VISUALIZING BIOLOGICAL DATA VIZBI

We are delighted to announce VIZBI 2011, the 2nd workshop on ‘Visualizing Biological Data’, to be held at the Broad Institute, Cambridge-MA (USA), March 16-18, 2011. VIZBI 2011 brings together scientists actively using or developing computational visualization to study a diverse range of biological data. The workshop features an impressive list of high-profile speakers who will each review the state-of-the-art and challenges with visualization in their field. VIZBI 2011 also features an art and science evening (Thursday) during which we will be joined by medical illustrators, graphic designers, and artists interested in biological visualization. On Saturday, March 20, immediately after the workshop, participants can choose from a range of tutorials and take part in a hands-on ‘bring-your-own-data’ session. All workshop participants are encouraged to submit a poster on their work, plus an image for the art & science evening. Participants also have the opportunity to be part of an authoritative book co-authored with the VIZBI speakers; the book will be the first to comprehensively review this topic – essentially an expanded version of the Nature Methods focus issue – and will be distributed by a major scientific publisher. We hope you can join us for this exciting event!

The VIZBI 2011 chairs
Seán O’Donoghue, EMBL
James Procter, U. Dundee
Larry Hunter, U. Colorado
Bang Wong, Broad

The company Illumina recently announced their ‘iDEA challenge’ to recognize new, creative ideas on how to visualize and analyze genomics data. Entries are due March 15, 2011 and the winners will be announced June 15, 2011. The  winning academic entry will be awarded US$50,000, while the winning  commercial entry will be awarded a co-marketing agreement with Illumina. Seperate prizes will also be awarded for the most creative visualization, and most creative algorithm. If you are working on visualizing genome data, it sounds like a great opportunity to achieve recognition.

Drew Berry, a VIZBI 2011 keynote speaker, has been awarded a MacArthur Fellow. He  is a animator who uses scientifically accurate and aesthetically rich visualizations to elucidate cellular and molecular processes for a wide range of audiences. A video about the award is available here that includes an interview with Dr Berry, and features some of his work.

A Workshop on Recent Advances and Future Prospects for Visualizing Macromolecular Complexes and Cellular Structures is planned for Oct 12-13 at the NIH in Bethesda, Maryland, USA. Invitations to submit abstracts are now open – for more details, see https://respond.niaid.nih.gov/conferences/

David Leader –  one of the participants in VIZBI 2010 – wrote a short article about the workshop in The Biochemist http://www.biochemist.org/bio/03204/0041/032040041.pdf

Bang Wong just published an interesting article in Nature Methods on the use of colors in figures – http://www.nature.com/nmeth/journal/v7/n8/full/nmeth0810-573.html
Actually this is planned to be the first in a series of regular ‘graphical tips’  in Nature Methods, a plan that was hatched at VIZBI 2010.

At the ISMB 2010 ‘Birds of a Feather’ (BoF) later today, we will lead a discussion through a range of topics related to the major challenges in visualization, plus current and future the community efforts towards meeting these challenges. Notes from the meeting will be available at a Google doc here – any BoF participant that want to contribute to writing this document is welcome – just write to to be added as an author of the document.

At ISMB 2010 we will be hosting a 1-hour ‘Birds of a Feather’ discussion on visualizing biological data (see here for details). We plan to cover the major visualization challenges identified in VIZBI 2010, and to discuss community efforts aimed at improving integration, effectiveness, and usability of visualization in biology. Please contact us if you would like to propose topics or disseminate announcements. All are welcome!

Time: Monday, July 12, 6:00 p.m. – 7:00 p.m.
Room: 304

In preparing the Nature Methods special issue on visualizing biological data, our goal was to create a useful resource for the experimental biology community. In the last month since it was published, there are indications that it is having an impact. It was featured prominently on the websites of Nature and Nature Biotechnology, and has also been featured on several blogs related to visualization and biology: e.g., Vizworld, Bioephemera, Timothy M. Kunau, ISPRS WG II/6 blog on Geographical Visualization and Virtual Reality, Getting Genetics Done, HENRY, Vallve’s Blog, QuimBiología, and Serialized Thoughts. In addition the special issue was covered in several FriendFeeds from Simon Cockell, Brad Chapman, and Abhishek Tiwari (who runs an interesting blog called fisheye perspective on visual analytics and bioinformatics). The issue was also covered by tweetmeme from joergkurtwegner. The PDFs from the special issue are still freely available, but I believe that soon they will be available only to Nature Methods subscribers – so best to grab them now if you want them, and tell any colleagues who may be interested.

Here are links to upcoming or recent meetings that include talks or sessions related to both visualization and biology. If you know of others, leave a comment or contact me and I’ll add them to this post. Eventually this post will probably evolve into a separate page.

• List of Conferences on Computer Image Analysis & Computer Vision
• BioImage Informatics
• IllustraVis09
• VizWeek
• EuroViz
• ISMB Special Session on Visualization of biological networks
• VCBM -Workshop on Visual Computing for Biology and Medicine
• ‘Have You Seen a Molecule’
• IVBI – Information Visualization in Biomedical Informatics
• Visualization In Science & Education – Gordon Conference Series

You may be interested in some Wikipedia pages we started that aim to provide a comprehensive list of computational tools for visualizing biological data. Starting from http://en.wikipedia.org/wiki/Biological_data_visualization you can access  lists of tools for different areas, e.g., alignment, phylogeny, molecular graphics. The pages for systems biology and microscopy currently have only very few tools, and for MRI there is currently no ‘list of’ page. So, we encourage everyone to add their favorite tools! This will give visibility to your favorite tools, and will make these Wikipedia pages a more valuable resource for the community.

Actually there is a back-story to these pages: due to space limitations, in the Nature Method special issue we were very restricted in the number of visualization tools we could mention. As a result, the list of tools cited was ultimately a subjective selection. This was a bit frustrating, as we were forced to remove for the tables several tools we liked. Thus the idea came about to create a more comprehensive list of visualization tools in each field. And the Wikipedia ‘list of’ pages seemed like an ideal place.

In this video of the final 30 minutes of VIZBI, the session chairs shared their impressions of the most important themes and challenges to emerge during the meeting.

There are already some photos from VIZBI 2010 on flickr – we would encourage others to put their photos there and use both tags ‘vizbi2010’ and ‘vizbi’ – here are some examples:

We have now switched to using http://feeds.feedburner.com/vizbi – please update your RSS reader to be sure you get all future blog entries.

In case you missed it, here are the winners of the 2009 international Science & Engineering Visualization Challenge.

This week in Cambridge, UK, is a 2-day meeting on science, art and visualisation called ‘Have you seen a molecule’