Posts Tagged ‘VIZBI 2013’

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.

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.

VIZBI 2013 Keynote Speaker – Sara Irina Fabrikant

Tuesday, March 19th, 2013

VIZBI 2013 first keynote speaker will be Dr. Sara Irina Fabrikant. She is currently an Associate Professor of Geography and head of the Geographic Information Visualization and Analysis (GIVA) group in the GIScience Center at the Geography Department of the University of Zurich, Switzerland. Her research and teaching interests lie in geographic information visualization and visual analytics (geovis), GIScience and cognition, graphical user interface design and evaluation, including dynamic cartography.

She was awarded a Rotary International Ambassadorial Scholarship to study Geographic Information Science for one academic year at the University of Canterbury, Christchurch, New Zealand, in 1993. She is the current elected chair of the International Cartographic Association’s Cognitive Visualization Commission. She publishes in a variety of GIScience/geovis related journals and is currently a member of the Editorial Boards of the Annals of the Association of American Geographers, Cartographica, Cartographic Perspectives, Computers Environment and Urban Systems, Journal of Spatial Information Science, Revue Internationale de Géomatique, and Transactions in GIS, in addition to her Program Committee memberships for various international GIScience/geovis related conferences (e.g., GIScience, COSIT, InfoVis (UK), etc.). She has been the Program Committee Chair of the GIScience 2010 conference. She has made various presentations at national and international professional meetings, including invited keynotes and other lectures at universities in North America, Europe, Asia, and New Zealand. Other service includes memberships of the Association of American Geographers, the International Cartographic Association’s Commission on Geovisualization, the North American Cartographic Information Society, and the Swiss Society of Cartography.

VIZBI 2013 Art & Biology Keynote Address – Felice Frankel

Friday, March 15th, 2013


This year’s Art & Biology keynote address will be delivered by Felice Frankel, a renowned science photographer and a researcher in the Center for Materials Science and Engineering at the Massachusetts Institute of Technology. The CSIRO-sponsored outreach keynote titled “Communicating Science Visually” will also be simulcast live to Melbourne, Australia as part of the CSIRO workshops on “Effective Visualisation for Science” and “Bioinformatics Focus on Analytical Methods”.

Working in collaboration with scientists and engineers, Felice’s images have been published in over 200 journal articles and/or covers and various other publications for general audiences such as National Geographic, Nature, Science, Angewandte Chemie, Advanced Materials, Materials Today, PNAS, Newsweek, Scientific American, Discover Magazine, and New Scientist among others. Felice foundered the IMAGE AND MEANING workshops and conferences, which promote public understanding of science through visual expression. She was principal investigator of the National Science Foundation-funded program, Picturing to Learn, which studies how visual representations aid in learning. She and her work have been often profiled in the mainstream press, and she exhibits throughout the United States and in Europe. Her limited edition photographs are included in a number of corporate and private collections.

VIZBI 2013 Tutor Spotlight – Graham Johnson’s uPy Tutorial

Thursday, March 14th, 2013

Graham Johnson is an outstanding medical illustrator, animator and visualisation expert with over 15 years of professional experience. He holds a masters degree in Medical and Scientific Illustration from the John Hopkins School of Medicine and a PhD in Biophysics from the Scripps Research Institute. He illustrated the textbook Cell Biology (written by Pollard and Earnshaw) and has created numerous scientific visuals ranging from journal covers to pedagogic animations and game designs. He currently works at the UCSF as a qb3@UCSF Faculty Fellow. His visuals have won numerous prizes including the best video at the 2011 NSF International Science and Engineering Visualization Challenge as well as the best poster at VIZBI 2012. He was a speaker at the VIZBI 2012 meeting where he spoke about the challenges of visualizing “mesoscale” data and the application of uPy and autoFill frameworks  (the video can be viewed here). As part of this year’s tutorial series, Graham will give an introduction on uPy (ubiquitous Python API), a system that facilitates interaction with molecular graphics software with animation systems such as Maya, Cinema 4D and Blender.