Bioinformatics course timetable
June 2016
| 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. |
|
| 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. |
| Wed 29 |
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. |
| Thu 30 |
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. |
July 2016
| Fri 1 |
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. |
| Wed 6 |
Data Analysis and Visualisation in R
Finished
This course introduces some relatively new additions to the R programming language: dplyr and ggplot2. In combination these R packages provide a powerful toolkit to make the process of manipulating and visualising data easy and intuitive. 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. |
| Fri 8 |
DECIPHER is a collaborative data sharing and interpretation platform that enables the secure upload, analysis and subsequent sharing of anonymised phenotype-linked patient variant data in rare genetic disorders. DECIPHER is a worldwide user community of over 250 clinical genetics centres and research groups from over 40 countries that utilise the built-in tools for aiding the interpretation of variants as well as to discover other patients that share similar phenotype and genomic findings. DECIPHER facilitates collaboration and exchange of information between a global community of clinical centers and researchers leading thereby accelerating discovery and diagnosis. Access to consented anonymised records is free to all users. User accounts are provided to bona-fide clinicians and lab scientists to enable deposition and sharing of anonymised patient data. The purpose of this half-day workshop is to acquaint participants with the DECIPHER website and database and introduce the various built-in tools for visualisation and interpretation of phenotype-linked genomic variation in anonymised consented patient data. It is hoped that by the end of this workshop, users will be able to carry out effective searches of data, use the built-in genome browser to visualise variation in context of other pathogenic and reference data sources, find other patients with similar variants and shared phenotypes, and identify most likely causes of phenotypic presentation by gene prioritisation. 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 11 |
Train the Trainer
Finished
This course aims to provide new 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). |
| Tue 12 |
Train the Trainer
Finished
This course aims to provide new 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). |
| Wed 13 |
The Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data. OME has three components:
In this one day course, we will present the OMERO platform, and show how Facility Managers can use it to manage users, groups, and their microscopy, HCS and digital pathology data. Help pages on 'Using OMERO for Facility Managers' can be found here. This course is organized alongside a one day course on Biological Imaging Data Management for Life Scientists. More information on this event are available here. This course will be delivered by members of the OMERO team. The OME project is supported by BBSRC and Wellcome Trust. 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. |
| Thu 14 |
The Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data. OME has three components:
In this one day course, we will present the OMERO platform, and show how to import, organise, view, search, annotate and publish imaging data. Additionally, we will briefly introduce how to use a variety of analysis tools with OMERO. This course is organized alongside a one day course on Biological Imaging Data Management for Facility Managers. More information on this event are available here. This course will be delivered by members of the OMERO team. The OME project is supported by BBSRC and Wellcome Trust. 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. |
| Fri 15 |
This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks. 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. |
| Mon 18 |
The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughout 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. 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. |
| Tue 19 |
The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughout 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. 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. |
| Fri 22 |
Version control is the management of changes to documents, computer programs, and other collections of information. Changes are usually identified by a number named the "revision number". Each revision is associated with a timestamp and the person making the change. Revisions can be compared, restored, and with some types of files, merged. Version control systems like subversion (svn) and git are frequently used for groups writing software and code, but can be used for any kind of files or projects. Many people share their git repositories on GitHub. This course will provide an introduction to git and how you can use github to share your projects, or for your own private use if you wish. 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. |
August 2016
| Thu 4 |
LithoGraphX is a software to visualize, process and analyse 3D images and meshes. On the first day of this course, we will demonstrate how to use LithoGraphX to visualize, clean and process 2D and 3D images. We will cover: (i) how to extract cell shape from 2D or 3D images by marking the cell wall or membrane, (ii) how to extract key morphological features and (iii) how to use these features to build a cell classifier. The first day is intended for biologists and computer scientists interested in using LithoGraphX. On the second day, we will see how to write and distribute extensions to LithoGraphX. To this purpose, we will learn more about the internals of LithoGraphX and its API both in C++ and Python. The second day is intended for computer scientists wanting either to write their own algorithm or automate complex protocols. Participants can choose to register for both days or for individual days, depending on their interest and background knowledge. The timetable for this event can be found here. This course is organized in collaboration with Dr Susana Sauret-Gueto from the OpenPlant Lab of the Department of Plant Sciences of the University of Cambridge. 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 5 |
LithoGraphX is a software to visualize, process and analyse 3D images and meshes. On the first day of this course, we will demonstrate how to use LithoGraphX to visualize, clean and process 2D and 3D images. We will cover: (i) how to extract cell shape from 2D or 3D images by marking the cell wall or membrane, (ii) how to extract key morphological features and (iii) how to use these features to build a cell classifier. The first day is intended for biologists and computer scientists interested in using LithoGraphX. On the second day, we will see how to write and distribute extensions to LithoGraphX. To this purpose, we will learn more about the internals of LithoGraphX and its API both in C++ and Python. The second day is intended for computer scientists wanting either to write their own algorithm or automate complex protocols. Participants can choose to register for both days or for individual days, depending on their interest and background knowledge. The timetable for this event can be found here. This course is organized in collaboration with Dr Susana Sauret-Gueto from the OpenPlant Lab of the Department of Plant Sciences of the University of Cambridge. 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. |
September 2016
| Thu 1 |
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. |
| Fri 2 |
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. |
| Mon 5 |
The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches. Lectures will give insight into how biological knowledge can be generated from High-throughput sequencing 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 sequencing data under the guidance of the lecturers and teaching assistants. The timetable can be found here. |