a biological sample. With the increase in genomic, transcriptomic and proteomic information there is a growing need to understand the metabolic phenotype that these genes and proteins ultimately control. The aim of this course is to provide an overview of metabolomics and its applications in life sciences, clinical and environmental settings. Over 2 days we will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways. The course content will predominantly be based on analysing samples from model plant species such as Arabidopsis thaliana but the procedures are transferable to all other organisms, including clinical and environmental settings. 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 by linking here. |
This course provides a refresher on the foundations of statistical analysis. The emphasis is on interpreting the results of a statistical test, and being able to determine the correct test to apply. Practicals are conducted using a series of online apps, and we will not teach a particular statistical analysis package, such as R. For courses that teach R, please see the links under "Related courses" . This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute. 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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Wed 22 |
Analysis of single cell RNA-seq data
Finished
Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging. In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq. Materials for this 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 by linking here. |
Thu 23 |
This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. 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. |
Fri 24 |
This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. 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. |
Mon 27 |
Ensembl API workshop
Finished
The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers the core, compara, variation and functional genomics (regulation) databases and APIs. The Ensembl Perl API Documentation can be found here. For each of these, the database schema and the API design as well as the most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put theoretical learning into practice by writing their own Perl scripts. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Tue 28 |
Ensembl API workshop
Finished
The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers the core, compara, variation and functional genomics (regulation) databases and APIs. The Ensembl Perl API Documentation can be found here. For each of these, the database schema and the API design as well as the most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put theoretical learning into practice by writing their own Perl scripts. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |