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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: Feb 1, 2005

Following is a description of a recently published research paper recommended by a scientist involved in integrated biology. The recommender, Anuj Kumar, is an assistant professor in molecular, cellular, and developmental biology at the Universityof Michigan. This installment was reported and written by Meredith Salisbury, Genome Technology editor.

 

For a complete list of recommended papers, read Genome Technology, a GenomeWeb News sister publication.


"In silico simulation of biological network dynamics," Lukasz Salwinski and David Eisenberg. Nature Biotechnology. 2004; 22 (9): 1017-1019.

 

"In this paper, the authors describe an approach to simulating biological networks using field programmable gate arrays, whose parallel architecture allows for more realistic simulation of the reaction steps in biological networks, according to the paper's abstract. They say that in the past such large-scale simulations have been limited both by data availability and by the vast computational demands for the stochastic algorithms needed to model the networks.

 

"'With the rise of various -omics approaches, the limitation of experimental data is being lifted, but the computational demands remain staggering for simulating networks of thousands of reactions involving thousands of reactants,' the authors note. 'The problem stems from the sequential nature of microprocessor architecture and the highly parallel nature of biological systems, with the result that simulation times become prohibitively long.' The authors say using FPGAs can improve simulation run times by 'at least an order of magnitude' over what conventional microprocessors can achieve."

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.