University of Cambridge Bioinformatics Training

We offer a broad range of undergraduate and postgraduate hands-on training courses focused on bioinformatics and computational biology. These training activities aim at enabling life scientists to effectively handle and interpret biological data.

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  • Image Analysis for Biologists

    26 - 28 Jun 2017

    Cambridge, United Kingdom

    Image Analysis for Biologists https://tess.oerc.ox.ac.uk/events/image-analysis-for-biologists-ec80f491-a531-450e-85aa-90d91a030248 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](http://fiji.sc/), an extensible open source software package. On day 2, we will describe the open [Icy platform](http://icy.bioimageanalysis.org/) 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). On day 3, we will cover time series processing and cell tracking using [TrackMate](http://imagej.net/TrackMate). 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. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2046117&course-title=Image%20Analysis%20for%20Biologists).'' 2017-06-26 08:30:00 UTC 2017-06-28 15:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC

    17 May 2017

    Cambridge, United Kingdom

    EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC https://tess.oerc.ox.ac.uk/events/embl-ebi-network-analysis-with-cytoscape-and-psicquic-7db489c7-b89a-4d0c-8230-da5dae2cb6fb This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1991376&course-title=EMBL-EBI:%20Network%20Analysis%20with%20Cytoscape%20and%20PSICQUIC).'' 2017-05-17 08:30:00 UTC 2017-05-17 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Protein Structure Analysis

    10 - 11 Jul 2017

    Cambridge, United Kingdom

    Protein Structure Analysis https://tess.oerc.ox.ac.uk/events/protein-structure-analysis-2af3f1c0-641d-44b1-99f2-007a33ac4707 This course covers data resources and analytical approaches for the discovery and interpretation of biomacromolecular structures. Day 1 focuses on public repositories of structural data ([Protein Data Bank](http://www.ebi.ac.uk/pdbe/) and [Electron Microscopy Data Bank](https://www.ebi.ac.uk/pdbe/emdb/)) and resources for protein analysis and classification ([Pfam](http://pfam.xfam.org/), [InterPro](https://www.ebi.ac.uk/interpro/) and [HMMER](https://www.ebi.ac.uk/Tools/hmmer)). Day 2 covers how to find information about the structure and function of your protein sequence using [CATH](http://www.cathdb.info/), principles of modern state-of-the-art protein modelling with [ Phyre2](http://www.sbg.bio.ic.ac.uk/phyre2/) and methods for predicting the effects of mutations on protein structure and function using the [SAAP family of tools](http://www.bioinf.org.uk/saap/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2052063&course-title=Protein%20Structure%20Analysis).'' 2017-07-10 08:30:00 UTC 2017-07-11 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Variant Analysis with GATK

    12 - 14 Jul 2017

    Cambridge, United Kingdom

    Variant Analysis with GATK https://tess.oerc.ox.ac.uk/events/variant-analysis-with-gatk-d9b30a6d-2da2-41d4-b9e4-7f62bd187f97 This workshop will focus on the core steps involved in calling variants with the [Broad’s Genome Analysis Toolkit](https://www.broadinstitute.org/gatk/), using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the 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. In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, RNAseq­ specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. The workshop is composed of one day of lectures and two days of hands­on training, structured as follows. Day 1: theory and application of the Best Practices for Variant Discovery in high­throughput sequencing data. Day 2 and the morning of Day 3: hands­on exercises on how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to various use cases and data types. Day 3 afternoon: hands-on exercises on how to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through a publicly accessible cloud-based service. Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non­human data, and we will address some questions regarding adaptations that are needed for analysis of non­-human data, but we will not go into much detail on those points. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2047357&course-title=Variant%20Analysis%20with%20GATK).'' 2017-07-12 08:30:00 UTC 2017-07-14 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Ensembl REST API workshop

    25 - 26 May 2017

    Cambridge, United Kingdom

    Ensembl REST API workshop https://tess.oerc.ox.ac.uk/events/ensembl-rest-api-workshop The [Ensembl project](http://www.ensembl.org/) 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 using the [REST API](http://rest.ensembl.org/) to query the core, variation, compara and functional genomics (regulation) databases. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2027436&course-title=Ensembl%20REST%20API%20Workshop).'' 2017-05-25 08:30:00 UTC 2017-05-26 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Analysis of small RNA-seq data

