More from Kokichi Sugihara (including an explanation of how this works) can be found here.

(thanks to my mother-in-law, who sent the link)

From the explanation:

The picture clearly shows the path of the sun through the sky over the last six months. I believe you can see we didn’t have a great summer by the broken lines at the top. More sun shone in the month of October.

The post also links to a description of how to make your own.

Dear colleagues,

We invite you to participate in the first EMBO Workshop on Visualizing Biological Data (VizBi) 3 – 5 March 2010 at the EMBL’s new Advanced Training Centre in Heidelberg, Germany.

The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). We have assembled an authoritative list of 29 invited speakers who will present an exciting program, reviewing the state-of-the-art and perspectives in each of these areas. The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.

The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a ‘fastforward’ presentation about their work (limited to 30 seconds and 1 slide).

To apply to join the workshop, please go to http://vizbi.org and submit an abstract and image related to your work. Submissions close on 16 November 2009. Since places are limited, participants will be selected based on the relevance of their work to the goals of the workshop.

Notifications of acceptance will be sent within three weeks after the close of submissions.

We plan to award a prize for the submitted image that best conveys a strong scientific message in a visually compelling manner.

Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring!

Seán O’Donoghue, EMBL
Jim Procter, University of Dundee
Nils Gehlenborg, European Bioinformatics Institute
Reinhard Schneider, EMBL

If you have any questions about the registration process please contact:

Adela Valceanu

Conference Officer
European Molecular Biology Laboratory
Meyerhofstr. 1
D-69117 Heidelberg
Tel: +49-6221-387 8625
Fax: +49-6221-387 8158
Email: valceanu@embl.de

For full event listings please visit our website or sign up for our newsletter.

Which also reminds me, I oughta finish cooking a few back-burner genetics projects before they go bad…

To quote myself, because it looks important:

We often think of scientific ideas, such as Darwin’s theory of evolution, as fixed notions that are accepted as finished. In fact, Darwin’s On the Origin of Species evolved over the course of several editions he wrote, edited, and updated during his lifetime. The first English edition was approximately 150,000 words and the sixth is a much larger 190,000 words. In the changes are refinements and shifts in ideas — whether increasing the weight of a statement, adding details, or even a change in the idea itself.

The idea that we can actually see change over time in a person’s thinking is fascinating. Darwin scholars are of course familiar with this story, but here we can view it directly, both on a macro-level as it animates, or word-by-word as we examine pieces of the text more closely.

This is hopefully the first of multiple pieces working with this data. Having worked with it since last December, I’ve been developing a larger application that deals with the information in a more sophisticated way, but that’s continually set aside because of other obligations. This simpler piece was developed for Emily King’s “Quick Quick Slow” exhibition opening next week at Experimenta Design in Portugal. As is often the case, many months were spent to try to create something monolithic, then in a very short time, an offshoot of all that work is developed that makes use of that infrastructure.

Oddly enough, I first became interested in this because of a discussion with a friend a few years ago, who had begun to wonder whether Darwin had stolen most of his better ideas from Alfred Russel Wallace, but gained the notoriety and credit because of his social status. (This appealed to the paranoid creator in me.) She cited the first edition of Darwin’s text as incoherent, and that it gradually improved over time. Interestingly (and happily, I suppose), the process of working on this piece has instead shown the opposite, and I have far greater appreciation for Darwin’s ideas than I had in the past.

Specter’s defection is only relevant (if it’s relevant at all) until the next election cycle, so it’s frustrating to see something that could affect us for five to fifty years pre-empted by what talking heads are more comfortable bloviating about. It’s a reminder that with all the progress we’ve made on how quickly we can distribute news, and the increase in the number of outlets by which it’s available, the quality and thoughtfulness of the product has only been further undermined.

Update, a few hours later: it’s a battle of the readers! now Jamie Alessio passed along a high quality video of the the President’s speech from the White House channel on YouTube. Here’s the embedded version:

I believe it is not in our American character to follow – but to lead. And it is time for us to lead once again. I am here today to set this goal: we will devote more than three percent of our GDP to research and development. We will not just meet, but we will exceed the level achieved at the height of the Space Race, through policies that invest in basic and applied research, create new incentives for private innovation, promote breakthroughs in energy and medicine, and improve education in math and science. This represents the largest commitment to scientific research and innovation in American history.

