VISUALIZING BIOLOGICAL DATA VIZBI

Last chance to publish your paper on biodata visualisation at ECCB 2012: in case you missed the March 30 deadline for paper submission, the organisers announced they have extended the deadline to Sunday April 8, 2012 (midnight GMT). For details, see http://www.eccb12.org/proceedings.

Another key bioinformatics meeting has created a paper track specifically for biodata vis & imaging papers. The European Conference on Computational Biology is the key European computational biology event in 2012, taking place 9-12 September 2012 in Basel, Switzerland. This year, ECCB specifically invites papers on biodata visualisation – the deadline for papers is 30 March 2012.

At VIZBI 2012 last week, the NVIDIA award for best poster was decided by popular vote; the winning poster was D18 – uPy: a ubiquitous Python API with biological modeling applications enables ePMV & autoFill by Ludovic Autin, Graham Johnson, Johan Hake, Arthur Olson, Michel Sanner from Scripps & USCF, California, USA. uPy provides a Python interface that lets users drive several computer graphics programs (Blender, Maya, Cinema4D, DejaVu) as well as two Graphical User Interface toolkits (Tkinter and Qt). The uPy group received an NVIDIA Quadro 6000 professional video card, one of the world’s fastest GPUs. Congratulations!

As the current VIZBI web server has become slow and has had recent crashes, we have been preparing to transfer the site to a new, much faster server. The new server still has minor glitches but is close to fully functional: the speed-up is particularly useful to navigating the VIZBI posters. Thus, we have decided to make it available as a back-up server during VIZBI 2012 under a temporary URL (http://bioviz.info/). Many thanks Jean-Karim Hériché and Venkata Satagopam!

VIZBI 2012 posters are now online at http://vizbi.org/Posters/2012; the collection of 75 images and abstracts can be navigated graphically (via image thumbnails), browsed by author or title (via list view), or searched by full text (via VIZBI site search). To help explore these high-resolution images, we made them easily zoomable in any browser using Seadragon Ajax (uses Javascript only, no plugins needed). I believe that in the near future zoomable, high-resolution images will become indispensible in science and beyond; the VIZBI zoomable poster collection can be a showcase, highlighting how this technology can benefit scientific meetings and scientific communication. Many thanks to everyone who contributed, especially Jim Procter & Sven Haag.

We have just confirmed NVIDIA as our latest bronze sponsor, joining Amira and Bitplane, together with our silver sponsor Autodesk. NVIDIA have generously donated a very attractive prize that will be awarded to the best poster at VIZBI 2012: their Quadro 6000 professional video card. One of the world’s fastest GPUs, this card can render 1.3 billion triangles per second, and retails for US$4,999. If you are looking for some extra motivation to improve your VIZBI poster before the submission deadline this weekend, check out these videos demonstrating how the Quadro 6000 can produce photorealistic, interactive 3D scenes as well as detailed, interactive biomedical animations.

Winners of the annual International Science and Engineering Visualization Challenge have just been announced. Outstanding entries featuring biological visualisation include: a video from Graham Johnson (VIZBI 2012 speaker), Andrew Noske, and Bradley Marsh showing a system for interactively visualising cellular compartments (1st Place and People’s Choice); a photograph from Bryan Jones showing a mouse eye with colouring used to highlight 70 distinct cell types (1st Place); a 3D illustration from Andrew Noske, Thomas Deerinck, Horng Ou, and Clodagh O’Shea showing mitosis (People’s Choice); and a poster from Ivan Konstantinov, Yury Stefanov, Alexander Kovalevsky, and Anastasya Bakulina showing the Ebola virus (honourable mention).

In case you missed it, late last year the book Visual Complexity appeared from Manuel Lima (VIZBI 2011 keynote speaker), and has been very well received.

A few months ago, Drew Berry released a video with the musician Björk for her song ‘Hollow’ from the album ‘Biophilia’. The video features a beautiful collection of cellular and molecular animations, smoothly zooming between scales, plus a homage to the fruit portraits of Giuseppe Arcimboldo. I highly recommend tracking down the ‘Hollow’ video – it’s great for engaging friends and colleagues; you can probably find it on YouTube, but it is best viewed on an iPad or iPhone, where it has been released as part of the Biophilia app. You can access a preview of the video here.

Last week, Apple announced several upcoming iPad textbooks that promise a new level of engagement and interactivity: one of the books - E.O. Wilson’s Life on Earth – is being lead by Gaël McGill (VIZBI 2011 speaker and VIZBI 2012 tutor) together with Drew Berry (VIZBI 2011 keynote speaker) as animation director.

For participants facing financial difficulties, a limited number of fellowships are still available that effectively provide free registration. The remaining fellowships will be awarded on a first-come, first-served basis. To apply, you must submit a poster and application letter – see the CPP section of the VIZBI registration page for details.

As VIZBI 2012 draws nearer, a quick reminder that early registration closes at midnight today (January 29) in any time zone. After this date, registration costs €50 more.

A quick reminder that early registration for VIZBI 2012 closes in just under three weeks: the deadline is midnight on January 29 in any time zone. After this date, registration costs €50 more. The deadline for poster submission is 26 February 2012.

