semeiotica recombining contemporary art, design strategy and life science
Archive for bioinformatics
August 3, 2008 at 9:31 am · Filed under bioinformatics, host-parasite, maps, public health
HealthMap
A project called HealthMap (http://www.healthmap.org) makes epidemiological information available to all corners of the world via the web. As reported in the July issue of PLoS Medicine, it extracts, categorizes, filters and integrates a variety of Web-based data sources, even analyzing blogs, listservs, chatrooms, and online news reports as sources for monitoring global health.
The idea is that people’s discussion can serve as signals of disease outbreaks which can then be scraped and fed to a map…
Brownstein JS, Freifeld CC, Reis BY, Mandl KD (2008) Surveillance Sans Frontières: Internet-Based Emerging Infectious Disease Intelligence and the HealthMap Project. PLoS Med 5(7): e151 doi:10.1371/journal.pmed.0050151
July 25, 2008 at 12:04 pm · Filed under bioinformatics, biology, interaction, visualization
A comparison of interaction records in two group of hens. This figure illustrates the comparison feature of the music notation program showing the interaction records in two groups of hens interleaved in two-hour blocks.
Ivan Chase demonstrates a compelling use of musical notation for visualizing social interactions and (conceivably) networks using musical notation. Chase suggests that:
music notation graphs can be of particular help in a variety of fields interested in social interaction in humans, animals, and machines such as behavioural ecology, behavioural economics, social organization in animals, development of social networks in humans, human conversational analysis, and the coordination of actions in social robots.
Read the entire article: Frontiers in Zoology 2006, 3:18
June 20, 2008 at 4:21 am · Filed under bioinformatics, community interaction design, design ecology, ecoregionalism, science
The Owl Project is a community space for interacting with owls in their natural habitat. I stumbled across it while visiting the MIT Media Lab. It is part of the Ecology Media group that “explores the potential of computational media as access point to natural systems and global ecology”.
Try exploring the aviary to hear some owl sounds!
The Owl Project
June 7, 2008 at 7:19 pm · Filed under bioinformatics, community interaction design, complex systems, cybernetics, heterarchy, making it public, technology
A letter to this week’s Nature describes a study that reveals an interesting model of human movement patterns. The study is the first of its kind for the simple reason that the researchers were able to objectively track people in the natural environment by using mobile phone locations as proxies for their movement.
location tracking phone
Biologists have been performing similar studies on animals for years, using radio tracking devices and similar forms of locations awareness. However, because people tend to be difficult to keep track of, subject to influence from experimental methods, and resistant to monitoring by others, it has been previously difficult to get this kind of accurate data about humans.
Without recapping the study itself (you can read the original abstract and related news stories from the links below), there are many reasons why these data are interesting and useful. The least of which concern us with how people behave and how their behavior translates into public health practice, urban planning, education and communication. For me, the most interesting questions come when we understand what kinds of heterogeneity exist in populations. Understanding what motivates people to behave and respond differently is curious, especially when it relates to their cognitive capacities, their environment, and their learned behaviors. Thus we can begin to ask questions about how systems like architecture or policy, at very different scales, affect systems at other scales–like human reproductive choices for instance.
This study demonstrated that people aren’t really all that interesting in the movements, which is to simply say that we are predictable. We generally stay close to home or work and move in small bursts around these areas most of the time. Occasionally we make wider forays across the landscape.
There are privacy concerns to be negotiated. Many have been critical of the use of this information for the study. To my mind I don’t find the use of the data in the current study problematic for two reasons: 1) there is no identifying information available in the data, and 2) the mobile phones companies have been collecting this data, often out of legal obligation for billing precision, and using it for proprietary purposes with contractual consent from subscribers. I think it is important that some public good be made of the information, even if it means simply bringing to light the fact that these kinds of data are ubiquitously collected under the terms of cell phone contracts. Furthermore, a sample of people in the study explicitly consented to having their movements tracked as part of a value-added service, associated with navigation or weather for example.
Still, the study raises questions and begs for further social questioning and negotiating. I think where it starts to become problematic is when these studies begin to impede personal autonomy. Then again, the negotiations are where all the fun is…
BARABÁSI LAB
For a rundown on how the press is selling the story-via Google
Cellphone Tracking Study Shows We’re Creatures of Habit-NYTimes
Cell phone users secretly tracked in study-CNN
How Will Disease Spread?-ABC News
Mobile phones expose human habits-BBC
May 26, 2008 at 6:03 pm · Filed under bioinformatics, community interaction design, complex systems, cybernetics, ecoregionalism, making it public, public health
This is an interesting report I came across from a UN-Vodaphone partnership designed to provide “research and recommendations on how to use technology and telecom tools to effectively address some of the world’s toughest challenges” (found via THDblog)
The story I was most interested in was Case Study 10: Environmental Monitoring with Mobile Phones (Ghana) carried out by Intel Research. I was struck by this paragraph, detailing the convergence of locative sensing and personal health status:
Another area for further exploration is the ability of mobile sensing to contribute to public health by linking health with environmental factors that have not been available before. For example, even though we know that there is a link between asthma symptoms and air pollution, previously it was not possible to directly correlate an individual’s symptoms with their exposure to air pollutants. Measuring people’s lung performance while measuring ambient air pollution exposure could shed new light on the links between air pollution and asthma, perhaps resulting in better treatments.
Clearly there are many thorny privacy concerns, but that’s the difficult (and fun) part to work out and begin to address.
Still, I think this example is on the mark in trying to link infrastructure, natural or man-made and population health patterns.
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.
April 21, 2008 at 7:24 pm · Filed under bioinformatics, digital design, ecoregionalism, india, making it public, maps
Screenshot of one of the mapunity community interfaces.
Last week I visited the Mapunity folks who are building projects at NSRCEL in the Indian Institute of Management, Bangalore. They are a really great, super-keen group dedicated to building IT solutions for the purposes of development…often using geographic systems as a segue to action. I think they are most well-known for their work on the Bangalore Traffic Information System, which, if you’ve visited Bangalore recently, you know how bad the traffic is here.
The Mapunity folks are creating tools for users to make their own maps for whatever purpose they choose. The ones I like the most are these, dealing with innovation in rural parts of India. Here is where local, user based solutions to problems like disease control in cumin crops or remedies for animal wounds can be mapped to particular areas and described.
http://honeybee.mapunity.org/main
and a regional innovation listing here: http://ruralinnovations.mapunity.org/main
More projects are in the works, and they were working on a new interface even as we talked. Go check them out…maybe even create your own community!
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.
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