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Primeur weekly 2011-05-30

EuroFlash

Altair Engineering announces successful 7th CAE Technology Conference held on the 10th May 2011 at the Heritage Motor Centre, Gaydon, Warwickshire ...

The quantum computer is growing up - Repetitive error correction in a quantum processor ...

Acorn: A Grid computing system for constraint based modelling and visualization of the genome scale metabolic reaction networks via a web interface ...

2011 International Supercomputing Conference is the forum for latest HPC news ...

World record in ultra-rapid data transmission ...

USFlash

Cray unveils the Cray XK6 supercomputer ...

Sandia and Cray Inc. to tackle "big data" in new supercomputing institute ...

D-Wave Systems sells its first quantum computing system to Lockheed Martin Corporation ...

Pittsburgh Supercomputing Center accelerates machine learning with GPUs ...

Zenoss demonstrates scalable monitoring for one of the world's most powerful supercomputers ...

University of Arizona Engineering selected as High-Performance Parallel Computing Teaching Center ...

Iowa State physicists explain the long, useful lifetime of carbon-14 ...

IBM unveils breakthrough software and new services to exploit big data ...

Penguin Computing supplies PACMAN supercomputer to University of Alaska Fairbanks ...

LG U+ implements Oracle Communications Applications for efficient network resource management of 3G and 4G LTE networks ...

New bandwidth management techniques boost operating efficiency in multi-core chips ...

HP trusted advisors reduce complexity of designing and building data centres ...

IBM donates top undergraduate computing capability to Union College ...

Citrix broadens footprint in Cloud infrastructure market with "Project Olympus" ...

Worldwide server market revenues increase 12.1% in first quarter as market demand continues to improve, according to IDC ...

NVIDIA Tegra 2 super chip wins 'Best Choice' Award at Computex 2011 ...

Citrix unveils end-to-end Cloud networking line-up ...

Veeam back-up and replication to support Microsoft Hyper-V ...

University of Toronto to award quantum mechanics prize to renowned physicist Sandu Popescu ...

HP technology helps DreamWorks Animation high-kick "Kung Fu Panda 2” onto the big screen ...

Zenoss delivers monitoring for applications built on Cloud Foundry ...

Acorn: A Grid computing system for constraint based modelling and visualization of the genome scale metabolic reaction networks via a web interface

24 May 2011 Warsaw - Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering.

These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment.

Therefore Acorn is presented, an open source (GNU GPL) Grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The Grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users) increase.

The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts.

Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available.

Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment.

To illustrate these features the development team has deployed Acorn and created a web server allowing constraint based simulations of the genome scale metabolic reaction networks of E. coli, S. cerevisiae and M. tuberculosis.

Acorn is a free software package, which can be installed by research groups to create a web based environment for computer simulations of genome scale metabolic reaction networks. It facilitates shared access to models and creation of publicly available constraint based modelling resources.

Authors are Jacek Sroka, Lukasz Bieniasz-Krzywiec, Szymon Gwozdz, Dariusz Leniowski, Jakub Lacki, Mateusz Markowski, Claudio Avignone-Rossa, Michael Bushell, Johnjoe McFadden, and Andrzej Kierzek. Their research apperas inBMC Bioinformatics2011, 12:196.
Source: BMC Bioinformatics

Back to Table of contents

Primeur weekly 2011-05-30

EuroFlash

Altair Engineering announces successful 7th CAE Technology Conference held on the 10th May 2011 at the Heritage Motor Centre, Gaydon, Warwickshire ...

The quantum computer is growing up - Repetitive error correction in a quantum processor ...

Acorn: A Grid computing system for constraint based modelling and visualization of the genome scale metabolic reaction networks via a web interface ...

2011 International Supercomputing Conference is the forum for latest HPC news ...

World record in ultra-rapid data transmission ...

USFlash

Cray unveils the Cray XK6 supercomputer ...

Sandia and Cray Inc. to tackle "big data" in new supercomputing institute ...

D-Wave Systems sells its first quantum computing system to Lockheed Martin Corporation ...

Pittsburgh Supercomputing Center accelerates machine learning with GPUs ...

Zenoss demonstrates scalable monitoring for one of the world's most powerful supercomputers ...

University of Arizona Engineering selected as High-Performance Parallel Computing Teaching Center ...

Iowa State physicists explain the long, useful lifetime of carbon-14 ...

IBM unveils breakthrough software and new services to exploit big data ...

Penguin Computing supplies PACMAN supercomputer to University of Alaska Fairbanks ...

LG U+ implements Oracle Communications Applications for efficient network resource management of 3G and 4G LTE networks ...

New bandwidth management techniques boost operating efficiency in multi-core chips ...

HP trusted advisors reduce complexity of designing and building data centres ...

IBM donates top undergraduate computing capability to Union College ...

Citrix broadens footprint in Cloud infrastructure market with "Project Olympus" ...

Worldwide server market revenues increase 12.1% in first quarter as market demand continues to improve, according to IDC ...

NVIDIA Tegra 2 super chip wins 'Best Choice' Award at Computex 2011 ...

Citrix unveils end-to-end Cloud networking line-up ...

Veeam back-up and replication to support Microsoft Hyper-V ...

University of Toronto to award quantum mechanics prize to renowned physicist Sandu Popescu ...

HP technology helps DreamWorks Animation high-kick "Kung Fu Panda 2” onto the big screen ...

Zenoss delivers monitoring for applications built on Cloud Foundry ...