skip to navigation skip to content

All Bioinformatics courses

Show:
Show only:

Showing courses 51-75 of 107
Courses per page: 10 | 25 | 50 | 100

EMBL-EBI: Interactions & Pathways Tue 13 Mar 2018   09:30 Finished

This workshop is aimed at giving life scientists training on how to explore and use protein interaction and pathway bioinformatics resources. This course looks at the data repositories, resources and tools available and shows attendees how to both find information on a single molecule and how to build high-quality networks to enable network analysis.

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.

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.

EMBL-EBI: Interactions & Pathways - Reactome Tue 28 Feb 2017   09:00 Finished

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.

EMBL-EBI: Introduction to Chemogenomics Resources Mon 6 Feb 2017   09:30 Finished

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.

EMBL-EBI: Introduction to EMBL-EBI resources Mon 23 Jan 2017   09:30 Finished

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.

EMBL-EBI: Introduction to Interpro new Tue 27 Feb 2018   09:00 Finished

Employ InterPro to help you answer your research questions!

This workshop will help you find out why there is a need to automatically annotate proteins, how protein family databases can help meet this challenge, and how InterPro pulls together a number of such databases, allowing you to classify unknown protein sequences and identify their function. The module is a combination of presentations and hands-on practical exercises. You will explore the various features of an InterPro entry, and design a workflow to utilise InterPro in the analysis of real world 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.

The European Nucleotide Sequence Archive (ENA) is a global database for storing experimental nucleotide data and also interpreted data (alignment files, variant calling, analysis results). The data is submitted by scientists conducting sequencing experiments and publishing research in the area. Data is fully searchable and available for download. Sequence data includes raw NGS files (FastQ, BAM…), assembled genomes and transcriptomes, and annotated sequences (protein coding genes, non coding RNA, barcode genes, HLA genes)

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.

EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC Wed 22 May 2019   09:30 Finished

This module provides an introduction to the theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to analyse large-scale datasets generated these to by techniques such as RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of Cytoscape and selected network analysis apps.

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.

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.

This course will give an introduction to the basic concepts of ontologies and how they are useful in biological applications. We will explain what a biomedical ontology is and present the two primary types of ontology: (i) domain ontology and (ii) application ontology, using examples as Gene Ontology (GO) and Experimental Factor Ontology (EFO). The module will also go into details of why big data need ontologies and the ontology capabilities in advanced computational biology.

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.

EMBL-EBI: Protein Sequence Databases with UniProt Mon 5 Feb 2018   09:30 Finished

This workshop aims to give the scientific community hands on experience on how to access and effectively use protein data in UniProt. UniProt is a high-quality, comprehensively and thoroughly annotated protein resource. Participants will be able to access detailed information on protein function and millions of protein sequences in the UniProt knowledgebase, including isoforms and disease variants.

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.

EMBL-EBI: Transcriptomics Data and Tools Fri 17 May 2019   09:30 Finished

This workshop is designed for researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. This will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

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.

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.

Ensembl REST API workshop Thu 11 Apr 2019   09:30 Finished

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.

This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.

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.

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.

This event will consist of two parts. The first part of the workshop aims to provide new trainers with guidance and tips for developing and delivering training in bioinformatics, exploring a range of methods appropriate to different learning styles and examining the requirements for a successful course (both scientific and logistic). It will be based on the EXCELERATE Train-the-Trainer (TtT) course materials and content will be tailored to trainers that are involved in teaching bioinformatics to clinical audiences.

The second part of the workshop will focus on "Best practices in clinical bioinformatics training", providing an opportunity for people already involved in this kind of training, or in the process of developing it, to come together and exchange best practice/experiences. Participants will include training providers of the Health Education England’s MSc in Genomics Medicine from several UK Universities as well as other providers active in this area, from around Europe and beyond.

This event is co-sponsored by ELIXIR-EXCELERATE and Health Education England (HEE).

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 by linking here.

Extracting biological information from gene lists new Fri 1 Mar 2019   09:30 Finished

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists.

This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication.

Course materials are available 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 or register your interest by linking here.

Finding and accessing human genome data new Mon 13 Mar 2017   09:30 Finished

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.

