Bioinformatics course timetable
December 2018
Tue 4 |
Bioinformatics for Biologists: An introduction to programming, analysis and reproducibility
Finished
This 1-week course aims to provide an introduction to the best practises and tools needed to perform bioinformatics research effectively and reproducibly. Focusing on solutions around handling biological data, we will cover introductory lessons in programming in R, statistical analyses, data management and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility. More information about the course can be found here. The training room is located on the first floor and there is currently no level access. 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. |
Wed 5 |
Bioinformatics for Biologists: An introduction to programming, analysis and reproducibility
Finished
This 1-week course aims to provide an introduction to the best practises and tools needed to perform bioinformatics research effectively and reproducibly. Focusing on solutions around handling biological data, we will cover introductory lessons in programming in R, statistical analyses, data management and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility. More information about the course can be found here. The training room is located on the first floor and there is currently no level access. 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 6 |
Bioinformatics for Biologists: An introduction to programming, analysis and reproducibility
Finished
This 1-week course aims to provide an introduction to the best practises and tools needed to perform bioinformatics research effectively and reproducibly. Focusing on solutions around handling biological data, we will cover introductory lessons in programming in R, statistical analyses, data management and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility. More information about the course can be found here. The training room is located on the first floor and there is currently no level access. 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 7 |
Bioinformatics for Biologists: An introduction to programming, analysis and reproducibility
Finished
This 1-week course aims to provide an introduction to the best practises and tools needed to perform bioinformatics research effectively and reproducibly. Focusing on solutions around handling biological data, we will cover introductory lessons in programming in R, statistical analyses, data management and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility. More information about the course can be found here. The training room is located on the first floor and there is currently no level access. 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. |
Mon 10 |
Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection. This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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. |
Tue 11 |
Microscopy experiments have proven to be a powerful means of generating information-rich data for biological applications. From small-scale microscopy experiments to time-lapse movies and high-throughput screens, automatic image analysis is more objective and quantitative and less tedious than visual inspection. This course will introduce users to the free open-source image analysis program CellProfiler and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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. |
Wed 12 |
Data Science in Python
Finished
This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes. Note: this course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. The training room is located on the first floor and there is currently no level access. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Thu 13 |
Data Science in Python
Finished
This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes. Note: this course is the continuation of the Introduction to Solving Biological Problems with Python; participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. The training room is located on the first floor and there is currently no level access. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Fri 14 |
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. The training room is located on the first floor and there is currently no level access. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Mon 17 |
R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. The course website providing links to the course materials is here. Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on Data Analysis and Visualisation in R course. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no level access. 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. |
Tue 18 |
R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. The course website providing links to the course materials is here. Please note that although we will demonstrate how to perform statistical analysis in R, we will not cover the theory of statistical analysis in this course. Those seeking an in-depth explanation of how to perform and interpret statistical tests are advised to see the list of Related courses. Moreover, those with some programming experience in other languages (e.g. Python, Perl) might wish to attend the follow-on Data Analysis and Visualisation in R course. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no level access. 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. |
January 2019
Wed 9 |
Statistics for Biologists in R
Finished
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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 10 |
Statistics for Biologists in R
Finished
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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. |
Tue 15 |
CRUK: Data Carpentry in R
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, using a combination of tools with a main focus in R. 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. 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 |
CRUK: Data Carpentry in R
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, using a combination of tools with a main focus in R. 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. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Statistics for Biologists in R
Finished
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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. |
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Thu 17 |
Statistics for Biologists in R
Finished
This course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences using the R software package. In this course we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to multiple linear regression. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques. This event is supported by the BBSRC Strategic Training Awards for Research Skills (STARS) grant (BB/P022766/1). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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 24 |
This course will present a set of R/Bioconductor packages to access, manipulate, visualise and analyse mass spectrometry (MS) and quantitative proteomics data. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. 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 25 |
CRUK: Image Analysis with Fiji
Finished
Fiji/ImageJ is a popular open-source image analysis software application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience with Fiji. This course is run by the CRUK CI Light microscopy core facility. 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 short (0.5 day) intensive course serves to introduce you to the command-line interface in Linux. It is based upon elements of the Software Carpentries Shell(novice) and Shell(extras) courses. It is recommended for those CI personnel planning on attending the CI High Performance Computing facilities (Cluster) course. This course is run by the CRUK CI Bioinformatics and IT core. 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 30 |
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. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
February 2019
Tue 12 |
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 the Bioinformatics Core Facility 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. |
Tue 19 |
Data Carpentry in R
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, using a combination of tools with a main focus in R. 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. This course is organized in collaboration with ElixirUK and the Software Sustainability Institute. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Wed 20 |
Data Carpentry in R
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, using a combination of tools with a main focus in R. 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. This course is organized in collaboration with ElixirUK and the Software Sustainability Institute. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here. |
Tue 26 |
CRUK: Managing your Research Data
Finished
How much data would you lose if your laptop was stolen? Have you ever emailed your colleague a file named 'final_final_versionEDITED'? Have you ever struggled to import your spreadsheets into R? Would you be able to write a Data Management Plan as part of a grant proposal? As a researcher, you will encounter research data in many forms, ranging from measurements, numbers and images to documents and publications. Whether you create, receive or collect data, you will certainly need to organise it at some stage of your project. This workshop will provide an overview of some basic principles on how we can work with data more effectively. We will discuss the best practices for research data management and organisation so that our research is auditable and reproducible by ourselves, and others, in the future. Course materials are available here 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. |