Archive for genomics
May 20, 2008 at 11:18 am · Filed under bioinformatics, biotechnology, cognitive justice, digital design, genes, genomics, heterarchy, visualization, yeast
Yeast Cell Cycle
Here is a new visualization of the cell cycle using a combination of Virtual Reality Markup Language (VRML), Flash, and database-driven graphics. This new version from Chris Landau and Jamie Cope’s nformation design demonstrates the yeast cell cycle in 3D cycle stages along with educational information about the process.
Try zooming in and see changes in the nucleus as the cycle progresses.
Yeast Cell Nucleus During Metaphase
This project started as a collaboration at the University of Michigan with Anuj Kumar’s lab in the Life Sciences Institute and first led to the OrganelleView project.
April 26, 2008 at 8:23 pm · Filed under Uncategorized, bioinformatics, biology, boundary objects, genes, genomics, making it public, maps, visualization
Here is a sketch I made showing the locations and extent of intellectual property claims on 22 chromosomes and the X and Y. These data are from 2005. The extent is larger today.
Click on the image to visit the full-size sketch.
February 2, 2008 at 8:19 am · Filed under bioinformatics, biotechnology, boundary objects, genes, genomics, maps, visualization
I ran across this today while searching for some mitochondrial gene information. It’s the MitoWheel (re:blogged via pimm). Gábor Zsurka, a mitochondrial geneticist, produced it in flash with actionscript.
click image to visit
When compared to, say, The National Center for Biotechnology Information’s mapviewer of human mitochondria, the difference and accessibility are unmistakable.
November 28, 2007 at 12:32 am · Filed under biotechnology, genes, genomics, semantics
“Genetics Just Got Personal” is the new tagline for 23andme, a new start-up that aims to take people’s saliva samples, genotype them, and make their genetic “plot points” accessible and searchable. Individuals can compare their single-nucleotide polymorphisms (SNPs) to identify ancestral locations, compare them with celebrities, and see what diseases are associated with these SNPs. If an entire family submits their samples for testing, each of them can compare themselves to each of their family members. 
In 23andme’s letter to the medical community, they state that “the information [23andme service] provides is tailored to genotypes, not to individuals”.
It’s surprising then, given the history of genetics, that 23andme decided to use the “Genetics Just Got Personal” tagline. When someone says that something just got personal, it usually points to conflict, and that a specific individual, rather than a group, stands to loose as a result. Likewise, when someone says it’s not personal, it often refers to some effect that has had an asymmetrical effect on an individual even though it was not directly intended for them. The 23andme tagline sounds like something Arnold Shartzeneggar would say. It does sound tough and too the point, but it also raises suspicions about what getting personal means. Does this mean that my SNPs, which were previously unknown to me, will enter the forefront of my individual decision-making and social interactions? Will it become a part of the design ecology that other will consider when making medicines, devices, or services?
If genetic information does enter our everyday decision-making processes, a central concern is how that information is conveyed and how the information design biases or constrains the decisions we make. Given that 23andme is providing incomplete information, should I make a health decision based on what’s available? I don’t think they’re advocating that anyone make health or reproductive decisions based on the information they provide. They do, after all, provide suggestions for a range of resources (including genetic counseling) for contextualizing the costs and benefits of these kinds of decisions.
Still, I’m left with questions about how the visual design of bioinformatic resources like 23andme creates and constrains different ways of thinking about and engaging with the information.
23andme’s stated goals include advancing research and being world’s most trusted source of genetic information. Can we imaging any scenarios where these goals would come into conflict?
Given that the value of the resource increases with each additional genotype, are those that contribute to the resource entitled to any of the database’s value over time?
November 16, 2007 at 9:31 pm · Filed under bioinformatics, genes, genomics, semantics
Well, it looks like 23andMe finally went online. It’s been over a year since I did this sketch (left) and less than that since Google invested heavily in their startup costs. So when I opened up the New York Times today and saw their article on 23andMe’s launch (that’s effective PR), I still couldn’t help but be surprised that they had gotten going so quickly.
The key question for me is about their interface and interaction design. Will it compare to the same old bioinformatic machine style gene representations (square genes; primary colors), or will there be evidence of a concerted effort to push the visual language of the genome into something that connects with the wide array of meaning associated with genes? After I’ve had a chance to browse their site a bit, I’ll
report back with some visual analysis. One thing is certain; they’ve definitely internalized the web 2.0 visual style of rounded corners and big type!
