Posts Tagged ‘visualization’

VIZBI 2014 tutorial – Network visualisation and analysis of high dimensional data using BioLayout Express3D

Thursday, January 16th, 2014

BioLayout Express3D is a powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high dimensional data. In biology, networks can be generated from interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. BioLayout Express3D has been specifically designed for visualisation, clustering, exploration and analysis of very large network graphs in 2- and 3-dimensional space derived primarily, but not exclusively, from biological data.

This tutorial is designed to cover the basics of network visualisation and analysis using this tool with particular emphasis on the analysis of high dimensional data such as that generated by microarray analysis or RNA-seq analyses. If time is available we will also demonstrate the use of the tool in the context of pathway modelling.

Participants will need to bring with them a laptop of any flavour (the program does not run on tablets) with the program and Java installed. To make the most use of the session it would be preferable to have at least a medium range graphics card e.g. AMD or Nvidia and a three-button mouse to allow to exploration of reasonable sized graphs in 3D space.

If in doubt – run the webstart version on the website and if you have any issues or questions contact support@biolayout.org.

VIZBI 2014 tutorial – ‘UCSC Genome Browser’

Tuesday, January 7th, 2014

The UCSC Genome Browser integrates information from a wide variety of genomic resources, including gene predictions; disease associations, including HGMD, OMIM and locus-specific databases; gene-expression data; copy-number variation; comparative genomics; SNPs; HapMap data; gene-chip mappings; and histone- and DNA- modification data.

The large number of genome-wide datasets available on the Browser allows users to pursue inquiries requiring multiple lines of evidence all in one location. By allowing users the flexibility to select only those data relevant to making a particular scientific argument, the Browser allows the pursuit of inquiry-driven data analysis by displaying all pertinent information in one graphical view.

This workshop will introduce participants to functions of the Genome Browser often missed by casual users, especially new features. Navigation and Browser search strategies, Custom Tracks, and the Session tool for sharing the results of inquiries with colleagues will be presented, as will export of camera-ready .pdf files for publication.

The Table Browser, a powerful tool for direct mining of the underlying data tables will be demonstrated. New functionality, including the user-hosting of new organisms and the analysis and display of user-generated variants will be demonstrated.

Participants should bring laptops and be prepared to learn the Browser by solving biological data problems.

VIZBI 2014 tutorial – ‘Exploring biological networks by means of visualization: Use R and NetBioV’

Tuesday, January 7th, 2014

The analysis of biological networks starts with the visualization of the networks. This can be seen as a form of an exploratory analysis. The main aim of an effective visualization is to highlight key structural properties of a network. Besides the connectivity of the nodes, there is a large variety of structural features of a network that can instead be exploited for an effective visualization. For example, modules, shortest paths or hierarchical levels.

We developed an R package called NetBioV (network biology visualization) that provides many easy to use functions, layout styles and color schemes to visualize biological networks

The tutorial is organized as follows:
• Introduction of biological networks
• Overview of standard graph layout algorithms
• Overview of visualization software
• Network visualization using R
• Visualization of biological networks using NetBioV, emphasizing structural components:
– Global view
– Modular view
– Hierarchical view
• Conclusions

VIZBI 2014 tutorial – ‘A Sampling of Open Source Visualization, Analytics, and Informatics Tools’

Monday, January 6th, 2014

This is an introductory tutorial on several open source and freely available tools recently introduced, extended, or improved at Kitware. Among the tools we will cover are web-based adaptations of our widely used ParaView Tool (ParaViewWeb) for viewing big data, Computational Fluid Dynamics (CFD) simulations and volume rendering; new developments in chemical simulation and cheminformatics; recently released Informatics tools such as Visomics, new D3 based libraries, and geospatial visualizations for omics, medical informatics research, and web based visualizations; and open source medical imaging tools for viewing and analysing CT, MRI and microscope derived images.

Attendees will gain introductory level knowledge of several key open source platforms developed at Kitware and will leave the session with the software installed on their computers. Attendees will also be introduced to the concept of open source and collaborative tools such as bug trackers, mailing lists, wikis, source code repositories and dashboards; and will know where they can be found for the tools discussed in the course.

