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Bioinformatics 2017

Programme of events provided by Bioinformatics
(Wed 18 Jan 2017 - Thu 14 Dec 2017)

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Wed 18 Jan 2017 – Wed 15 Mar 2017

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January 2017

Wed 18
Data Carpentry new (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Course materials are available here.

This course is organized in collaboration with ElixirUK and the Software Sustainability Institute.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Thu 19
Data Carpentry new (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Course materials are available here.

This course is organized in collaboration with ElixirUK and the Software Sustainability Institute.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Mon 23
EMBL-EBI: Introduction to EMBL-EBI resources Finished 09:30 - 13:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

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.

Thu 26
Data Analysis and Visualisation in R new Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Fri 27
EMBL-EBI: Introduction to ontologies new Finished 14:00 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to the basic concepts of ontologies and how they are useful in biological applications. The workshop will have three sections:

  • A brief, practical introduction to ontologies and semantics
  • Focus on Gene Ontology (GO), annotations made using GO and tools leveraging those annotations for biomedical discovery.
  • A practical exercise in annotating data with ontologies using EBI tools. A standard annotation exercise will be provided, but attendees are encouraged to bring examples of their own data for annotation, preferably in spreadsheet form.

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.

February 2017

Wed 1
EMBL-EBI: Introduction to Interpro new Finished 09:30 - 13:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to the protein sequence analysis & classification database Interpro.

Interpro is a bioinformatics resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro Consortium.

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.

Thu 2
EMBL-EBI: An Introduction to Sequence Searching Finished 14:00 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop introduces the area of sequence similarity searching and focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases. This session will include tips on which tool and database to use, input formats, how to change parameters and how to interpret the results pages.

Further information 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 or register your interest by linking here.

Fri 3
EMBL-EBI: Interactions & Pathways - IntAct & Complex Portal Finished 14:00 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to the protein interaction database IntAct and the Complex Portal service. You will also briefly learn how to visualise protein interactions using the Cytoscape application.

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.

Mon 6
EMBL-EBI: Introduction to Chemogenomics Resources Finished 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

An introduction to the chemogenomics resources available from the EBI. The workshop will cover resources such as ChEMBL, SureChEMBL, UniChem and Open Targets.

This session is one of a series of short introductions to EBI Services, run together, but bookable separately (see Related Courses section below).

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 7
Introduction to Scientific Figure Design Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Further information and access 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 your interest by linking here.

Tue 14
EMBL-EBI: Transcriptomics Data and Tools Finished 09:30 - 13:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to the functional genomics resources provided by EMBL-EBI and hands-on practical experience of searching and accessing appropriate data and information. The session will also cover data submission to ArrayExpress using Annotare.

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.

Thu 16
EMBL-EBI: Exploring genetic variation data new Finished 09:15 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to exploring variation data by the use of the European Variation Archive (EVA), Ensembl Variant Effect Predictor (VEP) and UniProt. The workshop will include a mixture of tutorials and hands-on sessions covering a number of key resources to both find and analyse variation data.

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.

Mon 20
CRUK: Analysis of publicly available microarray data (1 of 2) Finished 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

Although microarrays have been superseded by high-throughput sequencing technologies for gene expression profiling, years of experience gained from analysing microarray data has led to a variety of analysis techniques and datasets that can be exploited in other contexts. In this course, we will focus on retrieving and exploring microarray data from public repositories such as Gene Expression Omnibus (GEO).

Course materials can be found here.

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.

Tue 21
An Introduction to Solving Biological Problems with Python (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 and customize more complex code to fit their needs.

Course materials are available here.

Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Python functions and modules: best practices.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

CRUK: Analysis of publicly available microarray data (2 of 2) Finished 09:30 - 17:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

Although microarrays have been superseded by high-throughput sequencing technologies for gene expression profiling, years of experience gained from analysing microarray data has led to a variety of analysis techniques and datasets that can be exploited in other contexts. In this course, we will focus on retrieving and exploring microarray data from public repositories such as Gene Expression Omnibus (GEO).

Course materials can be found here.

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.

Wed 22
An Introduction to Solving Biological Problems with Python (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 and customize more complex code to fit their needs.

Course materials are available here.

Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Functions and modules are now the focus of a new 1-day course, Python functions and modules: best practices.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Thu 23
An Introduction to Solving Biological Problems with R (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 your interest by linking here.

Fri 24
An Introduction to Solving Biological Problems with R (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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 your interest by linking here.

Tue 28
EMBL-EBI: Interactions & Pathways - Reactome Finished 09:00 - 11:45 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

This workshop will give an introduction to the Reactome pathway database website and analysis tools, using short presentations and practical hands-on exercises. The session will also explain where to learn more, get help, and how to become involved in adding more pathway information to Reactome.

Further information 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.

March 2017

Fri 3
Using the Ensembl Genome Browser Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This 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.

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 7
CRUK: Introduction to Galaxy: Data Manipulation and Visualisation Finished 09:30 - 16:30 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

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.

A Galaxy introduction course covering basic functions, simple data manipulation using use cases and examples and visualisation mostly targeted at first time users.

Further information is available from the course website.

This event is part of a series of training courses organised 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.

Mon 13
Finding and accessing human genome data new Finished 09:30 - 12:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Researchers rely on acquiring external data to validate, benchmark and supplement research findings. Funders require researchers to make their datasets accessible for further reuse.

The goal of this workshop is to bring to the fore existing challenges with genomic data access and reuse. We will introduce a number of tools and resources to simplify #dataaccess and #datasharing.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

CRUK: Basic Unix Finished 11:00 - 17:00 Room 215, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE

The Unix shell has existed since the early days of computers, and yet is still the preferred way to run many popular Bioinformatics tools. This course aims to take the novice and turn them into a beginning Linux user. We will describe the Linux environment so they can start to utilise command-line tools and feel comfortable using a text-based way of interacting with a computer.

This event is part of a series of training courses organised 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.

Tue 14
An Introduction to Solving Biological Problems with PERL (1 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.

Wed 15
An Introduction to Solving Biological Problems with PERL (2 of 2) Finished 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

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.