VISUALIZING BIOLOGICAL DATA VIZBI

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

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.

We are delighted to announce VIZBI 2012 (http://vizbi.org/2012/), the 3rd international meeting on ‘Visualizing Biological Data’ – and the first in a series of EMBO conferences on this topic – to be held at the European Molecular Biology Laboratory, Heidelberg (Germany), 6-8 March, 2012. VIZBI 2012 brings together scientists actively using or developing computational visualization to study a diverse range of biological data; the conference also attracts participation from medical illustrators, graphic designers, and graphic artists. VIZBI 2012 features 22 invited talks from high-profile speakers that will review the state-of-the-art and challenges in visualizing data from genomes, transcripts, proteins, cells, organisms, and populations. Prior to the meeting (5 March), there will also be tutorials on visualization tools & methods. All VIZBI participants have the opportunity to present a poster describing their work. Just before your poster session, you will be given ~60 seconds and 2 PowerPoint slides to briefly introduce yourself and your poster to all VIZBI participants (details here). If you cannot join us in Heidelberg, you have the option of virtual registration, which allows participation via streaming video and chat. Registration is now open, and early registration closes 29 January 2012. The first two VIZBI meetings were timely and energized and have fostered some significant advances in the field; VIZBI 2012 promises no less, and is supported by a greatly expanded organizing team – we hope you can join us for this exciting event!

Now available for download in PDF or PPT format are slides for the following VIZBI 2011 talks: Yoseph Barash, Susumu Goto, Des Higgins, Robert Macleod, Tamara Munzner, Rod Page, John Quakenbush, Herve Tettelin, and Eric Westhof. These slides can also be downloaded from the corresponding video pages.

In addition, slides are also available from the recent workshop on “Data visualization and user interfaces” at ISMB 2011. There were talks on user interfaces by Scooter Morris, on data visualization by Nils Gehlenborg, on visual analytics by Carsten Goerg, and some discussion points by myself.

We are seeking someone to give a hands-on, 1/2-day tutorial on Processing.js as part of the VIZBI 2012 tutorial day (Monday, 5 March 2012, in Heidelberg, Germany). At VIZBI 2011, we offered tutorials for the first time and they were quite popular, with the Processing tutorial attracting the most students. For VIZBI 2012 we would like to offer a Processing.js tutorial; the tutor will receive a share of the tutorial registration fee plus a complementary pass to the VIZBI conference, which takes place on the three days following the tutorial day. To get a flavor of the conference, check out the videos from previous VIZBI meetings. If you are interested in this opportunity, or if you can suggest someone ideal for spreading the word about Processing.js to computational biologists, please get in touch:

If you are attending ISMB 2011 in Vienna, don’t miss today’s 2-hour workshop on “Data visualization and user interfaces”:

Date: Monday, July 18
Time: 10:45 a.m. – 12:40 p.m.
Room: Hall N/O

10:45 – 11:10 User Interface Design (Speaker: Scooter Morris)
11:15 – 11:40 Data Visualization (Speaker: Nils Gehlenborg)
11:45 – 12:10 Visual Analytics (Speaker: Carsten Görg)
12:15 – 12:40 Discussion (Moderator: Seán O’Donoghue)

Eric Lander’s opening remarks elegantly articulated the urgent need for an increased focus on data visualization in biological research, and, from the strong positive feedback, it’s clear that VIZBI helps address this need. The first VIZBI meeting was an experiment – it was not certain if this very diverse group would want, need, or be able to effectively communicate, let alone collaborate. However it is now clear the experiment is a success: the two meetings so far have already led to many fruitful collaborations and outcomes. Personally, I was also surprised to see that a large number of participants from 2010 came again in 2011, including many from Europe and even more remote places like Australia: clearly VIZBI has already begun to form a community, and indeed many people suggested that the website evolves to support this. Thus, the need to continue VIZBI is clear: now, what about the means to do so?

Here, I am delighted to report good news: EMBO recently accepted our application to start a VIZBI conference series at EMBL, Heidelberg. Together with the NIH grant awarded last year for a VIZBI conference series at the Broad Institute, we now have funds to run VIZBI annually – alternating between Europe and the USA – until at least 2016. We are now enlarging the organizing team and improving aspects of the meeting, especially the website. We are also finalizing the program for VIZBI 2012, which will be held 6-8 March 2012 at the EMBL in Heidelberg, Germany. As with previous years, VIZBI 2012 will have outstanding speakers, and will give all participants the opportunity to present their work via the fast-forward and poster sessions. For some, traveling to Heidelberg is difficult, so we plan to offer virtual participation via streaming video and chat. We will announce the detailed VIZBI 2012 program in August. Until then, together with the 2012 organizing team, I look forward to meeting many of you again in Heidelberg, 6-8 March 2012.

Videos of the VIZBI 2011 talks are now available at http://vizbi.org/videos/. These are high-quality video recordings of great presentations from outstanding scientists: feel free to share the videos with colleagues. I would like to thank again all who made this possible, especially the speakers, Lars-Erik Siren from the Broad for his dedicated video-production work, and the VIZBI 2011 co-chairs Jim Procter, Lawrence Hunter, and particularly Bang Wong for engaging the full support of the Broad Institute.