3D becomes a standard web data type

Trevor F Smith — Tue, 06 May 2008 15:49:29 -0700

Description

It can be argued that no data type has seen widespread use on the web until the default browsers on the top operating systems ship with native support. For example, in the recent past there were installable plugins and external applications which could render streamed video, but the massive uptake of online video applications like YouTube were not possible before default browser support because most users will not download and run installers.

The same pattern is happening right now for 3D content. There are several competing third party plugins which can render 3D data (e.g. Unity3D) but they suffer from the same reluctance on the part of users to install third party plugins. They also use standard but incompatible data formats to represent scene graphs and behaviors.

There are several open projects using Flash to render 3D scenes in software (e.g. Papervision3D and Away3D) and Adobe is working on hardware accelerated 3D APIs for the next version of Flash. In addition, members of the Gecko project (which underlies the Firefox browser) have prototypes of OpenGL bindings for a new canvas3D HTML element.

On the web server side there are also efforts like the Ogoglio project and Paperworld3D to create web standards based servers for shared 3D spaces.

Source

The Ogoglio Project: http://ogoglio.com/
Papervision3D: http://blog.papervision3d.org/
Unity3D: http://unity3d.com/

Web services for chemoinformatics

Andrew Walkingshaw — Fri, 02 May 2008 17:40:52 -0700

Description

Chemoinformatics algorithms are moving onto the Web, alongside the datasets they operate on.

For example, the University of Indiana provides a wide range of both data-driven and computation-driven services. Scientists don't need to download large datasets to use these, they don't need to install software, and they're easier to integrate with the rest of the Web on workflows and mashups (especially if they use the RESTful architecture style).

As the rest of the Web includes databases like the US-government-backed PubChemPubChem:

PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.

there's quite a bit of power there, potentially; Web-accessible large databases and algorithms which work on them, all without having to install anything or even provide the computational resources, and all in public.

Future of chemistry

Source

http://www.chembiogrid.org/
http://en.wikipedia.org/wiki/Representational_State_Transfer
http://pubchem.ncbi.nlm.nih.gov/

Social networks constructed by blog and SMS in China

Jess Hemerly — Tue, 05 Feb 2008 10:06:48 -0800

Description

From the blog post:

Blog was not invented in China, but it has been hugely popular in this country. Nowadays, almost everybody has a blog, presenting whatever he/she feels like to. Its users range from Nintendo DSL gamers to pop stars, and its hosts range from Windows Live Spaces to the Chinese native blog host www.bokee.com. And nonetheless, many of these hosts are reported to have attracted a large number of users.

This popularity can be probably attributed to the common Chinese character of being self-contained. Many Chinese prefer to keep their opinions to themselves rather than speaking out aloud. However, they do have a desire to share their experiences and knowledge, if the communications channel is right. Blogs are clearly one of those. Very often, the Chinese simply exchange their blog addresses, and then, when sitting back at home, they talk to each other over the blog. Blogs have obviously facilitated information flow and the construction of social networks in this country and particularly among the youth.

China: Science & Technology

Source

"Social networks constructed by blog and SMS in China." Xtract blog, November 14, 2007.

Social networking XY.0: building genetic communities

Attila Csordas — Sat, 24 Nov 2007 18:51:58 -0800

Description

In these days, tech companies with MISSIONS are flourishing. I guess you’ve already heard about the company, whose mission is to organize the world’s information and make it universally accessible and useful. The newly launched, Mountain View based 23andMe seems similar in the mission respect. 23andMe is the first web - based biotech company offering personalized genome service to its customers including interpreted and highly probabilistic information on the health risks of the customer’s genetic profile.

But 23andMe has much more to offer in these early days and I think that mainly the biggest mission behind the company will be to show how different people are irreversibly connected and similar through their genetic material and variants. The company’s Global Similarity Map based on the comparison of the evaluated SNP (single nucleotide polymorphism) variants amongst customers and the Ancestry Service based on the by and large maternally inherited mitochondrial DNA. They will make this mission more explicit by introducing a social networking service around shared genotypes or as it claimed in the Wired article on 23andMe:

This is also where a novel use of social-networking tools comes in. Wojcicki envisions groups of customers coming together around shared genotypes and SNPs, comparing notes about their conditions or backgrounds and identifying areas for further scientific research on their own. “It’s a great way for individuals to be involved in the research world,” Wojcicki says. “You’ll have a profile, and something almost like a ribbon marking participation in these different research papers. It’ll be like, How many Nature articles have you been part of?’” (Social networking will be included in version 2.0 in a matter of months, Avey says.)

Indeed, on one of the slide of the company's webcast media launch this aim was highlighted this way: "building genetic communities: 23andMe users can connect themselves to their families and friends."

