Archive for genes
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!
May 1, 2007 at 9:20 pm · Filed under Design, bioinformatics, genes, visualization
The transdisciplinary project “I Gene Visions” of the Cologne artist and researcher Karsten K. Panzer PerZan is developing a visionary grammar of science and the arts, of biology and the esthetics. PerZan creates a connecting and binding meta-language between the binary codes of the genetic DNA and the archaic Chinese opus “Yijing”, Book of Changes, by using a binary color system (FR 64) as a mediator and transmitter www.PerZan.de.
A collaboration with the Arts & Genomics Centre
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
March 10, 2007 at 9:26 pm · Filed under Design, bioinformatics, boundary objects, digital design, evolution, genes, genomics, making it public, maps, molecular biology, network entrepreneurship, visualization, yeast
The collaborative work of graduate student Gabriel Harp and Chris Landau (MFA ‘06) on the Organelle View project was published in the January issue of Nucleic Acids Research.
“The project makes a gigantic leap in the distribution of biological data–moving it beyond the conventional representations of names and numbers to embrace the visual and organismal aspects of cellular and molecular forms”, says Harp.
“Organelle View is a scientific visualization application allowing users to dynamically generate a visual interpretation of data from Organelle DB. Organelle View presents a searchable interface with a three-dimensional representation of an archetypical cell. Rather than representing organelles and subcellular structures by text, Organelle View offers an artist’s rendering of a cell and its major organelles. At present, we have chosen a budding yeast cell (S.cerevisiae) as the model for Organelle View, largely because protein localization has been studied quite extensively in yeast; future versions of Organelle View will incorporate additional cell types from other organisms.”
(Wiwatwattana, N., Landau, C.M., Cope, G.J., Harp, G.A., & Kumar, A. (2007). Organelle DB: an updated resource of eukaryotic protein localization and function. Nucleic Acids Research, 35, D810-D814.)
full text via PubMed
February 23, 2007 at 9:42 am · Filed under genes, genomics, visualization
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