Bioinformatics course timetable
March 2016
| Thu 10 |
This course is aimed at those new to programming and provides an introduction to programming using Perl. During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures. The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside. 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 by linking here. |
| Fri 11 |
This course is aimed at those new to programming and provides an introduction to programming using Perl. During this course you will learn the basics of the Perl programming language, including how to store data in Perl’s standard data structures such as arrays and hashes, and how to process data using loops, functions, and many of Perl’s built in operators. You will learn how to write and run your own Perl scripts and how to pass options and files to them. The course also covers sorting, regular expressions, references and multi-dimensional data structures. The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside. 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 by linking here. |
| Mon 14 |
Using the Ensembl Genome Browser
Finished
The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This one-day 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. |
| Tue 15 |
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. 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. |
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Galaxy 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. 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 by linking here. |
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| Wed 16 |
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. 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 17 |
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. 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 18 |
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. 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. |
| Mon 21 |
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. |
| Tue 22 |
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. |
April 2016
| Mon 4 |
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 5 |
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 6 |
A hands-on interactive course that will introduce you to how to analyse genomic sequences in the command line environment. Examples will focus on metagenomics data but the course is suitable to anyone starting to analyze high-throughput sequencing data. This course will be taught by Dr. Adina Howe from Iowa State University. Her group focuses on integrating traditional microbiology approaches with metagenomics and computational biology as investigative tools to understand environmental microbial populations Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book by linking here. |
| Thu 7 |
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 8 |
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 11 |
The course will teach intermediate R object-oriented programming and how to build a fully functional R package. The course page includes slides and handouts; other 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 register Interest by linking here. |
| Thu 14 |
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. |
| Fri 15 |
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. |
| Mon 18 |
This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:
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. |
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The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This one-day 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. 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 19 |
This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:
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. |
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This course will provide participants with an introduction to EMBL-EBI and its data tools and resources, which cover the whole spectrum of biological / life sciences. Sessions with trainers from ArrayExpress, Expression Atlas and the GWAS catalog will explore SNP-trait associations and show how further understanding can be gained on the location and level of gene expression across the body. 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 20 |
Molecular Phylogenetics
Finished
The 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. Course timetable 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. |
| Thu 21 |
Molecular Phylogenetics
Finished
The 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. Course timetable 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. |
| Fri 22 |
Molecular Phylogenetics
Finished
The 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. Course timetable 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. |