    2 - 3 May 2017

    Cambridge, United Kingdom

    Analysis of small RNA-seq data https://tess.oerc.ox.ac.uk/events/analysis-of-small-rna-seq-data This course focuses on methods for the analysis of small non-coding RNA data obtained from high-throughput sequencing (HTS) applications (small RNA-seq). During the course, approaches to the investigation of all classes of small non-coding RNAs will be presented, in all organisms. Day 1 will focus on the analysis of microRNAs and day 2 will cover the analysis of other types of small RNAs, including Piwi-interacting (piRNA), small interfering (siRNA), small nucleolar (snoRNA) and tRNA-derived (tsRNA). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2010014&&course-title=Analysis%20of%20small%20RNA-seq%20data).'' 2017-05-02 08:30:00 UTC 2017-05-03 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Introduction to RNA-seq and ChIP-seq data analysis

    22 - 23 Jun 2017

    Cambridge, United Kingdom

    Introduction to RNA-seq and ChIP-seq data analysis https://tess.oerc.ox.ac.uk/events/introduction-to-rna-seq-and-chip-seq-data-analysis-744f24d3-0d96-4b53-a91a-137d752b9031 The aim of this course is to familiarize the participants with the primary analysis of datasets generated through two popular high-throughput sequencing (HTS) assays: ChIP-seq and RNA-seq. This course starts with a brief introduction to the transition from capillary to high-throughput sequencing (HTS) and discusses quality control issues, which are common among all HTS 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. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2017446&course-title=Introduction%20to%20RNA-seq%20and%20ChIP-seq%20data%20analysis).'' 2017-06-22 08:30:00 UTC 2017-06-23 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Analysis of RNA-seq data with Bioconductor

    4 - 5 May 2017

    Cambridge, United Kingdom

    Analysis of RNA-seq data with Bioconductor https://tess.oerc.ox.ac.uk/events/analysis-of-rna-seq-data-with-bioconductor This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq data. We will present a workflow for the analysis RNA-seq data starting from aligned reads in bam format and producing a list of differentially-expressed genes. We will also describe the various resources available through Bioconductor to annotate, visualise and gain biological insight from the differential expression results. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2036601&course-title=Analysis%20of%20RNA-seq%20data%20with%20Bioconductor).'' 2017-05-04 08:30:00 UTC 2017-05-05 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • An introduction to metabolomics and its application in life-sciences

    19 - 20 Jun 2017

    Cambridge, United Kingdom

    An introduction to metabolomics and its application in life-sciences https://tess.oerc.ox.ac.uk/events/an-introduction-to-metabolomics-and-its-application-in-life-sciences The goal of metabolomics is to identify and quantify the complete biochemical composition of a biological sample. With the increase in genomic, transcriptomic and proteomic information there is a growing need to understand the metabolic phenotype that these genes and proteins ultimately control. The aim of this course is to provide an overview of metabolomics and its applications in life sciences, clinical and environmental settings. Over 2 days we will introduce different techniques used to extract metabolites and analyse samples to collect metabolomic data (such as HPLC or GC-based MS and NMR), present how to analyse such data, how to identify metabolites using online databases and how to map the metabolomic data to metabolic pathways. The course content will predominantly be based on analysing samples from model plant species such as Arabidopsis thaliana but the procedures are transferable to all other organisms, including clinical and environmental settings. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2013503&course-title=An%20introduction%20to%20metabolomics%20and%20its%20application%20in%20life-sciences).'' 2017-06-19 08:30:00 UTC 2017-06-20 17:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Introduction to genome variation analysis using NGS

    18 - 19 May 2017

    Cambridge, United Kingdom

    Introduction to genome variation analysis using NGS https://tess.oerc.ox.ac.uk/events/introduction-to-genome-variation-analysis-using-ngs This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including: *an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis; *an overview of available analytical tools and discussion of their limitations; and *hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1923651&course-title=Introduction%20to%20genome%20variation%20analysis%20using%20NGS).'' 2017-05-18 08:30:00 UTC 2017-05-19 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Statistical Analysis using R

    26 Apr 2017

    Cambridge, United Kingdom

    Statistical Analysis using R https://tess.oerc.ox.ac.uk/events/statistical-analysis-using-r-ea9ff23f-1d5f-40ec-b8c9-6cec0a89f873 Statistics are an important part of most modern studies and being able to effectively use a statistical package will help you to understand your results. This course provides an introduction to some statistical techniques through the use of the R language. Topics covered include: Chi2 and Fisher tests, descriptive statistics, t-test, analysis of variance and regression. Students will run analyses using statistical and graphical skills taught during the session. The course manual can be found [here](http://www.bioinformatics.babraham.ac.uk/training/R_Statistics/Introduction%20to%20Statistics%20with%20R.pdf). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1923506&&course-title=Statistical%20analysis%20using%20R).'' 2017-04-26 08:30:00 UTC 2017-04-26 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • An Introduction to MATLAB for biologists