August 6, 2007 at 7:40 am · Filed under art, genomics
Announcing the launch of a new genomic art website curated by Holly Longstaff and Jordan Miller. The gallery is graciously supported by Genome British Columbia. The purpose of this project is to spark public dialogue and debate about genetic and genomic science.
The site describes the “Allegories of the Genome” project, which also included an exhibition that was held in Winnipeg, Manitoba at outworks Gallery in February, 2007. The online gallery expands beyond the February show to showcase the work of 14 international artists working in a variety of mediums.
We hope you all will take a few minutes to view the artists’ work and read what they have to say about novel technologies.
Visit the site here:
http://www.genomic-art.com/
July 27, 2007 at 9:47 pm · Filed under genomics, making it public, visualization
Mostly these are notes to myself.
http://www.bootstrap.org/dkr/discussion/1316.html
…. Because documents are simply points on the map, it is possible for
ThemeScape to show thousands of documents at once without overwhelming
the user. Zooming into the map reveals greater detail. For any region on
the map, a click of the mouse pops up a list of documents with related
content. Pointing to any document title displays a short text summary.
A mouse click links the user directly to the original document…..
http://www.pnl.gov/news/1995/nws95-07.htm
In Themescape, themes in the documents are layered and appear on the computer screen as a relief map of natural terrain. The mountains in Themescape indicate where themes are concentrated in the underlying documents; and their shapes — a broad butte or a high pinnacle — reflect how the thematic information is distributed and related across documents.
http://availabletechnologies.pnl.gov/technology.asp?id=129
July 24, 2007 at 10:56 pm · Filed under art, biology, complex systems, critical theory, genomics, interdisciplinary, metaphors
Gabriel A. Harp
Leonardo. August 2007, Vol. 40, No. 4, Pages 376-381
Evidence from language, history and form suggest an analogy between the cinema and the genome. The author describes some of the relationships between cinema and the genome and points to opportunities for discovering unmarked categories within the genome and new methods of representation. This is accomplished by evaluating existing metaphors presented for the understanding of genetics and revealing how current scientific understanding and social concerns suggest a cinematic alternative. The formal principles of function, difference and development mediate discussion and serve as heuristics for investigating creative opportunities.
June 3, 2007 at 7:46 am · Filed under genomics, maps
Zack Denfeld and I had the opportunity to make a visit to The Institute for Transgeneography* in Troy, NY as part of (very brief) residency in association with our former advisor Rich Pell.
It was a valuable experience–if even just for the two days of freedom form dstraction to cognitively focus on the design and implementation of a visual analysis of the identity and distribution of patents on the Y chromosome.
One of the visual precedents we’ve started to develop relates to traditional Japanese woodblock prints and the ways that this approach organizes information. Here are some sketches.
The Institute for Transgeneography is a project whose primary objective is to create the world’s first comprehensive map of engineered transgenic flora and fauna. The project will consist of a database of transgenic organisms and the web interface that will make the information available to the public at large.
March 26, 2007 at 8:45 pm · Filed under art, bioinformatics, genes, genomics, interdisciplinary, visual culture
As part of the Penny Stamps Lecture Series at the University of Michigan School of Art & Design, the Liz Lerman Dance Exchange will perform excerpts from Ferocious Beauty: Genome on April 5th at 5pm in the Michigan Theatre, Ann Arbor, MI.
Liz Lerman, founder and artistic director of the Liz Lerman Dance Exchange, recently completed a four-year collaboration between scientists and choreographers culminating in Ferocious Beauty: Genome, a multi media dance/theater work that explores the human implications of discoveries in genetic science. Created with geneticists from organizations including The Institute for Genomic Research, Wesleyan University, Stanford University, Princeton University and Howard University, Ferocious Beauty has toured from Connecticut to California, deepening dialogue between science and the arts. Lerman will be joined by two dancers who will perform excerpts from Ferocious Beauty: Genome.
more…
http://www.art-design.umich.edu/ev_lectures.php?aud=e&menucat=ne#lerman
http://www.danceexchange.org/performance/ferociousbeautygenome.html#ff
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