For VIZBI 2012, a limited number of free registrations are offered to students via the EMBL’s Corporate Partnership Programme. To be eligible, students need to submit a poster for VIZBI 2012 before January 7 at 12 noon UTC/GMT. For details, see here.

A quick reminder that next Friday, January 13 is the deadline for submitting your work on Biological Data Visualization or Bioimaging to the upcoming Intelligent Systems for Molecular Biology (ISMB) in Long Beach, California (USA) July 15-17, 2012. Presenters of accepted papers are given a 20-minute speaking slot (plus 5 minutes for questions) in the conference schedule. Accepted papers will be published in an online part of the journal Bioinformatics, resulting in fully citable articles indexed by Medline and ISI. More information about ISMB paper submission is at:

http://www.iscb.org/ismb2012-submission/ismb2012-call-for-proceedings

Looking for a new career opportunity in biovis, either for yourself or a colleague? I am starting a new lab in Sydney focused on biological data visualization and I have a range of postdoc and programmer positions to offer – either at junior or senior level – as well as PhD studentships. The lab will be jointly associated with the Garvan medical research institute and with the CSIRO division of Mathematics, Informatics, and Statistics. A primary focus of the lab will be on using principles of usability, data visualization, and graphic design to develop state-of-the-art methods and tools that address cutting edge challenges in basic biomedical research. A second focus of the lab will be on using these methods to analyse experimental datasets in collaboration with groups at the Garvan. Projects will include leading the VIZBI initiative, leading user-interface development for the Reflect project (currently used to analyse ~20,000 documents per day), and developing methods for integrating 3D structures with genomics, proteomics, and other systems biology data: for further details see odonoghuelab.org.

I am seeking to recruit people with a range of skill sets, including a Javascript architect, a Java3D programmer interested in molecular graphics, plus several bioinformaticians and data visualization experts. The postdoc and programmer positions will be initially for five years, but may potentially be extended. Academic salaries in Australia are among the best in the world, and both CSIRO and Garvan both offer salaries, relocation and other benefits that are above the Australian average.

So, if you know anyone matching the above profiles who may be interested to work in one of the world’s most beautiful, lively, and livable cities, please put them in touch (sean@odonoghuelab.org). I will be attending BioVis/VisWeek and will be available from Oct 22-25 to meet and provide further details about these positions.

You are invited to consider submitting your work on Biological Data Visualization or Bioimaging to the upcoming Intelligent Systems for Molecular Biology (ISMB) meeting, to be held in Long Beach, California (USA) July 15-17, 2012. ISMB is organized by the International Society for Computational Biology, and is the most prominent and selective computational biology conference each year. Previous ISMB meetings have attracted over 230 submissions and had an acceptance rate between 15-20%. Accepted papers are invited to give talks at the main meeting, and are published in a special issue of the journal Bioinformatics.

Traditionally ISMB has had very few papers on biodata visualization or bioimage informatics, with only a scattered talk here and there or an occasional special session or workshop. One key reason for this was that there was no heading under which such papers could be submitted and reviewed properly. Therefore, in 2010, a “Bioimaging” track was added (chaired by Gene Myers and Bob Murphy) to encourage submission of papers and provide appropriate reviewing. It received an excellent response from the community, both in terms of people willing to serve on the program committee and papers submitted.

For ISMB 2012, the scope of the track has been broadened to “Bioimaging and Data Visualization”, and is being chaired by Robert Murphy and myself: we would now like to get the word out about the track so that people are aware of it and of the submission deadline.

Submission for ISMB papers opens soon, and the deadline for submission will be January 13, 2012 (with notification of decisions on March 16th). Please note that selection from submitted papers is the primary mechanism for choosing talks at the meeting, and that initial submissions do not have to be in the final OUP format. The focus during the initial review is on the quality of the work, with easily fixable problems with presentation not given too much weight. Presenters of accepted papers will be given a 20-minute time slot (plus 5 minutes for questions) in the conference schedule. Accepted papers will be published in an online part of the journal Bioinformatics, resulting in fully citable articles indexed by Medline and ISI. More information about ISMB paper submission is at:

http://www.iscb.org/ismb2012-submission/ismb2012-call-for-proceedings

We hope that you will consider submitting some of your best work to the track. Having a large number of submissions and accepted papers will be critical to continuing it at ISMB. We believe that it is very important for the broader computational biology community to be aware of the exciting results being generated in the areas of bioimaging and biodata visualization, and of the important role these results play in advancing our understanding of biology.

In the current issue of Nature Methods, Bang Wong has a useful 1-page article summarizing key principles for laying out text and graphics.

The National Science Foundation (NSF) and the journal Science have announced the 2011 International Science & Engineering Visualization Challenge. Entries due 30 September 2011.

We have completely updated the VIZBI website with a new design and some new features, including a video gallery, an improved poster gallery (including now thumbnails from the 2010 posters), galleries of photographs from 2011 and 2010, as well as information about the upcoming VIZBI 2012 conference. Check it out! Thanks especially to Christian Stolte for the great design, also to Janos Binder for help with Javascript.