Bioinformatics 2015
(Mon 16 Feb 2015 - Thu 17 Dec 2015)
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July 2015
Fri 24 |
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. |
August 2015
Thu 13 |
The aim of this course is to familiarise 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 and discusses quality control issues, which are common among all NGS 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 14 |
The aim of this course is to familiarise 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 and discusses quality control issues, which are common among all NGS 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. |
Wed 19 |
SeqMonk is a graphical program for the visualisation and analysis of large mapped sequencing datasets such as ChIP-Seq, RNA-Seq, and BS-Seq. The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets. This course provides an introduction to the main features of SeqMonk and will run through the analysis of a couple of different datasets to show what sort of analysis options it provides. 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. |
Thu 20 |
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 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 21 |
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 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. |
September 2015
Thu 10 |
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. Workshop Learning objectives & programme
This event is organized in collaboration with Data Carpentry. Corse materials are 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 11 |
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. Workshop Learning objectives & programme
This event is organized in collaboration with Data Carpentry. Corse materials are 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. |
Mon 14 |
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 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. |
Tue 15 |
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 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. |
Wed 16 |
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 17 |
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 18 |
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 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. |
Wed 23 |
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. |
Thu 24 |
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 25 |
Statistical Analysis using R
Finished
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Wed 30 |
What are the cognitive differences between novices, competent practitioners, and experts? Do different people really have different learning styles? Do flipped classrooms actually work better than regular lectures? This tutorial will explore recent research in these areas and more, and show participants how to apply that research in the classroom to improve teaching. This tutorial is a condensed version of the instructor training program that Software Carpentry has been running for the past three years. In it, we will explore a handful of research results in educational psychology, and see how to use those findings to build more effective lessons. Greg Wilson is the Executive Director of the Software Carpentry Foundation, a volunteer non-profit organization that teaches researchers basic lab skills for scientific computing. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
October 2015
Wed 21 |
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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book by linking here. |
Mon 26 |
This workshop is an introduction to EMBL-EBI and the life science data resources it provides. Participants will be shown how to navigate the website and search for appropriate database resources and tools, whilst also highlighting resources such as Train online (our e-learning portal) and the literature resources at Europe PMC. The timetable for this event can be found here. This workshop will not focus on a set of specific resources; for more focused workshops please see the others within this series (see the Related Courses section below) Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
The aim of this course is to introduce participants to the basics of statistical analysis and the open source statistical software R, a free software environment for statistical computing and graphics. Participants will actively use R throughout the course, during which they will be introduced to principles of statistical thinking and interpretation by example, exercises and discussion about a range of problems. The examples will be used to present a variety of statistical concepts and techniques, with no focus on any specific discipline. Important information: We have 12 configured laptops for use at the workshop. After these laptops have been allocated, participants will either need to share, or bring their own. These laptops will be allocated to the first individuals to express an interest in using them. When booking, please indicate under "Special requirements" if you wish to use one of the 12 laptops or bring your own. Participants bringing their own laptop will be given instructions on what software to install. 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 27 |
Mouse Genome Informatics workshop
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. |
Wed 28 |
This workshop will give an introduction to the resources provided by UniProt. Participants will be shown, and given hands-on experience in, how to navigate the website, search for data and run analysis tools. The session also covers what the sources of our data are and how they are curated. A basic introduction into accessing UniProt Knowledgebase programmatically will be given as well. The timetable for this event can be found here. Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
The aim of this course is to introduce participants to the basics of statistical analysis and the open source statistical software R, a free software environment for statistical computing and graphics. Participants will actively use R throughout the course, during which they will be introduced to principles of statistical thinking and interpretation by example, exercises and discussion about a range of problems. The examples will be used to present a variety of statistical concepts and techniques, with no focus on any specific discipline. Important information: We have 12 configured laptops for use at the workshop. After these laptops have been allocated, participants will either need to share, or bring their own. These laptops will be allocated to the first individuals to express an interest in using them. When booking, please indicate under "Special requirements" if you wish to use one of the 12 laptops or bring your own. Participants bringing their own laptop will be given instructions on what software to install. 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. |