Back to Table of contents

Primeur weekly 2012-08-13

Exascale supercomputing

Department of Energy awards $62 million in contracts to accelerate development of 'extreme scale' supercomputers ...

The Cloud

DreamWorks Animation drives innovation with HP Cloud Services ...

DDN and Alliance Technology Group enable data-intensive intelligence & surveillance organisations to economically harness the power of Big Data and Cloud collaboration ...

Applied Math Modeling releases Cloud-based, next-generation data centre design software ...

EuroFlash

Altair RADIOSS structural solver achieves unmatched performance using NVIDIA GPUs ...

UK’s Atomic Weapons Establishment selects Rogue Wave's ThreadSpotter ...

Future Internet PPP - Information Day on Call 2, Objectives 1.8 & 1.9 ...

What makes Paris look like Paris? Carnegie Mellon software finds stylistic core ...

USFlash

UC San Diego team aims to broaden researcher access to protein simulation ...

UC San Diego and Yale awarded collaborative NSF grant for Neuroscience Gateway ...

GPU acceleration of top genomics application with OpenACC promises to help speed delivery of life-saving drugs ...

DataDirect Networks debuts comprehensive management suite to simplify Big Data infrastructure scale up and scale out ...

DataDirect Networks announces rapid uptake of award-winning SFA technology across Australia's research computing community ...

EMC DLm8000 first mainframe virtual tape library to deliver synchronous replication ...

Swinburne to unveil the hidden universe ...

AMD launches first-ever AMD FirePro APU providing a powerful integrated visual computing platform for CAD and media and entertainment work flows ...

SGI reports fourth quarter and fiscal year 2012 financial results ...

Dell helps to power NASA's latest mission to Mars ...

Large private donation launches Institute for Advanced Computational Science at Stony Brook University ...

Computer models calculate systems-wide costs of gene expression ...

XSEDE brings in NCSA's Alan Craig as Digital Humanities Specialist ...

Computer models calculate systems-wide costs of gene expression

7 Aug 2012 San Diego - Bioengineers at the University of California, San Diego have developed a method of modelling, simultaneously, an organism's metabolism and its underlying gene expression. In the emerging field of systems biology, scientists model cellular behaviour in order to understand how processes such as metabolism and gene expression relate to one another and bring about certain characteristics in the larger organism.

In addition to serving as a platform for investigating fundamental biological questions, this technology enables far more detailed calculations of the total cost of synthesizing many different chemicals, including biofuels. Their method accounts, in molecular detail, for the material and energy required to keep a cell growing, the research team reported in the journalNature Communications.

"This is a major advance in genome-scale analysis that accounts for the fundamental biological process of gene expression and notably expands the number of cellular phenotypes that we can compute", stated Bernhard Palsson, Galetti Professor of Bioengineering, at the UC San Diego Jacobs School of Engineering.

"With this new method, it is now possible to perform computer simulations of systems-level molecular biology to formulate questions about fundamental life processes, the cellular impacts of genetic manipulation or to quantitatively analyze gene expression data", stated Joshua Lerman, a Ph.D. candidate in Bernhard Palsson's Systems Biology Research Group.

The team's method can be compared to understanding both the chemical reactions and the machinery that are required to refine crude oil into petrol in a large, industrial factory. Modelling metabolism tells you what biochemical reactions need to take place. Modelling the organism's gene expression tells you what kind of machinery you need. The team's method specifically accounts for the expression of enzymes, which are the molecular machines responsible for the biochemical processes of life. With this knowledge, it is possible to explore how an organism distributes its resources to promote growth and how genetic manipulation of these organisms alters this distribution.

"What you could hypothetically do with our model is simulate the total cost of producing a value-added product, such as a biofuel. That includes all the operating and maintenance costs", stated Daniel Hyduke, a project scientist in Bernhard Palsson's lab. Daniel Hyduke said the method has the potential to help streamline industrial metabolic engineering efforts by providing a near complete accounting of the minimal material and energy costs associated with novel strain designs for biofuel, commodity chemicals, and recombinant protein production.

Daniel Hyduke and Joshua Lerman prototyped the method on the minimal, yet metabolically versatile, hyperthermophile Thermotoga maritima. Because T. maritima is not currently ready for use in industrial applications, Daniel Hyduke and Joshua Lerman are working as part of a larger team to produce similar models for industrially relevant microorganisms, such as E. coli.

"We've built a virtual reality simulator of metabolism and gene expression for Thermotoga maritima, and shown that it much better approximates phenotypes of cells than modeling metabolism in isolation", stated Joshua Lerman.
Source: UCSD Jacobs School of Engineering

Back to Table of contents

Primeur weekly 2012-08-13

Exascale supercomputing

Department of Energy awards $62 million in contracts to accelerate development of 'extreme scale' supercomputers ...

The Cloud

DreamWorks Animation drives innovation with HP Cloud Services ...

DDN and Alliance Technology Group enable data-intensive intelligence & surveillance organisations to economically harness the power of Big Data and Cloud collaboration ...

Applied Math Modeling releases Cloud-based, next-generation data centre design software ...

EuroFlash

Altair RADIOSS structural solver achieves unmatched performance using NVIDIA GPUs ...

UK’s Atomic Weapons Establishment selects Rogue Wave's ThreadSpotter ...

Future Internet PPP - Information Day on Call 2, Objectives 1.8 & 1.9 ...

What makes Paris look like Paris? Carnegie Mellon software finds stylistic core ...

USFlash

UC San Diego team aims to broaden researcher access to protein simulation ...

UC San Diego and Yale awarded collaborative NSF grant for Neuroscience Gateway ...

GPU acceleration of top genomics application with OpenACC promises to help speed delivery of life-saving drugs ...

DataDirect Networks debuts comprehensive management suite to simplify Big Data infrastructure scale up and scale out ...

DataDirect Networks announces rapid uptake of award-winning SFA technology across Australia's research computing community ...

EMC DLm8000 first mainframe virtual tape library to deliver synchronous replication ...

Swinburne to unveil the hidden universe ...

AMD launches first-ever AMD FirePro APU providing a powerful integrated visual computing platform for CAD and media and entertainment work flows ...

SGI reports fourth quarter and fiscal year 2012 financial results ...

Dell helps to power NASA's latest mission to Mars ...

Large private donation launches Institute for Advanced Computational Science at Stony Brook University ...

Computer models calculate systems-wide costs of gene expression ...

XSEDE brings in NCSA's Alan Craig as Digital Humanities Specialist ...