Further material is openly available on the web using Kitware provided tutorials, documentation, and communities.
Training links:
http://www.kitware.com/media/protrainingwebinars.php
https://github.com/InsightSoftwareConsortium/ITKv4-TheNextGeneration-Tutorial

VM’s for the ITK Tutorial:
http://midas3.kitware.com/midas/folder/9388
https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks

Documentation:
http://www.itk.org/Wiki/ITK/Documentation
http://www.paraview.org/paraview/help/documentation.html
http://www.vtk.org/VTK/help/documentation.html

VIZBI 2014 tutorial – ‘Visualization and analysis of multi-dimensional images using Vaa3D’

Monday, January 6th, 2014

This tutorial will introduce the recent developments and techniques of 2D, 3D, 4D, and 5D microscopic image analysis and visualization, with a central theme of how to use Vaa3D, a powerful platform for various applications of bioimage informatics.

We will discuss new and exciting challenges in 2D/3D/4D/5D biological and microscopic image computing, as well as large-scale and very large-scale (gigabyte-size to terabyte-size images) visualization and interaction, – with a focus on microscopy images but can be generally useful for other large biomedical images and surface object visualization problems. We are also going to give a relatively detailed tutorial (and demonstration) on how to use Vaa3D for quantitative analysis.

Vaa3D itself (Nature Technology, 2010; Nature Protocols, 2013) is an increasingly used platform for multi-dimensional microscopic image related studies. This suite of software is open source, cross-platform, and has been used in many recent high-profile studies.

Join the tutorial for a hands-on, interactive half day experience to understand the key benefits of Vaa3D. Learn how to operate the software and streamline your analysis for complicated images. Learn how to write plugin programs within minutes and incorporate your favorite tools into Vaa3D.

VIZBI 2014 tutorial – ‘Gitools: data visualization and analysis using interactive heat-maps’

Sunday, January 5th, 2014

Gitools is a desktop application for analysis and visualization of multidimensional data using interactive heat-maps.

Participants will learn:
1. How to load data into Gitools
2. How to obtain the visualization that fits your needs.
3. How to interact with the heat-map (sort, filter, move, cluster, search)
4. How to integrate different data dimensions.
5. How to visualize column and row annotations.
6. How to perform analyses over the heat-map (e.g. sample level enrichment analysis, group comparison, correlations and others).
7. How to load predefined interactive heat-maps of interest for cancer research, including multidimensional data from The Cancer Genome Atlas, Cancer Cell Line Encyclopedia and IntOGen.
8. How to export heat-maps into a publication-ready figure.
9. How to share your data in the form of interactive heat-maps.

VIZBI 2014 tutorial – ‘Decorated, interactive multiple sequence alignments with HTML5 without Java’

Sunday, January 5th, 2014

Sequence alignment visualization is widely applied. Interactive capabilities, hyper-links, balloon messages and the option to shield annotations and sequences become increasingly important in the ‘omics-era. Java brought interactivity to web pages and has been successfully used for the visualization of sequence alignments. However, the Java runtime-environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for many tasks render Java unnecessary.

Alignment-to-html is the first HTML5 and JavaScript based interactive visualization platform for multiple sequence alignments. Alignment rendering and the user interface is implemented in JavaScript which is natively supported by all browsers. Since Java does not need to be loaded, alignments are rapidly displayed. Only for additional display options, Java needs to be activated: 3D-visualization, phylogenetic trees and Jalview.

Each participant will use a protein family of their own choice to create decorated interactive multiple sequence alignments within an intuitive graphical user interface. Some participants may be interested in non-interactive automated alignment rendering for alignment visualization for web services. They can use the scripting language from the command line.

The tutorial will cover:
– Similarity and diversity color modes
– Balloon texts, color and style for residue selections
– BioDAS sequence features
– Association of 3D-structures and 3D-rendering (Color, ribbons, balls, sticks, labels)
– 3D-Structure superposition
– Sequence icons
– Sequence groups
– Residue index number, number offsets, peptide fragments, PDB-residue number
– Coding triplets, exon number, nucleotide index offsets

VIZBI 2014 tutorial – ‘CELLmicrocosmos Workshop: Molecular Modeling’

Saturday, January 4th, 2014

The modeling of cells and its compounds is an important subject of biological visualization and simulation. The CELLmicrocosmos project develops open source tools and workflows which support students and scientists of various life science-related disciplines in generating the model needed for their specific task in a user-friendly way.