The idea of social networking based on genetic similarities and vulnerabilities: I would call it social networking XY.0 and the challenge for any other social networking sites will be huge. Also this mission could be interpreted as a nice and humanist aim, just like Google’s, although the interpretation space is bigger than that.

One for instance can argue that the idea of building "genetic communities" has a bad connotation thanks to racial prejudices. If 23andMe wants to introduce this social or rather genetic networking service, it will probably have to fight a semantic battle to turn the connotation of "genetic communities" neutral and finally positive, by recasting it as a means of connecting people together.

“We are all from the same seed” - that's how an interviewer summarized what she heard from Linda Avey, co-founder of 23andMe in a video interview below. Linda and the other founder Anne Wojcicki talked about the company’s ancestry, genetic comparison and similarity seeking services, the ones that will technologically turned into a social networking service later based on shared genotypes backed by the genetical connectedness of all people (in this case all 23andMe customers).

Linda’s thought was the following: “If genetics has the basis to bring people together, rather than differentiate them, that’s gonna be really interesting.”

In a recent Nature report called "So similar, yet so different" (1) we can find the following expert opinions on the very same topic that is commercialized and envisioned now by 23andMe (citing lengthy here, emphasis by me):

In his 2000 State of the Union Address, President Bill Clinton chose to emphasize something he had recently heard from a genome researcher: that humans are all, irrespective of race, 99.9% the same genetically. “Modern science,” he told his country’s legislators, “has confirmed what ancient faiths have always taught: the most important fact of life is our common humanity.” Seven years on, and four years after the final publication of the sequences from the Human Genome Project, new technologies and larger data sets are allowing genome biologists to answer a conundrum embodied in that unity-inspiring percentage: if our DNA is so similar, why do we seem different in so many ways?

The answer, in part, is that the genome is not as uniform as Clinton was led to believe; nor is it nearly as sedate, stable and homogeneous as scientists used to think. It’s less a ‘Book of Life’, more a wiki; many of its ho-hum elements don’t change, but some really interesting bits are constantly revised.

“Maybe 99% of our genome behaves in a nice, predictable way,” says Gilean McVean, a statistical geneticist at the University of Oxford, UK. “But it’s become clear that there is this pool of errant variants that are responsible for a lot of the dynamism in our genome, and we don’t understand its consequences for disease risk or normal variation.”

Over the past year, two large studies (2,3) have found evidence that many people carry around lots of large chunks of DNA that are deleted, copied, flipped or otherwise rearranged in other people. The findings confirm earlier studies that hinted at this type of ’structural’ variation but were not large enough to command assent (4). A study of the genome of sequencing pioneer Craig Venter also found much more variation from reference sequences than expected (5).

The larger analyses estimate that such variable regions could make up more than 10% of the genome, vindicating scientists, such as Evan Eichler of the University of Washington in Seattle, who have long argued that structural variation is a major source of diversity. Scientists are still investigating how much it contributes to differences between populations. But it is already clearly linked to some differences between individuals that can be correlated with behaviour or environment. For example, a study published in September reported5 that evolution has driven a starch-digestion gene to duplicate itself in people with traditionally starch-heavy diets.

“We’re getting away from this 0.1% figure that has been in our minds ever since the draft human genome sequence came out,” says Hunt Willard, head of the Institute for Genome Sciences and Policy at Duke University Medical Center in Durham, North Carolina. “We’re now looking at maybe half a per cent of content that is unique to individual genomes.” The actual variation is thus lower than the extent of the variable regions, but larger than previously thought. “Maybe Eichler always had that number in his head,” adds Willard, “but no one else did.”

What social networking XY.0 could mean for the future:

The rise of web based social networking services based on shared genotypes
Web based ancestry services tracking back the customer's family tree
Connecting customers with different genetic background together through personal genome services
Reinterpretation of genetic relationships between people

1. Erika Check So similar, yet so different Nature 449, 762-763 (2007)

2. Redon, R. et al. Nature 444, 444–454 (2006).

3. Stranger, B. E. et al. Science 315, 848–853 (2007).

4. Erika Check: Human genome: Patchwork people Nature 437, 1084–1086 (2005).

5. Nature 447, 358–359 (2007).

Blog:

Pimm: 23andMe: Genetics brings people together, rather than differentiate http://pimm.wordpress.com/2007/11/19/23andme-genetics-brings-people-together-rather-than-differentiate/

Pimm: 23andMe’s mission: connecting all people on the DNA level or social networking XY.0
http://pimm.wordpress.com/2007/11/18/23andmes-global-similarity-map-as-mission-connecting-all-people-on-the-dna-level/

Pimm: inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa?
http://pimm.wordpress.com/2007/11/20/infaq-for-23andme-what-if-i-have-mitochondrial-dna-from-pa/

Signals

Genetic information will make it onto social networking profile