The VIZBI 2014 art & biology submissions are now available at: http://vizbi.org/Posters/?category=Art&year=2014
The VIZBI 2014 art & biology submissions are now available at: http://vizbi.org/Posters/?category=Art&year=2014
The VIZBI 2014 posters are now online! As you will see, some quite exciting new work will be presented next week! Note that the art & biology submissions remain unpublished – they will first be revealed prior to the outreach keynote on Thursday evening, then displayed on various screens.
March 15 is now the deadline for BioVis 2014 papers. Possible contributions include full scientific papers, scientific posters, participation in a data contest, or in a redesign contest. BioVis 2014 (July 11-12) will be held as a special interest group (SIG) meeting associated with the ISMB conference in Boston, MA, USA. For further details see http://biovis.net/.
For the upcoming Faraday Discussion on Molecular Simulations & Visualizations (7-9 May 2014; Nottingham, UK), the deadline for submitting a poster has been extended until March 10. Organized by the Royal Society for Chemistry (RSC), the discussion will bring together internationally recognised experts in applying advanced visualization (visual analytics, virtual and augmented reality, immersive graphics, GP-GPUs, cloud computing) to analyse molecular simulations across a range of applications in biology, chemistry, and materials science.
Bursaries for students and early career scientists are still available, which are worth £150.
On the Tuesday evening before VIZBI (March 4), there will be a meeting of the Heidelberg Unseminar in Bioinformatics (HUB), a regular social event focused on design and visualisation in biology. Bring along any scientific figures you’re working on that you’d like to discus with others to brainstorm for ways to develop/improve. There is also the opportunity to give a 3-minute-max flash talk on your work in visualising biological data.
Come and meet VizBiers and local Heidelbergers, the evening before VIZBI!
VIZBI 2014 delegates can now propose and vote on topics for discussion during the two unconference breakout sessions scheduled after the afternoon coffee break on Wednesday 5th and Thursday 6th March.
With two unconference breakout sessions this year, and a Heidelberg Unseminars in Bioinformatics meeting on the evening of the tutorial day, there are lots of opportunities for you to get together with like-minded members of the biological visualization community for constructive discussion. So, if you are coming to VIZBI 2014 and have a topic you want to explore, then check your inbox for the link and propose your topic now!
Next Saturday (Feb 22), as part of the White Night Melbourne 2014, the renowned biomedical animator Drew Berry will transformed the Melbourne State Library’s domed reading room into a vast microscope with a magnifying power of 1 billion times. The artwork examines eight different types of human virus in ultra-high resolution detail. Every two minutes the room switches to a different type of virus, including herpes, influenza, HIV, polio and smallpox. Depending on the type of virus and the way it stores it’s genetic code, long snaking coils of DNA or it’s more ancient cousin RNA, grip and slide across the walls like agitated Chinese dragons.
All of the molecular models, including the virus outer shells on the ceiling and the long DNA molecule, has been built to scale, using the raw scientific data from X-Ray crystallography. Every two minutes, an immune defence is released from the floor of the host room – either fluttering antibodies or hormone swarms – removing the virus overhead, and transitioning to the next virus type.
Update: there is also an interview with Drew featuring scenes from the exhibit.
For the upcoming Faraday Discussion on Molecular Simulations & Visualizations (7-9 May 2014; Nottingham, UK), the deadline for submitting a poster closes soon (24 February), as does the deadline and for early-bird registration (17 March). Organized by the Royal Society for Chemistry (RSC), the discussion will focus on the use of advanced visualization (visual analytics, virtual and augmented reality, immersive graphics, GP-GPUs, cloud computing) to analyse molecular simulations across a range of applications in biology, chemistry, and materials science.
Note that the RSC offers bursaries for student and early career members to attend the meetings; for details, see the registration section of the web site (http://rsc.li/fd169).
Winners of the 2013 International Science and Engineering Visualization Challenge have just been announced. In total, 18 outstanding entries were announced as either winners or honorable mentions in 5 categories (Illustration, Posters & Graphics, Photography, Games & Apps, or Video). The four featured below are (from left to right): a stylized illustration of showing cerebral cortex, axons, and dendrites (Greg Dunn et al. from U. Pennsylvania & Johns Hopkins U., USA); a time-lapse photograph showing water swirling in a vortex above two millimeter-sized coral polyps (Vicente I. Fernandez et al. from MIT, USA); a photograph of stellate leaf hairs from the shrub Deutzia scabra (Steve Lowry Photography, UK); and a still from a video titled ‘Visualizing Leaf Cells from Within’ (Geoffrey J. Harlow et al. from UC Riverside, USA). To see all winning entries, click here.