The CELLmicrocosmos 2.2 MembraneEditor can be used to model membranes based on lipid and protein files in PDB format. It is possible to generate structural and compositional heterogeneous membrane patches as well as vesicles. The created structures can be used for visualization purposes, structural analysis or as a base for molecular simulations.

The attendees of this hands-on workshop will learn:
• How to acquire the information needed to generate their specific membrane
• Which data sources exist to solve their specific task(s)
• Which information is already provided by the MembraneEditor and applied to the semi-automatic membrane generation process
• How to use the MembraneEditor and its plug-in interface
• How to create renderings by exporting PDB files to Blender
• How to prepare and start a simple MD simulation in GROMACS by using the GMX-Plugin of the MembraneEditor
• How to make a structural analysis using the tool APL@Voro

All software packages utilized during this workshop are freely available and will be put to practical use. The documentation as well as the software is available at http://Cm2.CELLmicrocosmos.org.
Participants should bring their own laptop. No previous experience with modeling tools is required.
Please install Blender before the workshop starts. All participants who want to do experiments with the GMX-Plugin should install GROMACS on their Linux system.

VIZBI 2014 tutorial – ‘Data hierarchies and ‘omics data: How to use treemaps and related tools for data visualization’

Saturday, January 4th, 2014

In the different field of ‘omics technologies or metaanalyses of biocommunities large sets of abundance or change data on taxonomic or gene expression level have to be explored. Due to the complexity of these data new visualizaton tools have been developed linking experimental data with already available knowledge from gene functional classificatons, taxonomy or metabolic and regulatory networks.

In our tutorial participants will learn to visualize and explore hierarchically or quasi-hierarchically organized data. Metabolic modules, similarly regulated gene clusters, gene functional classes will be extracted and visualized in Voronoi- and swarm-based treemaps, path treemaps or stream graph views, respectively. For this purpose the Paver package will be used.

Participants will learn:
1. The basics of using the Paver application.
2. How to integrate and visualize metabolic data, gene functional classification data and other hierarchically structured data sets in a space saving and aesthetically appealing way.
3. How different visual channels (cell size, color gradients, color saturation, containment and others) support data visualization and how this is implemented in Paver.
4. How brilliant interactive as well as static artwork can be made from expression data tables that helps you with an immediate and intuitive interpretation of your data.

We will give you the essential elements to construct and visualize powerful integrative functional genomics analyses.

The tutorial includes both lectures and hands-on exercises, so bring a laptop with a spreadsheet application and a text editor such as notepad++ or similar. We will provide you with a two month Paver licence, and give you some insights into other available software.

VIZBI 2014 tutorial – ‘Visualisation, Segmentation and Quantitation of 3D Images using Amira’

Friday, January 3rd, 2014

Amira is an advanced general-purpose visualization and 3D reconstruction software for the life sciences. Notably, it displays 3D image data and has a number of versatile editors. For example, it has a powerful segmentation editor that can be used to segment data sets and surface reconstruct the result to produce 3D representations. Amira can import a wide variety of image formats, visualize images in various ways, provide tools for segmentation, analysis and measurement, allow scripting and integration with MATLAB and then export the results in a variety of formats.

This tutorial is divided into two parts, with the following key outcomes and learning objectives:
• Part A will introduce a newcomer to Amira by explaining its interface, how to load and visualise data, resample and crop data, volume and surface render 3D data sets, and make movies.
• Part B will then consider some of the advanced features available such as applying various editors in image transformation, warping and quantification.

In the workshop, hand-outs will be provided to compliment the information displayed on an overhead projector. The session will involve students using Amira on their own laptops (trial licenses will be available).

VIZBI 2014 tutorial – ‘Great images and movies with Chimera’

Friday, January 3rd, 2014

This hands-on tutorial will provide the participants with the tools to interpret macromolecular complexes and produce meaningful images and movies of the complex of interest using the software UCSF Chimera. You will be guided step by step trough the different aspects of this application from the loading of the molecules to the production of a movie in a way that will be understandable for total beginners and enjoyable for users with some experience. The course is intended for 10-20 participants and designed to be interactive, so any specific question proposed by the participant will be warmly welcome and some time will be dedicated to address specific issues.

