3rd BiVi Annual Meeting Workshops

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Workshop Timetable for 21st April 2017

Registered delegates, please make Workshop Preferences by 10th April 2017. See Delegate Information for instructions on making preferences.

09:30-10:45 11:15-12:30 12:30-13:30 13:30-14:45 15:15-16:30
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

Workshop Descriptions


Morning Session Short Workshops

These two shorter workshops can both be taken as one combined option for the morning session.

 MARender web-based 3D model visualisation (9:30 – 10:45)

Richard Baldock, MRC Human Genetics Unit, IGMM, University of Edinburgh, UK.

Tool: MARender

The Mouse Atlas project (emouseatlas.org) has created a series of 3D reconstructions of the mouse embryo with associated segmentations of anatomy. To make these large data-sets available to the community we have developed a javascript library extension to three.js to deliver a simple mechanism to publish an interactive 3D visualisation of surface-based and grey-level section data in a standard web-browser. In this tutorial we will walk through the various tools that can be used to go from grey-level image to a segmented volume and then to a webGL visualisation.

Further materials

Examples of use of the MARender library:

- http://aberlour.hgu.mrc.ac.uk/MARenderTests/ema103-test.html

- http://aberlour.hgu.mrc.ac.uk/Educational_Tutorials/MARenderView.html?config=cardiovascular_system/marender-def.json

- http://www.emouseatlas.org/eAtlasViewer_ema/application/ema/anatomy/EMA24.php


The key javascript library is available from github: https://github.com/ma-tech/MARender. To build the 3D models, generate the segmentation and to provide a json data-file for a specific renderer can be developed using a range of tools. In this demonstration we will show applications that we use within the MouseAtlas for this purpose. These we can provide for Mac OSX and some varieties of linux. If you want to come to this session please contact Richard.Baldock@igmm.ed.ac.uk


 Gene Expression Commons (11:15 – 12:30)

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:

  • Firefox 27 and above
  • Chrome 30 and above
  • IE 11 on Windows 7 and above
  • Edge
  • Opera 17 and above
  • Safari 9 and above
  • Android 5.0 and above

Making your account on Gene Expression Commons in advance would be great.


Morning Session Workshops

 Aequatus and the Galaxy workflow (09:30 – 12:30)

Anil Thanki, Earlham Institute, Norwich, UK
Nicola Soranzo, Earlham Institute, Norwich, UK

Tool: Aequatus

Aequatus.js is a JavaScript library that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignments and gene feature information typically generated through the Ensembl Compara GeneTree pipeline.

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.

Intended Audience

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.


 Visualising structured data with Python, pandas and seaborn (09:30 – 12:30)

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.

What will be covered in the session:

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:

  • jupyter
  • pandas
  • seaborn

You are also strongly encouraged to bring your own datasets to play with!


 Phyre (09:30 – 12:30)

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.

Further materials






Mac, PC, Unix with internet browser Firefox, Chrome or Safari


 Zegami Workshop (09:30 – 12:30)

Update (12/04/17): Unfortunately, this workshop will no longer be running

Stephen Taylor, University of Oxford
Roger Noble, Zegami Limited

Tool: Zegami

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:

  1. Introduction to Zegami, basic and advanced features
  2. Generation of collections
  3. Using advanced features such as dashboards and other plugins with your collections
  4. Integrating with existing image analysis tools/pipelines

Example collections will be supplied but it is encouraged to bring your own images and metadata.

Further materials



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.


Afternoon Session Workshops

 Reactome (13:30 – 16:30)

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.

Further materials

- http://www.ebi.ac.uk/training/online/course/reactome-quick-tour/what-reactome


Modern web browser (Chrome, Firefox, IE, Safari etc.)


 Using SeqMonk to visualise and explore large NGS datasets (13:30 – 16:30)

Simon Andrews, Babraham Institute

Tool: SeqMonk

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.


 Workshop on Gene Network Analysis using Miru (13:30 – 16:30)

Prof. Tom Freeman, University of Edinburgh, Founder, Kajeka Ltd

Tool: Miru (formerly known as BioLayout Express3D)

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.

Further materials

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.

See also http://www.biolayout.org/about/publications/


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.


 Jalview 2.10.2, tips, tricks, and undocumented bits (13:30 – 16:30)

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.

Target audience

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.

Further materials


Introduction to Jalview manual

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.


All-day Workshop

 Creating data visualizations (09:30 – 16:30)

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.

In this workshop, we will look into the process of visual design focussing on three different aspects: the investigator, the data, and the visualisation itself. Most of the time will be spent on learning and practising how to explore the design space. Our weapon of choice will be pen and paper. The last part of the workshop will be dedicated to D3.js, a JavaScript library which became the industry standard for creating customized web-based visualisations. Together we will go through the basics of HTML, CSS, SVG, JavaScript, and finally D3.js.