July 2008 Archives

The database generation

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Writing in last week's Nature, Nobel laureate Paul Nurse came down on the side of systems biology but was careful to distance the concept from the 'big biology' tag that the field's critics are attaching to it.

For Nurse, "biology stands at an interesting juncture". Previous advances, he argued were based mostly on molecular biology: "applying the ideas that the gene is the fundamental unit of biological information and that chemistry provides effective mechanistic explanations of biological processes". But he warned:

"...comprehensive understanding of many higher-level biological phenomena remains elusive. Even at the level of the cell, phenomena such as general cellular homeostasis and the maintenance of cell integrity, the generation of spatial and temporal order, inter- and intracellular signalling, cell 'memory' and reproduction are not fully understood."

ISMB 2008 on FriendFeed

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I haven't really got into FriendFeed just yet but one of the useful things about it is the concept of the room. A group of bloggers who went to the ISMB conference in Toronto created one such room into which they could tip a bunch of micro-blogs that covered the key points of the keynote.

According to a comment from one of the bloggers on Nature's Seven Stones blog, there is talk of pulling microblogs into next year's conference.

(Via The Seven Stones.)

Cellumen is spinning off a unit to work on personalised medicine:

"Cellumen's successful application of Cellular Systems Biology (CSB(TM)) to drug discovery, drug development and personalized medicine over the last three years has yielded strong interest across each of these application areas," stated D. Lansing Taylor, Ph.D., CEO of Cellumen. "As a result, we are spinning out our personalized medicine unit to better address the market demands. Cernostics Pathology will focus on digital imaging pathology and personalized medicine using Tissue Systems Biology (TSB(TM)), which is CSB applied to tissues."

Sometimes, I can't help feeling that some people really haven't grasped the concept of systems biology.

Designing the library

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Jean Peccoud and colleagues at the Virginia Bioinformatic Institute have published their work analysing one of the clone banks derived from the BioBrick registry of parts for synthetic biology.

What they found reflects the way in which the registry has grown, particularly the ready-made clones. Peccoud and his team argues that future registries will have to pay closer attention to what the concept of a 'part' means in synthetic biology as the current definitions do not necessarily work all that well.

The VBI researchers see registries such as the BioBrick Foundation's as "complementary to de novo synthesis since both approaches can be used to fabricate designer DNA sequences".

When he spoke at BioSysBio earlier this year, Peccoud said there is a role for many types of registry. Some will be kept inhouse by companies to allow them to include their own parts. Others will tend to use publicly available libraries.

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