The topics covered include:
• Loading of an EM map and basic manipulation of a structure (select atom/sequence/change size of the atoms etc.).
• Fitting a pdb structure in an electron density map, align pdbs.
• Transparency and color, how to use them to underline the biological significance.
• How to get a nice movie/ How to get your movie played everywhere (animated gif).
• Few command-line tips to make of you an “expert user”.
• Topic selected on the basis of students feedback.

The participants should bring your own laptops and have the latest stable release of Chimera and ImageJ installed prior to the tutorial. Handouts will be provided.

Sheelagh Carpendale to Give a Keynote on ‘Usability & Computer Interfaces’

Thursday, January 2nd, 2014

The final keynote of the VIZBI 2014 meeting on the Usability and Computer Interfaces will be given by Sheelagh Carpendale. Sheelagh Carpendale is a professor in the Department of Computer Science at the University of Calgary where she holds the Canada Research Chair in Information Visualization and heads the InnoVis (Innovations in Visualization) laboratory. She uses her combined background in visual arts and computer science to enable the design of accessible visual representations of data. Her research interests include information visualization, user interface design, human-computer multi-touch tabletop interaction, visual languages and graph layout. She has received several major awards in the recognition of her contribution to information visualization including the Canada Foundation for Innovation Award, E. W. R. Steacie Memorial Fellowship from the Natural Sciences and Engineering Research Council of Canada and a BAFTA for Off-Line Learning among others.

Jeffrey Heer to give the opening keynote at VIZBI 2014

Friday, December 20th, 2013

Jeffrey Heer is an Associate Professor of Computer Science and Engineering at the University of Washington. His work focuses on social computing, human-computer interaction and interactive visualization particularly in relation to large data collections with the aim of developing novel interactive systems for visual analysis and communication.

His lab has developed numerous visualization tools (D3, Protovis, Flare, Prefuse) which are widely used by the research community, companies and thousands of data enthusiasts around the world. Jeff is the recipient of a Sloan Research Fellowship, an ACM UIST Notable Paper Award, and a Technology Review TR35 Award for the top innovators under the age of 35. He will deliver the opening VIZBI 2014 keynote on on Data Visualization Principles.

VIZBI 2013 – ‘Alignments and Phylogenetics’ videos now available

Friday, December 20th, 2013

The videos of talks from VIZBI 2013 final session on ‘Alignments & Phylogenetics” are now available on http://vizbi.org/videos/. Bruno Sobral talks about development and deployment of cyberinfrastructure supporting infectious disease research. Bruno demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance of human-computer interface professionals in the design process. Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but acknowledges that more effort into analysis and visualisation solutions are required at the microbial community and ecosystem level. In the final talk, Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.

VIZBI 2013: ‘Visualizing Organism Data’ videos now available

Thursday, December 19th, 2013

The videos from the ‘Vizualizing Organism Data’ session of VIZBI 2013 are now available on http://vizbi.org/videos. Sean Megason gives the opening talk which focuses on visualisation challenges of in toto imaging in developmental biology. Mark Henkelman then talks about how imaging of randomly or targeted mutagenized mice can be used to look for phenotypes that represent human diseases. Finally, Daniel Haehn talks about visualising medical and scientific data in 3D (such as MRI and CT scans, microscopy scan stacks etc.) and introduces some of the open-source tools available.

VIZBI 2013 – ‘Visualising Cellular Systems’ videos now available

Wednesday, December 18th, 2013

‘Visualising Cellular Systems’ is the topic of the fourth session of VIZBI 2013 and the session videos can be found on http://vizbi.org/videos. The first talk is by Martin Miller who speaks about data visualisation in proteomics. Scooter Morris then gives an introduction into visualising biological networks and a primer on the features of Cytoscape, an open source platform for integration and visualization of biological data. Finally, Peter Sorger and Bang Wong talk about the challenges of visualisation of large sets of multidimensional data such as single-cell imaging data, multiplex biochemistry, dose-response assays and drug polypharmacy among others.

