The organizers of the EMBO Workshop on Visualizing Biological Data (a conference I’m very sad to miss as it is occurring this week!) have been working with a group of scientists to prepare a series of reviews on visualizing biological data. These reviews have been published in a supplementary issue of Nature Methods (Volume 7 No 3 ppS1-S68). In addition to five reviews covering visualization of data from systems biology, genomics, 3D macromolecular structures, alignments and phylogenies, and image-data. The supplement also contains a commentary on future visualization.

I’m especially interested in functional network mapping, though at first pass there appears to be little new in that area. Perhaps it is left as an exercise for the reader.

(See also: EMBO Workshop on Visualizing Biological Data (VizBi))

(See also: Nature Methods: March 2010, Volume 7 No 3 ppS1-S68)
(See also: Supplement on visualizing biological data)
(See also: Visualizing biological data—now and in the future)
(See also: Visualizing genomes: techniques and challenges)
(See also: Visualization of multiple alignments, phylogenies and gene family evolution)
(See also: Visualization of image data from cells to organisms)
(See also: Visualization of macromolecular structures)
(See also: Visualization of omics data for systems biology)

An early morning earthquake shook the central coast of Chile today, killing over 700 people and injuring thousands more. The Magnitude and location of the quake prompted tsunami warnings throughout the Pacific. The details are as follows:

2010/02/27 06:34:14 (UTC)
Preliminary Magnitude: 8.8
Latitude: -36.1 Longitude: -72.6
Location: near the coast of central Chile

It is interesting to see the differences between the 1960 (9.5) and 2010 (8.8) events. Both examples are drawn on Mercator projections, where rhumb lines are drawn as straight lines. The linear scale is constant in all directions around any point and preserves the angles and shapes of small objects. This is useful for plotting paths but it distorts the size and shape of large objects, exaggerating the size of objects far from the equator. This would likely have a magnifying effect on the visualization of seismic events at the poles.

I wonder if NOAA has a sphere with the ability to display these events in their proper proportion?

Tsunami:

(See also: Chilean Tsunami energy map)
(See also: Tsunami Advisory: Sat Feb 27 22:48:29 GMT 2010)
(See also: Tsunami Advisory: XML)

(See also: NOAA Center for Tsunami Research)
(See also: NOAA: Chilean event)

(See also: Carleton: Ocean System: Data, Models and Visualization)
(See also: Oregon State: Tsunami Visualization)
(See also: PDF: Data Visualization Strategies for Tsunami Research)

Earthquake:

(See also: NYTimes: ‘State of Catastrophe’ After Chile Quake)
(See also: NYTimes: Underwater Plate Cuts 400-Mile Gash)
(See also: NYTimes: Maps of the Chile Earthquake)

(See also: USGS: Historic World Earthquakes)
(See also: USGS Worldwide Deadly & Destructive Earthquakes between Magnitudes 6 and 8)

Finished the book. Review in progress, somewhere between zero and infinity. Each chapter begins with a quote to set the tone. Here is my favorite:

“When you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meager and unsatisfactory kind: it may be the beginning of knowledge, but you have scarely, in your thoughts, advanced to the stage of science. “

- William Thomson, Lord Kelvin

This is largely the problem traditional HPC sciences have with Life Sciences. Apart from statistical analysis, we simply haven’t risen to the level where we can express biological systems numerically.

(See also: amazon: Zero: The Biography of a Dangerous Idea)
(See also: wikipedia: Charles Seife)
(See also: Charles Seife)

(See also: amazon: The Nothing that Is: A Natural History of Zero, by Robert Kaplan)

I spent some time today exchanging Tweets and Email with friends about Apple’s new iPad and I think we’re on the same page. While I think it would be fun to have, much of the function is found in my iPod touch in a far more portable format.

The iPad does not replace my MBP laptop, or even my netbook (Toshiba N205). It’s tasks are very different. It is interesting to note I can use Adobe Flash apps and video on my laptops and netbook, but not the iPod or iPad. During the product introduction it was obvious Flash didn’t work for the video on the front page of the New York Times site. Yet the image of the Times front page on the Apple website shows content were the Flash video would appear. (update)

The name is dreadful. It was bad when Fujitsu used it in 2002. The Hamming distance between iPod and iPad was simply too powerful for marketing. It also plays on the idea that accessories for the iPod should work on the new device. This remains to be seen. (I preferred something more organic, iSlate, perhaps. Though this suffers from the same ‘i-ing’ of nouns.)

Increasingly, and my deepest concern, I feel left out of the loop on this class of devices. (iPod touch, Kindle, Nook, SonyReader, iPad, etc.) I don’t like being relegated to the role of consumer when I want to be a creator. It is almost as if I’m a ‘revenue stream’ first. Kris’ comment ‘designed for consuming, not creating’ hit home with me. That said, if you are looking to consume media, I don’t know why you would buy a Nook or Kindle, if you had a chance to see the iPad.

A killer app for the iPad could be home automation systems, using the ‘pad to control lights, heat & HVAC, A/V, and security (cameras?). Though the lack of multi-tasking limits monitoring capabilities. Touch panel or voice controled lights and heat, family logistics, ‘iPad, set the heat to 68′,’iPad, did we get any mail today?’, ‘iPad, do we need milk?’, ‘iPad, where are all my children?’.

I’m sure the iPad is beautiful and I intend to test is when it becomes available. It is compelling as a multi-touch development platform. Currently I don’t need a bigger iPod, but I might consider replacing my iPod touch with an iPad when the time comes.

I hope this doesn’t herald the end of ownership or the general purpose computer. A future in which I own nothing, but merely rent access. Where is the Terminal.app, rsync, Perl, Ruby? There is nothing raw or vulnerable about this device. My view of the world is limited to what I’m allowed to buy, not what I’m enabled to create. The iPad is a consumer, not a creator device. The expansion of slick, safe, closed systems prevent users from writing their own utilities or solving their own problems. Not all solutions can be downloaded from an app store. Ultimately, the iPad may be too safe for me.

Don’t protect me from myself. Provide the platform and get out of the way.

(See also: apple.com: iPad)
(See also: engadget: Fujitsu and Apple dispute iPad name)

(See also: engadget.com: Apple excises the false flash)

(See also: O’Reilly Radar: The iPad is the iPrius: Your Computer Consumerized)

The Star Wars of our time? (Spoiler alert.)

(See also: scifiwire.com: Making of Avatar)