The 4th Symposium on Biological Data Visualization (BioVis 2014, July 11-12) has announced its call for participation, inviting contributions on all aspects of visualization in biology, from molecular to cell, tissue, organism and population biology. Possible contributions include full scientific papers, scientific posters, participation in a data contest, or in a redesign contest. For the first time, BioVis will be held as a special interest group (SIG) meeting associated with the ISMB conference in Boston, MA, USA.
BioVis is an interdisciplinary event featuring original, peer-reviewed scientific work covering all aspects of visualization in biology. The symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. For further details see http://biovis.net/.
A quick reminder that the deadline for VIZBI 2014 registration is tomorrow, 31 January 2014 at 23:59 Pacific time (PST). For further information, go to http://vizbi.org/2014/Registration/.
If you have not yet registered for a VIZBI tutorial, fear not! The registration deadline for tutorials has now been extended to February 15. There are 14 tutorials to choose from, details of which can be found in the posts below or on the VIZBI 2014 Program page. Please note this applies only to tutorials: the registration deadline from the VIZBI 2014 conference is still January 31.
Some more exciting news: Autodesk have once again offered a free Maya license as a prize for the best Art & Biology poster at VIZBI 2014. Normally retailing for $3,675, Maya is widely used for creating interactive 3D applications, video games, animated film, TV series, and visual effects. This very generous prize is offered to participants from academia and industry alike, but cannot be resold.
Each conference participant can upload one artistically-inspired Art & Biology image with accompanying text. The deadline for entering is 23:59 PST on 15 February 2014. These images will first be revealed during a special event as part of the Art & Biology evening. The award for best Art & Biology submission will be decided by popular vote and announced at the Awards Ceremony during the VIZBI 2014 closing session. Participants are asked to choose their favourite Art & Biology submission based on how visually compelling and original it is; it may help to see Art & Biology submissions from previous VIZBI meetings. Further details on submission and upload are here.
So, if you’re still waiting for another reason to register for VIZBI, here it is: submit an Art & Biology poster and win a Maya license!
NVIDIA have confirmed they will again sponsor a fantastic prize for the best scientific poster at VIZBI 2014: their high-end Quadro K5000 professional video card, retailing for US$2,199. One of the world’s fastest GPUs, this card is designed for large-scale visualization of complex data; it supports up to four displays, has 1,536 CUDA Cores, 4GB of GDDR5 memory, a single-precision performance of 2.1 Teraflops, and the ability to render 1.8 billion triangles per second. Such performance allows real-time rendering of stunning photorealistic, interactive 3D scenes. The deadline for poster upload is 23:59 PST, February 15. In addition to scientific posters, each participant can also upload an artistically-inspired ’Art & Biology’ poster (see here for more details). The award for best scientific poster will be decided by popular vote.
VIZBI 2014 tutorial – Network visualisation and analysis of high dimensional data using BioLayout Express3DPosted by Lidija on 16, January, 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.
As VIZBI 2014 draws nearer, we would like to remind you that the registrations will close on 31 January 2014. Registration is on a first-come, first-served basis; places are limited and can only be confirmed after payment is received. You can register for tutorials without registering for the main conference. If you are unable to attend the meeting in person, you can register for ‘Virtual Participation’, which allows access to a live web stream of high-quality video covering all scheduled talks during the main conference (does not cover tutorials).
We’re looking forward to seeing you there!
VIZBI 2014 tutorial – ‘Compute, visualize and explore the folding landscape of your favorite RNA molecule with Assemble2′Posted by Lidija on 7, January, 2014
Understanding the biological functions of an RNA molecule is tightly linked to the comprehension of its folding abilities. The folding process for an RNA molecule is achieved through the establishment of secondary and tertiary structures. Both states are interconnected and made with complex biological objects that need adapted visualization tools for their interactive exploration.
In this tutorial, Fabrice Jossinet will expose the basic principles of RNA architectures and illustrate them with Assemble2. You will also practice with Assemble2 in order to reveal the folding properties of your RNA molecule. Among the different features that are available with Assemble2, you will more precisely learn how to:
• Combine bioinformatics predictions and experimental data (structure probing, NGS reads,…) to quickly identify the best candidates for a secondary structure.
• Identify the consensus secondary structure for a set a related/orthologous RNA molecules.
• Annotate a solved tertiary structure into a secondary one that can be used as a 3D exploration guide.
• Edit an RNA secondary structure interactively to fit your experimental data and/or hypothesis.
• Derive a new tertiary structure from a solved one using an user-driven mutagenesis approach (deletion, insertion and/or substitution of single residues).
• Use an RNA secondary structure to query a database of recurrent RNA 3D motifs extracted from solved structures.
• Construct a 3D model from scratch for an entire RNA molecule or domain.
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.
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