This 2-days workshop will bring together bioimage analysts, trainers and developers from NEUBIAS, EuroBioImaging and Global BioImaging, as well as ELIXIR’s Bioschemas and TeSS developers, and anyone willing to contribute, to foster new collaborations between ELIXIR and key initiatives from the image analysis community, to:

  • Build a collection of curated image analysis training materials. Many materials are currently available online for several topics but no consistent curation has been applied to them to make them easily discoverable. During the workshop we will collate materials and ensure that, for each image analysis workflow, a minimum set of training materials is available, including slides, practical exercises, Docker container, etc.
  • Improve materials’ annotations (introducing full BioSchemas compliance) and align them with existing ELIXIR efforts (linking to TeSS). During the workshop, materials will be curated to ensure that they are properly described, according to the existing ELIXIR guidelines, and BioSchemas compliant. Consequently the curation will enable materials, hosted by individual providers, to be discoverable via TeSS.
  • Increase the number of Docker/Virtual Machines (VMs) available for easy installation of image analysis training environments. We will focus on: (i) specific pipelines for which containers currently do not exist, (ii) workflows that are of interest to the NEUBIAS/GBI communities and (iii) for which expertise will be available among the workshop participants. This would be incredibly helpful for running future image analysis courses, including the next GBI course planned for October 2018, as it would increase portability of training environments, reducing the burden of lengthy, and often troublesome, software installations.
Genome Annotation with Artemis Thu 28 May 2015   09:30 Finished

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.

High Performance Computing: An Introduction Thu 18 Oct 2018   09:30 Finished

The course aims to give an introductory overview of High Performance Computing (HPC) in general, and of the facilities of the High Performance Computing Service (HPCS) available at the University of Cambridge.

Practical examples of using the HPCS clusters will be used throughout, although it is hoped that much of the content will have applicability to systems elsewhere.

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

A hands-on interactive course that will introduce you to how to analyse genomic sequences in the command line environment. Examples will focus on metagenomics data but the course is suitable to anyone starting to analyze high-throughput sequencing data.

This course will be taught by Dr. Adina Howe from Iowa State University. Her group focuses on integrating traditional microbiology approaches with metagenomics and computational biology as investigative tools to understand environmental microbial populations

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

Image Analysis for Biologists Mon 11 Dec 2017   09:30 Finished

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

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 on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate. The afternoon of day two will focus on understanding the basics of deconvolution and colocalisation, using tools in Fiji to look at basic examples of how to apply deconvolution and how to carry out colocalisation analysis in fluorescence microscopy.

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.

Image Analysis for Biologists Mon 24 Jun 2019   09:30 [Full]

This course will focus on computational methods for analysing cellular images and extracting quantitative data from them. The aim of this course is to familiarise the participants with computational image analysis methodologies, and to provide hands-on training in running quantitative analysis pipelines.

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 on Fiji, an extensible open source software package.

On day 2, we will cover time series processing and cell tracking using TrackMate and advanced image segmentation using Ilastik. Additionally, in the afternoon we will run a study design and data clinic (sign up will be required) for participants that wish to discuss their experiments.

On day 3, we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualisation, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager).

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.

Image Processing and Visualisation with LithoGraphX new Thu 4 Aug 2016   10:00 Finished

LithoGraphX is a software to visualize, process and analyse 3D images and meshes.

On the first day of this course, we will demonstrate how to use LithoGraphX to visualize, clean and process 2D and 3D images. We will cover: (i) how to extract cell shape from 2D or 3D images by marking the cell wall or membrane, (ii) how to extract key morphological features and (iii) how to use these features to build a cell classifier. The first day is intended for biologists and computer scientists interested in using LithoGraphX.

On the second day, we will see how to write and distribute extensions to LithoGraphX. To this purpose, we will learn more about the internals of LithoGraphX and its API both in C++ and Python. The second day is intended for computer scientists wanting either to write their own algorithm or automate complex protocols.

Participants can choose to register for both days or for individual days, depending on their interest and background knowledge.

The timetable for this event can be found here.

This course is organized in collaboration with Dr Susana Sauret-Gueto from the OpenPlant Lab of the Department of Plant Sciences of the University of Cambridge.

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.

Interpreting the clinical genome with DECIPHER new Fri 8 Jul 2016   09:30 Finished

DECIPHER is a collaborative data sharing and interpretation platform that enables the secure upload, analysis and subsequent sharing of anonymised phenotype-linked patient variant data in rare genetic disorders.

DECIPHER is a worldwide user community of over 250 clinical genetics centres and research groups from over 40 countries that utilise the built-in tools for aiding the interpretation of variants as well as to discover other patients that share similar phenotype and genomic findings.

DECIPHER facilitates collaboration and exchange of information between a global community of clinical centers and researchers leading thereby accelerating discovery and diagnosis. Access to consented anonymised records is free to all users. User accounts are provided to bona-fide clinicians and lab scientists to enable deposition and sharing of anonymised patient data.

The purpose of this half-day workshop is to acquaint participants with the DECIPHER website and database and introduce the various built-in tools for visualisation and interpretation of phenotype-linked genomic variation in anonymised consented patient data. It is hoped that by the end of this workshop, users will be able to carry out effective searches of data, use the built-in genome browser to visualise variation in context of other pathogenic and reference data sources, find other patients with similar variants and shared phenotypes, and identify most likely causes of phenotypic presentation by gene prioritisation.

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.

[Back to top]