I’m not much for patriotism rah-rah but it’s hard not to get fired up about this. I found the rest of his speech remarkable as well, listing specific technologies that emerged from basic research, too often overlooked:

The Apollo program itself produced technologies that have improved kidney dialysis and water purification systems; sensors to test for hazardous gasses; energy-saving building materials; and fire-resistant fabrics used by firefighters and soldiers.

And the announcement of a new agency along the lines of DARPA:

And today, I am also announcing that for the first time, we are funding an initiative – recommended by this organization – called the Advanced Research Projects Agency for Energy, or ARPA-E.

This is based on the Defense Advanced Research Projects Agency, known as DARPA, which was created during the Eisenhower administration in response to Sputnik. It has been charged throughout its history with conducting high-risk, high-reward research. The precursor to the internet, known as ARPANET, stealth technology, and the Global Positioning System all owe a debt to the work of DARPA.

The speech, nearly 5000 words in total (did our former President spill that many words for science during eight years in office?) continues with more policy regarding research, investment, and education–all very exciting to read. But perhaps my most favorite line of all, when he said to the members of the National Academy of Sciences in attendance:

And so today I want to challenge you to use your love and knowledge of science to spark the same sense of wonder and excitement in a new generation.

Our forty-fourth president:

That we are in the midst of crisis is now well understood. Our nation is at war, against a far-reaching network of violence and hatred. Our economy is badly weakened, a consequence of greed and irresponsibility on the part of some, but also our collective failure to make hard choices and prepare the nation for a new age. Homes have been lost; jobs shed; businesses shuttered. Our health care is too costly; our schools fail too many; and each day brings further evidence that the ways we use energy strengthen our adversaries and threaten our planet.

These are the indicators of crisis, subject to data and statistics. Less measurable but no less profound is a sapping of confidence across our land – a nagging fear that America’s decline is inevitable, and that the next generation must lower its sights.

For the politically-oriented math geek in me, his mention of statistics stood out: we now have a president who can actually bring himself to reference numbers and facts. I searched for other mentions of “statistics” in previous inaugural speeches and found just a single, though oddly relevant, quote from William Howard Taft in 1909:

The progress which the negro has made in the last fifty years, from slavery, when its statistics are reviewed, is marvelous, and it furnishes every reason to hope that in the next twenty-five years a still greater improvement in his condition as a productive member of society, on the farm, and in the shop, and in other occupations may come.

Progress indeed. (And what’s the term for that? A surprising coincidence? Irony? Is there a proper term for such a connection? Perhaps a thirteen letter German word along the lines of schadenfreude?)

And it’s such a relief to see the return of science:

For everywhere we look, there is work to be done. The state of the economy calls for action, bold and swift, and we will act – not only to create new jobs, but to lay a new foundation for growth. We will build the roads and bridges, the electric grids and digital lines that feed our commerce and bind us together. We will restore science to its rightful place, and wield technology’s wonders to raise health care’s quality and lower its cost. We will harness the sun and the winds and the soil to fuel our cars and run our factories. And we will transform our schools and colleges and universities to meet the demands of a new age. All this we can do. And all this we will do.

And how a swarm reacts to a falcon attack, via Burak Arikan:

For myself and all you designers out there just getting their heads around particle simulations, this is just a reminder: nature is better than you.

Last week the National Institutes of Health (NIH) modified their policy for posting and accessing genome-wide association studies (GWAS) data contained in NIH databases. They have removed public access to aggregate genotype GWAS data in response to the publication of new statistical techniques for analyzing dense genomic information that make it possible to infer the group assignment (case vs. control) of an individual DNA sample under certain circumstances. The Wellcome Trust Case Control Consortium in the UK and the Broad Institute of MIT and Harvard in Boston have also removed aggregate data from public availability. Consequently, UCSC has removed the “NIMH Bipolar” and “Wellcome Trust Case Control Consortium” data sets from our Genome Browser site.

