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Registered delegates, please make Workshop Preferences by 10th April 2017. See Delegate Information for instructions on making preferences.
|MORNING SESSION OPTIONS||Lunch||AFTERNOON SESSION OPTIONS|
|MARender - Richard Baldock||Gene Expression Commons - Jun Seita||Reactome - Steve Jupe|
|Aequetas with Galaxy - Anil Thanki||SeqMonk - Simon Andrews|
|Visualisation with Python - Martin Jones||Miru - Tom Freeman|
|Jalview - Jim Procter|
|Creating data visualisations - Jan Aerts & Marc Streit|
These two shorter workshops can both be taken as one combined option for the morning session.
Richard Baldock, MRC Human Genetics Unit, IGMM, University of Edinburgh, UK.
Examples of use of the MARender library:
Jun Seita, RIKEN Center for Integrative Medical Sciences, Japan
Tool: Gene Expression Commons
Each gene has a different dynamic-range of its expression. Gene Expression Commons provides dynamic-range of each gene by meta analysis of thousands of publicly available microarray data. By mapping your data onto it, you can profile absolute expression of any gene on the microarray through intuitive web interface.
This session covers how dynamic-range based gene expression profiling works, how to explore absolute gene expression profiles of existing data in Gene Expression Commons, and how to submit your own data to Gene Expression Commons.
Modern web browser:
Making your account on Gene Expression Commons in advance would be great.
Anil Thanki, Earlham Institute, Norwich, UK
Nicola Soranzo, Earlham Institute, Norwich, UK
The Ensembl GeneTrees pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover homologous gene families. Since expertise is required to configure and run the relatively complex pipeline via the command-line, we created GeneSeqToFamily, an open-source Galaxy workflow. GeneSeqToFamily helps users to run potentially large-scale gene family analyses without requiring the command-line while still allowing tool parameters, configurations, and the tools themselves to be modified.
Gene families discovered with GeneSeqToFamily can be visualised directly inside Galaxy using the Aequatus.js interactive tool, integrated as a visualisation plugin.
The course is aimed at researchers (graduate students, postdocs, and principal investigators) working in plant or animal genomic annotation and interested in applying comparative genomics approaches to find and visualise gene families.
Most of the workshop will be hands-on and teach participants how to integrate data, and perform simple and complex analysis within Galaxy. It will also cover data visualisation within Galaxy.
No programming or Linux command line experience is required.
Martin Jones, pythonforbiologists.com
Tool: Visualising structured data with Python, pandas and seaborn
The scientific Python ecosystem is at an exciting point for those of us that are interested in data visualisation. There has emerged over the last few years a reasonably standard "stack" of tools that work well together and are excellent for rapidly exploring complex datasets. In this workshop we will practise using the pandas package to import, filter, clean and generally manipulate data, and the seaborn package to visualise the results. We will use biological examples throughout and concentrate on exploring patterns in large datasets.
reading data into pandas; filtering and cleaning data; aggregating and grouping data; visualising distributions; splitting visualisations across categories and factors
The easiest way to obtain Python and all the packages we will use is to download and install Anaconda: https://www.continuum.io/downloads which has installers for Windows, OSX and Linux machines. Alternatively, if you are already using Python and want to work in your own environment, install the following packages:
You are also strongly encouraged to bring your own datasets to play with!
Update (14/04/17): Unfortunately, this workshop will no longer be running
Mike Sternberg, Imperial College London
Stefans Mezulis, Imperial College London
Tool: Phyre2, SuSPect, PhyreStorm and EzMol
The tutorial will focus on the Phyre2 web server which predicts a protein 3D structure from its sequence. Phyre2 provides a set of suggested models with confidences and the user can inspect in detail the alignment. Facilities are provided to assess the likely accuracy of the coordinates. Phyre2 also reports the results of our SuSPect server which predicts the phenotypic effect of a missense mutation in a protein.
PhyreStorm is a rapid method to take a protein coordinate and find similar structures in the PDB. A typical search takes minutes. The tutorial will also introduce the beta version of EzMol which is a simple-to-use web based graphics program to display protein structure. EzMol is designed for the occasional user who does not wish to recall command lines or extensive choices of menu options.
Mac, PC, Unix with internet browser Firefox, Chrome or Safari
Update (12/04/17): Unfortunately, this workshop will no longer be running
Stephen Taylor, University of Oxford
Roger Noble, Zegami Limited
Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a visual way of manipulating images and derived values (from the images themselves or annotated metadata) on a massive scale, allowing querying and organisation of large image based collections.
