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Bioinformatics Training

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Bioinformatics course timetable

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Fri 17 Apr 2015 – Fri 29 May 2015

April 2015

Fri 17	Protein Structure Modelling (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Mon 20	Image Analysis for Biologists (1 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Tue 21	Image Analysis for Biologists (2 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Wed 22	Image Analysis for Biologists (3 of 3) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Thu 23	Variant Analysis with GATK (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Fri 24	Variant Analysis with GATK (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Tue 28	An Introduction to Solving Biological Problems with R (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Wed 29	An Introduction to Solving Biological Problems with R (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Thu 30	An Introduction to Solving Biological Problems with Python (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.

May 2015

Fri 1	An Introduction to Solving Biological Problems with Python (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Mon 11	Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview (1 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Further information, including some training videos, is also available. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.
Tue 12	Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview (2 of 3) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Further information, including some training videos, is also available. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.
Wed 13	Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview (3 of 3) Finished 09:00 - 16:00 Bioinformatics Training Room, Craik-Marshall Building Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Further information, including some training videos, is also available. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.
Thu 14	Introduction to RNA-seq and ChIP-seq data analysis (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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 15	Introduction to RNA-seq and ChIP-seq data analysis (2 of 2) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Mon 18	CRUK: An Introduction to Solving Biological Problems with Python (1 of 2) Finished 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE 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 timetable for this event 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.
	An Introduction to MATLAB for biologists (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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. 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 or register Interest by linking here.
Tue 19	CRUK: An Introduction to Solving Biological Problems with Python (2 of 2) Finished 09:30 - 16:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE 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 timetable for this event 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.
	An Introduction to MATLAB for biologists (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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. 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 or register Interest by linking here.
Wed 20	Introduction to Metabolomics Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building The aim of this course is to provide an overview of the applications, laboratory equipment and online bioinformatic portals for metabolomics research. 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.
Thu 21	An Introduction to Solving Biological Problems with R (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Fri 22	An Introduction to Solving Biological Problems with R (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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.
Wed 27	Introduction to Scientific Figure Design Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building 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. Morning Timetable Introduction Data Visualisation Theory Coffee Data Representation Practical Ethics talk Afternoon Timetable Design theory talk Ethics practical GIMP Tutorial GIMP Practical Coffee Inkscape Tutorial Inkscape Practical Final practical Further information and access to the course materials is available. 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 28	Genome Annotation with Artemis Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building This one day workshop aims to give an introduction to Artemis and ACT (Artemis Comparison Tool). Both tools enable the visualization, analysis and comparison of genome data. They are freely available for all operating systems and can be downloaded here. This is a hands-on course with short talks introducing the tools. The course is taught by members of the Pathogen and Parasite Genomic Teams from the Wellcome Trust Sanger Institute. 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.
Fri 29	Nowomics: Track the latest data and papers relevant to your research Finished 10:00 - 11:30 Bioinformatics Training Room, Craik-Marshall Building Nowomics - Access to the latest data and papers relevant to your research Nowomics is a new website to help biologists stay up to date with the latest data and papers relevant to their research. Try it here. Nowomics tracks new papers and many types of data in online repositories. You ‘follow’ the genes and processes you work on to see a Twitter-like news feed of new papers, annotation, interactions, curated comments and more. For each gene you can also include information from orthologues and related genes directly in your news feed. Data are currently included for human, mouse, rat, fly and plant. This short workshop will show you how to use the Beta version of Nowomics to find the latest information for genes & keywords, how to set up your personalised news feed and configure email alerts. We’ll also demonstrate new portals to help researchers working on Drosophila or Arabidopsis find the latest and most popular papers. Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.