    15 - 16 May 2017

    Cambridge, United Kingdom

    An Introduction to MATLAB for biologists https://tess.oerc.ox.ac.uk/events/an-introduction-to-matlab-for-biologists-44edbb74-176f-4e4b-97d7-ab41f9f379aa This course aims to give you an introduction to the basics of Matlab. During the two day course we will use a practical based approach to give you the confidence to start using Matlab in your own work. In particular we will show you how to write your own scripts and functions and how to use pre-written functions. We will also explore the many ways in which help is available to Matlab users. In addition we will cover basic computer programming in Matlab to enable you to write more efficient scripts. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2059297&&course-title=An%20Introduction%20to%20MATLAB).'' 2017-05-15 08:30:00 UTC 2017-05-16 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Analysis of DNA Methylation using Sequencing

    14 Jun 2017

    Cambridge, United Kingdom

    Analysis of DNA Methylation using Sequencing https://tess.oerc.ox.ac.uk/events/analysis-of-dna-methylation-using-sequencing-1f6900ee-426e-416a-8bab-4f661f9fb246 This course will cover all aspects of the analysis of DNA methylation using sequencing, including primary analysis, mapping and quality control of BS-Seq data, common pitfalls and complications. It will also include exploratory analysis of methylation, looking at different methods of quantitation, and a variety of ways of looking more widely at the distribution of methylation over the genome. Finally the course will look at statistical methods to predict differential methylation. The course will be comprised of a mixture of theoretical lectures and practicals covering a range of different software packages. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1923832&course-title=Analysis%20of%20DNA%20Methylation%20using%20Sequencing).'' 2017-06-14 08:30:00 UTC 2017-06-14 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Working with Python: functions and modules

    28 Apr 2017

    Cambridge, United Kingdom

    Working with Python: functions and modules https://tess.oerc.ox.ac.uk/events/python-functions-and-modules-best-practices-173eaa37-660b-4c91-b93b-d462342af8d4 This course will cover concepts and strategies for working more effectively with Python with the aim of writing reusable code. In the morning session, we will briefly go over the basic syntax, data structures and control statements. This will be followed by an introduction to writing user-defined functions. We will finish the course by looking into how to incorporate existing python modules and packages into your programs as well as writing you own modules. Course materials can be found [here](https://github.com/pycam/python-functions-and-modules/blob/master/python_fm_intro.ipynb). Note: this one-day course is the continuation of the [Introduction to Solving Biological Problems with Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-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. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2052485&course-title=Working%20with%20Python:%20functions%20and%20modules).'' 2017-04-28 08:30:00 UTC 2017-04-28 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use

    22 - 24 May 2017

    Cambridge, United Kingdom

    ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use https://tess.oerc.ox.ac.uk/events/elixir-goblet-gtn-hackathon-for-galaxy-training-material-re-use This three day workshop will bring together representatives of the ELIXIR Galaxy Working Group, as well as trainers and developers working on the Galaxy project from Europe and beyond, to: *Build on an existing collection of [Galaxy training materials](https://github.com/galaxy-project/training-material). During the workshop we will collate additional materials, including topics relevant to the ELIXIR use-cases, and ensure that, for each workflow, a minimum set of training materials is available, including slides, practical exercises, Docker containers, and Galaxy tours. *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 they are properly described, according to the ELIXIR/GOBLET guidelines, and BioSchemas compliant. *Extend the existing “curated” dataset collection and assign DOI to individual datasets. *Increase the number of Docker/Virtual Machines available for easy installation of Galaxy training environments. *Explore the feasibility of developing a toolkit to facilitate plug in of different datasets in existing training material/workflows through a templating approach. 2017-05-22 08:30:00 UTC 2017-05-24 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • An Introduction to Solving Biological Problems with R

    15 - 16 Jun 2017

    Cambridge, United Kingdom

    An Introduction to Solving Biological Problems with R https://tess.oerc.ox.ac.uk/events/an-introduction-to-solving-biological-problems-with-r-4d582e5b-cd40-487c-b145-1a62c30639a1 [R](https://www.r-project.org/) 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](http://cambiotraining.github.io/r-intro/). 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](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-intR) course. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1923763&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20R).'' 2017-06-15 08:30:00 UTC 2017-06-16 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • An Introduction to Solving Biological Problems with Python

    12 - 13 Jun 2017

    Cambridge, United Kingdom

    An Introduction to Solving Biological Problems with Python https://tess.oerc.ox.ac.uk/events/an-introduction-to-solving-biological-problems-with-python-db575358-92e7-4588-b001-dd0fe0df5f8e 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](http://pycam.github.io). 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, [Working with Python: functions and modules](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-advpython/). Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=1923528&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2017-06-12 08:30:00 UTC 2017-06-13 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
scraper created University of Cambridge Bioinformatics Training at 2016-11-22 04:01:55 UTC.