The course will cover:
Example collections will be supplied but it is encouraged to bring your own images and metadata.
The trainee will require a modern web browser. Chrome is recommended. Example collections will be supplied but it is encouraged to bring your own images and metadata.
A cloud environment will be provided.
Steve Jupe, EMBL-EBI
Tool - Reactome
Reactome represents human biological processes as interconnected molecular events or 'reactions'. Reactions can be considered as 'steps' in a pathway. Pathways are organized hierarchically. Reactome uses a unique overview visualization of the hierarchy, representing pathways at the uppermost hierarchical level as central nodes (circles) with subpathways arranged concentrically (in rings) around them. Many have further concentric rings of ‘child’ subpathways. Pathway nodes are connected to their subpathways by edges (lines). Nodes in the overview link to detailed pathway diagrams that use a style based on SBGN. These have several features intended to ensure an appropriate level of information detail, including subpathway shading and fade-in of labels, commonly occurring small molecules and structures. Pathway analysis and expression tools use coloured overlays on the overview and pathway diagrams to indicate result location and significance. Pathway diagrams and analysis methods are available as reusable widgets.
Modern web browser (Chrome, Firefox, IE, Safari etc.)
Simon Andrews, Babraham Institute
SeqMonk is a well-established desktop application designed for biologists to take an explorative approach to the robust analysis of large sequencing datasets. In this workshop we will show how this software can be used to visualise, explore and analyse some common data types (ChIP-Seq and RNA-Seq) and how this type of interactive analysis can help to identify issues which might be missed by more automated pipelines.
The workshop has no specific requirements for previous experience in the analysis of sequencing data and is suitable for people with a computational, biological or bioinformatics background.
Prof. Tom Freeman, University of Edinburgh, Founder, Kajeka Ltd
The workshop will include a short general introduction to the principles of network visualisation and analysis and the use of networks as a generic medium to understand relationships between biological entities. I will introduce the basics of network visualisation and navigation within Miru, and principles of correlation analysis. The course will then explore how numerical data such as gene expression data (microarray or RNA-seq) can be explored and clustered within the tool, and how you can use the software to rapidly extract meaning from large and complex biological datasets.
Shih et al., Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders. J Pathol DOI: 10.1002/path.4864 (2017).
Theocharidis A., van Dongen S., Enright A.J. and Freeman T.C. Network Visualisation and Analysis of Gene Expression Data using BioLayout Express3D. Nature Protocols 2009; Vol.4 No.10:1535-50.
Participants will need to bring their laptop (all OS supported) and a 3 button mouse.
Ideally participants will download and install the tool prior to the course http://kajeka.com/miru/, a licence to the full version of the software will be provided on the day.
Jim Procter, University of Dundee, UK
Tool name: Jalview
Jalview is a stand-alone application for creation, interactive visualisation, annotation and analysis of multiple sequence alignments.
Originally designed for exploring sequence-structure relationships in protein sequence alignments, it now also includes support for working with RNA, analysis of protein coding regions, and integrates with UCSF Chimera for high-performance structure visualisation
In this workshop we will introduce the key features in Jalview, and give participants the opportunity to explore recently developed capabilities including linked CDS/Protein alignments, and interactive exploration of sequence variants on protein structure. We'll also introduce Jalview's scripting interface and demonstrate how Jalview can be extended with new types of alignment analysis calculations and annotation clients.
This workshop will provide an opportunity for anyone teaching bioinformatics with Jalview to bring themselves up to date with the latest developments. It is also aimed at people with an interest in adapting and improving Jalview for use in their own research or learning how Jalview could better integrate with tools they develop.
Additional materials will be provided closer to the time.
Familiarity with molecular sequence alignment and analysis. Laptop capable of running Java 1.8 or later with at least 2G memory. We recommend that you watch the Getting started with Jalview playlist and verify that you can launch the latest version of Jalview on your machine.
Jan Aerts, ESAT/STADIUS, Visual Data Analysis Lab KU Leuven
Marc Streit, Institute of Computer Graphics, Johannes Kepler University Linz
Techniques: Design workshop (pen & paper), D3.js
Creating Customized Visualizations: Design Workshop (pen & paper) + D3.js Introduction
With datasets becoming more and more complex, generic representations often cannot convey the richness hidden inside them anymore which can result in patterns being missed and insights that stay just across the horizon. As a result, custom visualization become necessary, which has led to circos, hive plots, ABySS Explorer and UpSet.