The ingredients for a genome-wide association study are a few hundred people, and a list of what genetic letter (A, C, G, or T) is found at a few hundred specific locations in the DNA of each of those people. Such data is then correlated to whether individuals have a particular disease, and using the correlation, it’s possible to sometimes localize what part of the genome is responsible for the disease.

Of course, the diseases might be of a sensitive nature (e.g. bipolar disorder), so when such data is made publicly available, it’s done in a manner that protects the privacy of the individuals in the data set. What this message means is that a bioinformatics method has been developed that undermines those privacy protections. An amazing bit of statistics!

This made me curious about what led to such a result, so with a little digging, I found this press release, which describes the work:

A team of investigators led by scientists at the Translational Genomics Research Institute (TGen) have found a way to identify possible suspects at crime scenes using only a small amount of DNA, even if it is mixed with hundreds of other genetic fingerprints.

Using genotyping microarrays, the scientists were able to identify an individual’s DNA from within a mix of DNA samples, even if that individual represented less than 0.1 percent of the total mix, or less than one part per thousand. They were able to do this even when the mix of DNA included more than 200 individual DNA samples.

The discovery could help police investigators better identify possible suspects, even when dozens of people over time have been at a crime scene. It also could help reassess previous crime scene evidence, and it could have other uses in various genetic studies and in statistical analysis.

So the CSI folks have screwed it up for the bipolar folks. The titillatingly-titled “Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays” can be found at PLoS Genetics, and a PDF describing the the policy changes is on the NIH’s site for Genome-Wide Association Studies. The PDF provides a much more thorough explanation of what association studies are, in case you’re looking for something better than my cartoon version described above.

Links to much more coverage can be found here, which includes major journals (Nature) and mainstream media outlets (LA Times, Financial Times) weighing in on the research. (It’s always funny to see how news outlets respond to this sort of thing—the Financial Times talk about the positive side, the LA Times focuses exclusively on the negative.) A discussion about the implications of the study can also be found on the PLoS site, with further background from the study’s primary author.

Science presents such fascinating contradictions. A potentially helpful advance that undermines another area of research. The breakthrough that opens a Pandora’s Box. It’s probably rare to see such a direct contradiction (that’s not heavily politicized like, say, stem cell research), but the social and societal impact is undoubtedly one of the things I love most about genetics in particular.

I’m not sure how useful they would be to novices in terms of usable data (raw numbers are not provided in any easy to harvest manner), but the information is
still useful and they provide for a basic, if clunky, presentation that follows the basic steps you laid out in your book. They data can be found here, and they occasionally compile it all into interesting visualizations. My favorite being the carbon map here.

The carbon map movie is really cool, though I wish the raw data were available since the strong cyclical effect seen in the animation needs to be separated out. The cycles dominates the animation to such an extent that it’s nearly the only takeaway from the movie. For instance, each cycle is a 24 hour period. Instead of showing them one after another, show several days adjacent one another, so that we can compare 3am with one day to 3am the next.

For overseas readers, I’ll note that the images and data are not all U.S.-centric—most cover the surface of the Earth.

I asked Chris about availability for more raw data, and he did a little more digging:

The raw data availability is slim. From what I’ve gathered you need to contact NASA and have them give you clearance as a researcher. If you were looking for higher quality photography for a tutorial NASA Earth Observations has a newer website that I’ve just found which offers similar data in the format of your choice at up to 3600 x 1800. For some sets it will also offer you data in CSV or CSV for Excel.

If you needed higher resolutions that that NASA’s Visible Earth offers some TIFF’s at larger sizes. A quick search for .tiff gave me an 16384 x 8192 map of the earth with city lights shining, which would be relatively easy to filter out from the dark blue background. These two websites are probably a bit more helpful.

Interesting tidbits for someone interested in a little planetary digging. I’ve had a few of these links sitting in a pile waiting for me to finish the “data” section of my web site; in the meantime I’ll just mention things here.

Update 31 July 2008: Robert Simmon from NASA chimes in.