Archive for category science

Next Gen Data in Genome Web

Article is here.

Nailing Down Next-Gen Data
April 2010
By Matthew Dublin

With all of the nail-biting that supposedly goes hand-in-hand with the next-generation sequencing “data deluge,” the non-informaticist may be surprised to learn that the real worry of the folks tasked with making sense of this data lies not in the quantity, but rather, in the ambiguity of the data these machines are spitting out. Issues such as error rates in data and how to improve base calls to account for those errors result in researchers developing a sort of informatics hoarding disorder in which they sometimes feel the need to store images, base calls, second-best base calls, third-best base calls, and process intensity information — all because of a lack of knowledge about the data.

Happy Birthday, Watson!

From the Writer’s Almanac:

It’s the birthday of molecular biologist James Dewey Watson, born in Chicago (1928). He went to England as a research fellow at Cambridge University, and there he met a graduate student, Francis Crick, who became a close friend and collaborator. They started work on the structure of DNA. They weren’t the only scientists working on it — Maurice Wilkins and Rosalind Franklin in London had done important research on the structure, and Franklin in particular had realized that the phosphate backbones were on the outside of the molecule, and that at least in one form, DNA took the shape of a helix. But female scientists weren’t taken as seriously as their male counterparts — they weren’t even allowed to eat lunch in the same room — and Wilkins was frustrated with Franklin, so he showed her data to Watson and Crick without her knowledge. The two took her research and made the next big leap, imagining DNA as a double helix of nucleotides, and in 1953 Watson and Crick published their findings in the journal Nature. Watson was only 25 years old.

AGBT: Ion Torrent Wows with Semiconductor Sequencing | MassGenomics

AGBT: Ion Torrent Wows with Semiconductor Sequencing | MassGenomics.

Here’s the future, folks. A breadbox sized sequencer that uses microchips to sequence DNA without dyes and reagents. I’m amazed, and can’t wait to see how these things work in the lab. I’m also impressed that they ship with ipads!

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Less Talk More Rock

lesstalkmorerock

There’s a great … I guess it’s an article …. over here about video game design and construction, but I really think it applies to all creative pursuits, even those work-related pursuits that might not seem creative at the time, but really are when you think about them.

Great read.

Why Hasn’t Scientific Publishing Been Disrupted Already?

Great article on The Scholarly Kitchen about the scientific publishing business. Notably, the breakdown of why publishing has worked for so long in the scientific fields (dissemination and registration), how that has evolved (into validation designation and filtration) and what technologies are moving to change the publishing landscape yet again (semantic and mobile technologies with open data standards).

A great read.

China’s R&D

An article from Thomson Reuters has some interesting facts about China’s R&D:

The study draws on data found in Web of Science®, available on the Web of Knowledge platform — the world’s largest citation environment of the highest quality scholarly literature. Key findings include:
• China’s output increased from just over 20,000 research papers in 1998 to nearly 112,000 in 2008, The nation doubled its output since 2004 alone. China surpassed Japan, the UK and Germany in 2006 and now stands second only to the USA.
• China is heading to overtake the USA in output within the next decade.
• China’s research is concentrated in the physical sciences and technology. Materials science, chemistry and physics predominate. Looking toward the future, rapid growth can be seen in agricultural sciences and life sciences fields such as immunology, microbiology, and molecular biology and genetics.
• The USA stands out in terms of collaboration with China., US-based authors contributed to nearly 9 percent of papers from China-based institutions between 2004 and 2008.
• Regional collaboration expansion is notable, especially with Japan, South Korea, Singapore and Australia.

Not surprising – given China’s size and scientific focus, but, hopefully a kick in the pants for the US and Europe to start emphasizing Research and Development not only in higher education, but also in high school, in large corporations and in government.

Commercial Break: Old school harem scarem Swine Flu jab ads don’t worry us | BitterWallet

Commercial Break: Old school harem scarem Swine Flu jab ads don’t worry us | BitterWallet.

Great embedded you tube about the 1976 swine flu epidemic.

Fun times.

Now wash your hands.

Swine Flu

swineflu

Props.

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Science on TV

phd040609s

From here.

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BBC NEWS | Science & Environment | Black hole found in Milky Way

There is a giant black hole at the centre of our galaxy, a study has confirmed.

German astronomers tracked the movement of 28 stars circling the centre of the Milky Way, using the European Southern Observatory in Chile.

The black hole is four million times heavier than our Sun, according to the paper in The Astrophysical Journal.

BBC NEWS | Science & Environment | Black hole found in Milky Way.

Thanks, Mr. Ellis. That really made my night.