NEWS
Cancer collaboration
identifies biomarkers
Genedata has collaborated on pre-processing and statistical captured secondary MS traces. Second, the reproducibility of
analysis of mass spectrometry analyses on LC-MS spectra. Professor James Mobley, this approach also increased
data with researchers at the Using the Expressionist system, director of the Comprehensive the confidence in our resulting
Comprehensive Cancer researchers first created matched Cancer Center Proteomics protein biomarker hits and
Center Proteomics Facility of peak lists across all samples with Facility, said: ‘Using enabled us to identify key
the University of Alabama at the Refiner MS module and then Expressionist in a systems biology associated pathways that were
Birmingham (UAB). performed uni- and multivariate approach advanced our research otherwise difficult to discern.
The collaboration made use statistical analyses with the in two fundamental ways. First, ‘The ability to compare
of the Genedata’s Expressionist Analyst module to identify because of the reproducibility samples prior to identification
system to identify protein peaks differentiating normal and inherent in the system, we were will enable our research to go
biomarkers for critical human disease states. After statistical able to identify key biomarkers into areas that might otherwise
diseases using animal models. analysis, researchers used standard with a relatively small cohort. remain unexplored.’
The collaboration spanned techniques to identify the peptides
three studies to date and found in the differentiating Web-exclusive features now online
covers research into pancreatic peaks. By doing the peak
cancer, prostate cancer and processing and analyses up front
l Cutty Sark’s high-tech salvation
cystic fibrosis. In each of these and using raw MS data, researchers
l FPGA technology provides boost to proteomics research
research areas the Genedata were able to identify biomarker l Accessibility and green issues dominate SC08
Expressionist Refiner MS and peptides that they would have l More cores means slower supercomputing
Analyst modules were used for otherwise missed had they only
www.scientific-computing.com/news
Painted warrior brought to life
Scientists from WMG at the the group’s expertise in surface of the bust and translated The Southampton team is
University of Warwick, the three key technologies: high that information into a computer now digitally re-modelling and
University of Southampton, and resolution laser scanning, rapid model. Dr Greg Gibbons, also re-painting the sculpture.
the Herculaneum Conservation prototyping and ultra-realistic of WMG, then used rapid They are using techniques
Project are helping to restore a computer graphics. Researchers prototyping to create a physical derived from the film industry to
2,000-year-old painted statue from WMG at the University 3D model of the head. recreate the original carved and
using modern technology. of Warwick, Southampton and Further recording was painted surfaces. In the final step
The Roman statue was Herculaneum are now scanning, carried out on site by experts Professor Alan Chalmers, head
discovered by the Herculaneum modelling and digitally in archaeological computing of WMG’s visualisation team
Conservation Project in the recreating the Amazon statue. from Southampton, led by Dr and an expert in ultra-realistic
ancient ruins of Herculaneum, Dr Mark Williams, a leader Graeme Earl. They used a novel graphics, will apply techniques to
a town preserved in the same in laser measurement at WMG, form of photography, which the computer model to exactly
eruption that buried nearby took his team and equipment provided an extremely detailed reproduce the lighting and
Pompeii in AD 79. It is to the site. He said: ‘The statue record of the texture and colour environmental conditions under
thought to represent a wounded is an incredible find. Although of the painted surfaces. Dr Earl which the painted statue would
Amazon warrior, complete with its age alone makes it valuable, said: ‘Cutting edge techniques have originally been created
painted hair and eyes preserved it is unique because it has are vital to the recording of and displayed. This visualisation
by the ash that buried the retained the original painted cultural heritage material, since will provide archaeologists with
town. Archaeologists at the surface, preserved under the so much remains unstudied an otherwise impossible view
University of Southampton volcanic material that buried or too fragile to analyse. Our of how the original statue may
and the Herculaneum Herculaneum.’ work at Southampton attempts have looked in context, and
Conservation Project contacted Dr Williams measured (within to bridge the gap between allow them to experiment with
WMG after hearing about 0.05 of a millimetre) every computing and archaeology.’ alternative hypotheses.
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SCIENTIFIC COMPUTING WORLD FEBRUARY/MARCH 2009 www.scientific-computing.com
SCWfeb09 pp04-07 News.indd 4 4/2/09 10:40:39
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