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LABORATORY & STATISTICAL SCIENCE
Researchers explore visualisation of genetic information
Researchers at the National Center for Supercomputing Applications (NCSA), Mayo Clinic and the Genomic Institute of Singapore have begun a pilot project to develop an effective way to visually present genomic data to clinicians. The project is one of several being carried out by the Mayo Illinois Alliance for Technology-Based Healthcare, a joint effort launched in 2010.
Biomedical researchers generate a tremendous amount of genomic data about cancer, which has the potential to improve clinicians’ ability to diagnose, treat and prevent the disease. But in order for this complex, heterogeneous data to be useful in a clinical setting, it must be clear and easy to understand, with the relevant information drawn from the overwhelming fl ood. ‘There are all sorts of ways in which visualisation tools could be deployed to inform students, clinical practitioners, genetic counsellors and patients about the role of genomics in health and disease,’ said Dr Frank Prendergast, director of Mayo’s Center for Individualised Medicine and a co-principal investigator for the pilot project. ‘I am especially taken with
how such tools can be used to explain genomics to patients; gene sequences by themselves can be stultifyingly uninformative.’
The goal of the project is to ‘bridge
the gap between research and clinicians,’ added Michael Welge, who leads the data-intensive technologies and applications research team at NCSA. ‘How do you visually represent information from the research laboratory to the clinician, so the clinician can use this in their workfl ow?’ Welge’s team brings substantial data visualisation expertise to the project, while the team from Singapore provides insight into the research perspective on the data and how it is currently visually represented. The clinicians from Mayo and other hospitals (including Carle Hospital in Urbana) can explain their typical workfl ow and how they could use genomic data in diagnosis and in formulating treatment plans. The plan is to have an initial prototype or mock-up in 2011, which will be used as the basis for follow-on proposals and research. Welge believes a system could be ready for clinical deployment in two to fi ve years.
Ablynx deploys data management solution
Biopharmaceutical company Ablynx has deployed IDBS’ E-WorkBook Suite to manage data associated with the discovery and development of Nanobodies, a new class of antibody-derived therapeutic proteins for the treatment of major disease areas including infl ammation, thrombosis, oncology and pulmonary disease. E-WorkBook Suite is a data management solution designed to simplify workfl ows and protect
4 SCIENTIFIC COMPUTING WORLD
Intellectual Property (IP) assets. It offers a compliant environment, enabling scientists to capture, analyse and share data in a single, secure environment. Dominique Vlieghe, senior bioinformatician at Ablynx commented: ‘In E-WorkBook we believe we have found a complete solution that will support both rigid and fl exible workfl ows. E-WorkBook contains native functionality suited to our requirements.’
Software partnership for DNA sequencing data analysis
Accelrys has announced the signing of a partnership agreement with Oxford Nanopore Technologies. Under the terms of the partnership, Accelrys and Oxford Nanopore will develop software to enable complex, real-time analyses of experimental data produced by the Oxford Nanopore single molecule analysis system. Accelrys’ workfl ow software Pipeline Pilot will be
offered as the preferred and supported solution for secondary and higher level data analysis for the Oxford Nanopore DNA sequencing system at the time of its commercial release. These pipelines will use a variety of collections including Accelrys’ newly launched NGS Collection for Pipeline Pilot, a software solution that is compatible with all leading DNA sequencing technologies.
CHEMIST SEEKS SOLUTION TO NERVE AGENT EXPOSURE
Scientists are working to develop a new drug that will regenerate a critical enzyme in the human body that ‘ages’ after a person is exposed to poison gas. Christopher Hadad, professor of chemistry at The Ohio State University (OSU), is utilising Ohio Supercomputer Center (OSC) resources to help develop a more effective antidote to lethal organophosphorus (OP) nerve gas. ‘This project is a combination of synthetic and computational organic chemistry conducted through OSC at Ohio State, and biochemical studies conducted by colleagues at the US Army Medical Research Institute of Chemical Defense at Aberdeen Proving Ground in Maryland,’ said Hadad. Hadad’s study is focused on the
identifi cation of compounds that would return an appropriate alkyl group to the aged nerve agent/ AChE molecule, thus allowing treatment with oximes to provide for complete recovery. The project is investigating common OP nerve agents Tabun, VX, VR, Sarin, Soman, Cyclosarin and Paraoxon – all of which take on a similar
molecular structure upon ageing. ‘Computational studies of the interaction of the alkylating compounds with AChE were used to provide insight for the design of selective reagents,’ Hadad explained. ‘Ligand-receptor docking, followed by molecular dynamics simulations of the interactions of alkylating compounds with aged OP-AChE, was carried out in conjunction with experimental studies to investigate the binding of alkylating compounds to AChE. These results were then used to suggest interactions that aided in the orientation of alkylating compounds for maximal effi cacy.’ Throughout the project, Hadad employed computational studies to guide the progress of each objective, as well as to rationalise the observed experimental results. ‘Dr Hadad’s work on this project has made use of a range of the tools of electronic structure theory, molecular docking, molecular dynamics and hybrid quantum mechanical/molecular mechanical methods,’ said Ashok Krishnamurthy, interim co-executive director of OSC.
www.scientific-computing.com
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