Archive by category | Systems Medicine

SciFoo: scientific fireworks

SciFoo: scientific fireworks

In his list of eight ‘generative’ values (Better Than Free), Kevin Kelly includes ’embodiment’–the actual physical realization of an item or event which could be otherwise freely distributed over the web. While we are all ‘hyperlinked’ on the Internet, the value of those unique qualities that cannot be generated or “copied” on the web is dramatically increased. The type of intense emulation and shared excitement sparked at the recent Science Foo Camp (SciFoo 2008), organized by Nature, Google and O’Reilly, gave a wonderful example of the unique value of direct human exchange during an exclusive event bringing together roughly 200 top scientists, ‘geeks’ and other technologists at the Googleplex in Mountain View, California.  Read more

Fascinating correlations or elegant theories?

Chris Anderson, Editor-in-Chief of Wired , wrote a few weeks ago a provocative piece “”http://www.wired.com/science/discoveries/magazine/16-07/pb_theory”>The End of Theory: The Data Deluge Makes the Scientific Method Obsolete“, arguing that in our Google-driven data-rich era (”The Petabyte Age”) the good old “approach to science —hypothesize, model, test — is becoming obsolete”, leaving place to a purely correlative vision of the world. There is a good dose of provocation in the essay and it was quite successful in spurring a flurry of skeptical reactions in the blogosphere, FriendFeed-land and lately in Edge’s Reality Club.  Read more

Google Health, Biomedical Mutual Organizations and Open Consent

Google Health, Biomedical Mutual Organizations and Open Consent

Google Health, the new service offered by Google is now online (via bbgm, Life as a Healthcare CIO, GTO). This service helps users to store, organize and share their health profile and medical records, to use a variety of health-related online services and to search for medical information. Understandably, Google places great emphasis on data security and confidentiality. In this regard, I thought it might be worth highlighting several recent and thought-provoking discussions around the issues of data privacy and participative medical investigations.  Read more

Top-down mapping of gene regulatory pathways

Top-down mapping of gene regulatory pathways

In a very recent lecture (see full video from NIH VideoCasting) given for the NIH Systems Biology Special Interest Group, Trey Ideker presents a great overview of the various strategies his group has been developing in the recent years in order to integrate multiple types of large scale datasets. While one of the most pervasive ‘meme’ about high-throughput measurement is that they are “notoriously unreliable” (see Hakes et al, 2008, for a recent example), Trey beautifully illustrates how predictive computational models and novel biological insights can be generated by sophisticated data integration strategies. Three types of applications are presented in his talk:  … Read more

Consumer Health Information Technology

Consumer Health Information Technology

I highly recommend to visit the NIH VideoCasting page, which hosts many interesting video/podcasts. Even if I realize that this is a bit old according to the blogosphere time scale, I would like to point to this one: “The Future: Consumer Health Information Technology”, featuring talks given at a NCI-sponsored meeting on Dec 10, 2007 by Adam Bosworth (formerly “Google Health architect”, now starting his own company Keas), Bern Shen (Intel) and Bill Crounse (Microsoft).  Read more

J Craig Venter’s Genome

J Craig Venter’s Genome

Many others have abundantly commented on the publication of Craig Venter’s genome this week in PLOS Biology (Levy et al, 2007). The sequence of his full diploid genome (HuRef) reveals that the degree of genetic variability between maternal and paternal chromosomes is much higher (0.5%) than expected. Part of this variability is due to insertion/deletions (indels represent only 22% of variant events but amount to up to 75% of the variant nucleotides), alterations that are typically missed by SNP genotyping (SNPs represent 78% of the variants). Copy number variations (62, amounting to 10Mb) are also reported, albeit not determined by sequencing but via microarray genomic hybridization. With regard to variability in gene exons, the analysis shows that at least 44% of the genes are in the heterozygous state.  Read more

The Human (Genetic) Disease Network

The Human (Genetic) Disease Network

The relationship between genetic mutations and human diseases is often complex and ambiguous: a given disease can be associated with mutations in distinct genes and, conversely, mutations in a given gene can be associated with several diseases. Can this many-to-many relationship be exploited to construct a human disease network and extract information on the human disease landscape?  Read more

Open Source Biology

Open Source Biology

Novartis, The Broad Institute, and Lund University today announced the completion of a genome-wide map of genetic differences in humans and their relationship to type 2 diabetes and other metabolic disorders. All results of the analysis are being made accessible, free of charge on the internet to scientists around the world (Novartis Media Release, Feb 12, 2007)  … Read more