Bioinformatics 2015

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.

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.

This practical-based course will deal with all aspects of the prediction of protein structure, concentrating on the prediction of secondary structure, fold recognition and comparative modelling of structures. Computational aspects of protein structure determination, validation and analysis will be covered. The course will be a mixture of talks and guided practicals. 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 practical-based course will deal with all aspects of the prediction of protein structure, concentrating on the prediction of secondary structure, fold recognition and comparative modelling of structures. Computational aspects of protein structure determination, validation and analysis will be covered. The course will be a mixture of talks and guided practicals. 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 will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

• It is aimed at researchers who are applying or planning to apply image analysis in their research

• 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 around Fiji, an extensible open source software package.

• On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.

• On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.

• A draft agenda can be found here.

• This event is sponsored by the Systems Microscopy NoE.

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 will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

• It is aimed at researchers who are applying or planning to apply image analysis in their research

• 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 around Fiji, an extensible open source software package.

• On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.

• On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.

• A draft agenda can be found here.

• This event is sponsored by the Systems Microscopy NoE.

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 will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

• It is aimed at researchers who are applying or planning to apply image analysis in their research

• 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 around Fiji, an extensible open source software package.

• On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.

• On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.

• A draft agenda can be found here.

• This event is sponsored by the Systems Microscopy NoE.

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 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 calling process, what are the key 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. Special attention will be given to the newest functionalities in GATK3, including joint discovery in cohorts and RNAseq analysis.

• The workshop will last two days, with a day and a half of lectures (including many opportunities for Q&A) and one half day of hands-on training.

• On the first day, we will explain the rationale, theory and real-life applications of our Best Practices for Variant Discovery in high-throughput sequencing data.

• On the second day, in the morning we will cover additional topics such as the differences between whole genome vs. exome analysis, sequence data QC metrics, and how to apply GATK to non-model organisms. In the afternoon, we will hold a hands-on session in which attendees will learn to interact with the GATK tools and apply them effectively.

• The lecture-based component of the workshop is aimed at a mixed audience of people who are new to GATK seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. The hands-on component is aimed mainly at beginners who have basic familiarity with the command line environment.

• A draft agenda can be found here.

• This event is sponsored by eLife.

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 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 calling process, what are the key 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. Special attention will be given to the newest functionalities in GATK3, including joint discovery in cohorts and RNAseq analysis.

• The workshop will last two days, with a day and a half of lectures (including many opportunities for Q&A) and one half day of hands-on training.

• On the first day, we will explain the rationale, theory and real-life applications of our Best Practices for Variant Discovery in high-throughput sequencing data.

• On the second day, in the morning we will cover additional topics such as the differences between whole genome vs. exome analysis, sequence data QC metrics, and how to apply GATK to non-model organisms. In the afternoon, we will hold a hands-on session in which attendees will learn to interact with the GATK tools and apply them effectively.

• The lecture-based component of the workshop is aimed at a mixed audience of people who are new to GATK seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. The hands-on component is aimed mainly at beginners who have basic familiarity with the command line environment.

• A draft agenda can be found here.

• This event is sponsored by eLife.

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.

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 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. 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.