Registration is now open for the EMBL Advance Course ‘Cytoscape Developer’

Wednesday, December 18th, 2013

A week after the VIZBI 2014, on March 10-11, EMBL Advanced Course ‘Cytoscape Developer’ will be held at EMBL Heidelberg. This two-day course will teach participants to develop Apps for the Cytoscape 3.x series.

Cytoscape is an open source software platform for visualisation of molecular networks and biological pathways. The system allows annotation and integration of these networks with gene expression profiles and other state data. While Cytoscape was initially built for biologists, the platform can be adapted to a broad range of network-related projects including bioinformatics, social network analysis and semantic web. Cytoscape has a very active App developer community which means that new functionalities and tailored solutions are constantly being added to the platform.

As part of the course, the participants will be introduced to the app development process as well as the key aspects of the Cytoscape API necessary to manipulate Cytoscape tables, networks, and user interface. The participants will then be guided on how to set up development environments on multiple platforms, and develop an initial Cytoscape App. The second day of this course will provide time for each participant to interact with the instructor and other participants to plan and develop their own Cytoscape app.

The registration is now open until Friday 31 January 2014. Please register here.

VIZBI 2013 – ‘Visualising Proteins and Complexes’ videos now available

Tuesday, December 17th, 2013

The video recordings of the talks from the ‘Visualising Cellular Systems’ session of VIZBI 2013 are now available on http://vizbi.org/videos. In the opening talk, Seán O’Donoghue talks about molecular spatial data and the emerging issue of sequence-structure gap arising from experimental difficulties in obtaining reliable (or any) structure information for a given protein. In his talk, Seán gives a brief demonstration of Aquaria, a web-based 3D molecular structure visualization tool that combines data from various databases and allows investigators to easily view and explore proteins and protein-protein interactions. Thomas Ferrin talks about visualization tools for interactive modelling of biological structures and showcases how various features Chimera, an extensible molecular modelling software, can be applied to visualise various protein structures. The third talk, given by Ian Sillitoe, introduces protein structure classification with particular emphasis on superfamily-centric taxonomy which is used in the CATH database. Finally, Martin Strauch briefly presents his BioVis Honorable Mention paper on visualising odours with insect brains.

VIZBI 2013 – ‘Visualising Transcript Data’ videos now available

Monday, December 16th, 2013

The videos from the second VIZBI 2013 session focusing on visualisation of transcript data are now available at http://vizbi.org/videos. The first talk by Paul Gardner is focusing on the challenges of visualising RNA structures and alignments with particular emphasis on Rfam database, a collection of non-coding RNAs, structured cis-regulatory elements and self-splicing RNAs. The topic or data reliability and co-relation of anti-sense RNA sequences is then discussed by Gisela Storz. She demonstrates that RNA-seq data across different experiments and from various sources can often be riddled with discrepancies and lack of overlap. She argues that, while the majority of RNA-seq data is robust and reliable, low abundance transcripts can be difficult to account for and the variations in experimental as well as computational conditions can lead to vastly different data. In the final talk of the session, Cole Trapnell talks about isoform-resolution analysis of RNA-seq. RNA-seq is an assay used to determine the abundance of RNA transcripts in a transcriptome, the results of which can be used for gene discovery and expression analysis. Cole highlights the inherent challenges associated with the analysis of isoform-resolution data and proposes several different areas that are open for improvement.

VIZBI 2013 – ‘Beyond Genome Browsers’ videos now available

Sunday, December 15th, 2013

As promised, the videos from the first VIZBI 2013 session are now available at http://vizbi.org/videos. The session’s topic is Genome Browsers and the rising challenges of epigenomic and genomic data visualization. Ester Rheinbay gives a  great introduction into the epigenetics and the current tools available for the visualization of epigenomic data including the UCSC Genome Browser. As the amount and complexity of epigenomic data increases it becomes increasingly challenging to navigate and explore the vast data sets. Ting Wang took the challenges raised during the VIZBI 2011 meeting and set out to address them in the WashU Epigenome Browser, which he showcases during his talk. Jim Zheng talks about the importance of understanding the 3D structure of genome and gives an introduction into Genome3D framework which allows integration of multi-scale structural and genomic data within 3D. The final talk of the session is presented by Alexander Lex, the winner of the BioVis 2012 Best Paper award. Alex introduces enRoute, a visualization technique that enables detailed analysis of complex data sets in the context of biological pathways.