Timothy M. Kunau

Nature Methods issue on Visualizing Biological Data

kunau — Wed, 03 Mar 2010 17:21:48 +0000

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.

Tsunami Visualization

kunau — Sun, 28 Feb 2010 02:16:30 +0000

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

Earthquake:

Book: Zero: The Biography of a Dangerous Idea

kunau — Fri, 05 Feb 2010 15:40:29 +0000

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)

iPad Wonderment

kunau — Thu, 28 Jan 2010 21:28:05 +0000

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.

Avatar: Creating the World of Pandora

kunau — Wed, 20 Jan 2010 22:37:13 +0000

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

Book: A Whole New Mind: Why Right-Brainers Will Rule the Future

kunau — Mon, 18 Jan 2010 21:33:33 +0000

Dan Pink’s book outlines the ’six essential aptitudes on which professional success and personal fulfillment now depend’. The era of left-brain dominance (L-directed thinking) will give way to those who are more right-brain oriented (R-directed). Individuals who develop their sense of inventiveness, empathy, and meaning will step into prominence.

Many technical careers in IT and academia are less creative than you might imagine. I have seen how the sausage is made and have turned the crank myself from time to time. I simply cannot live that way. I crave more than a creative outlet. My life must be creative.

In this book, Mr. Pink asks three critical questions:

Can a computer do it faster?

Is there a demand for my product in a time of abundance?

Can someone overseas do it cheaper?

In a world where information is almost free and access is immediate, the recitation of facts and figures in less important. Creativity will be in demand. Mr. Pink outlines six R-directed aptitudes:

Design: Moving beyond function to engage the sense.

Story: Narrative added to products and services, not just argument.

Symphony: Invention and big picture thinking.

Empathy: Beyond logic, engaging emotion and intuition.

Play: Bringing humor to business, products, and services.

Meaning: The purpose is the journey.

I must say, this is somewhat of a relief to hear.

gCal: Add Color to Weekend Columns

kunau — Mon, 11 Jan 2010 17:18:48 +0000

We are heavy Google Calendar users in our family and it has always bothered me that there was no visual cue between weekdays and weekends on ‘Week’ or ‘7 Days’ view options. If this bothers you as well, simply edit the userContent.css file for your respective browser and add the following:

/* bluegrey weekends on gCal. */
td.tg-weekend {
    background-color:#F0F8FF;
}

The result is a pleasant distinction as the 7 day window moves forward.

The file userContent.css sets the display rules for web content and is located in the sub-folder called chrome in your profile folder. This folder does not exist by default, so you may need to create it before you can start adding your preferences. On my Macintosh, the chrome folder may be found:

% pwd
/Users/kunau/Library/Application Support/Firefox/Profiles/j2am41kw.default/chrome
 
% ls -al
total 24
drwxr-xr-x@  5 kunau  kunau   170 Nov  5 18:44 .
drwx------@ 70 kunau  kunau  2380 Jan 11 11:00 ..
-rw-r--r--   1 kunau  kunau  1039 Nov  5 18:44 userContent.css

It is a little thing, but it makes all the difference.

Eyeos, your Web-Based Desktop in the Clouds?

kunau — Tue, 29 Dec 2009 22:10:05 +0000

Tinkering with remote desktops as supported by the eyeos.org project. The current version offers few applications including a simple Office-like suite and chess game. While not yet Citrix on the cheap, platforms like this could mature into an interesting VDI option.

Connectivity will become that much more critical if these tools are to be taken seriously. Connectivity and carriers will move to the center of the enterprise.

(See also: eyeos.org)
(See also: eyeos: eyedocs)

Air Travel no-longer Enjoyable?

kunau — Sun, 27 Dec 2009 21:25:13 +0000

It seems another sociopath has found his way on an airplane. As a result, the rest of us will endure increasingly invasive TSA checkpoints and restrictions while flying. According to a TSA press release:

Passengers flying from international locations to U.S. destinations may notice additional security measures in place. These measures are designed to be unpredictable, so passengers should not expect to see the same thing everywhere. Due to the busy holiday travel season, both domestic and international travelers should allot extra time for check-in.”

Interestingly Delta was quick to declare this flight was operated by Northwest Airlines. The official Delta statement sounds as if they are designed to create distance from the NWA subsidiary. Delta should declare their ownership and describe in detail how they will meet the challenges and coordinate with the TSA moving forward. All this posturing doesn’t increase our trust in their organization.

I’ve read the accounts and there is no mention of a sky marshall. Apparently, ultimately, we’re responsible for subduing our own terrorists. Lovely.

I prefer the Israeli Model. People are the threat, not the things they carry.

(See also: NYtimes: The Israeli Model)

One day of Traffic on the NYtimes.com

kunau — Thu, 17 Dec 2009 23:14:29 +0000

The New York Times site traffic, US, June 25, 2009 from Nick Bilton on Vimeo.

Site traffic visualization to nytimes.com from mobile and web users on June 25, 2009. Maps and animated data. I simply could not turn away. Design and programming by Michael Young, Noriaki Okada and Nick Bilton.