Research is in the Clouds for CIT's Bioinformatics Group

Research is in the Clouds for CIT's Bioinformatics Group

Published on: Thursday, 01 November 2012

CIT’s Bioinformatics research group has been awarded the highly coveted and prestigious Marie Curie Industry-Academia Partnerships and Pathways (IAPP) programme grant. The Award from the European Commission, which is worth over €1.3 million and will run over 4 years, is focused on the development of advanced cloud computing techniques for large-scale bacterial genome sequencing and medical diagnostics/prognostics.

The project, known as ClouDx-i, involves three partners: CIT (the lead institution), NSilico (a CIT spinout founded by Dr Paul Walsh from Computing and Dr Roy Sleator from Biological Science) along with The Division of Medical Pathways unit of the University of Edinburgh (recently ranked 32 in the Higher Education world University rankings).

This project is coordinated by Dr Sleator, who will provide expertise in bacterial genomics and large scale next generation sequencing of bacterial pathogens of clinical importance. Aisling O’Driscoll from CIT’s Department of Computing will lead the development and implementation of the cloud computing platform technology that will use distributed big data frameworks to perform parallelised processing of the developed biological algorithms. Dr Paul Walsh, CEO of NSilico, will lead the software development work in the project, which will entail detailed analysis of high performance computing techniques for computer based diagnosis and the development of a user friendly software package that will allow medics to easily and rapidly treat patients in clinics. NSilico has already developed a commercial cloud computing bioinformatics product known as BioMapper (a project which was part funded by an Enterprise Ireland Commercialisation fund) and so will bring significant commercial and software development expertise to the project.

The Division of Medical Pathways in the University of Edinburgh will lead the research on the identification of biomarkers that identify infection responses in humans (the host response) as well as the data analytic techniques that classify these markers accurately. Software developed by NSilico will be used to rapidly analyse and combine the bacterial genomics data generated in CIT with the human biomarkers identified in Edinburgh, creating a software package which will enable clinicians to easily and rapidly classify the source of infection in patients and the most appropriate treatment regimen to follow.

According to Dr Sleator the software envisioned in this project, when combined with modern molecular biology techniques, is likely to have a significant impact on patient care – dramatically improving diagnostic accuracy and prognostics value in patients – being faster, cheaper and better than current approaches.

“We plan to lead the development of new medical diagnostic techniques that will enable patients to be diagnosed and treated rapidly by harnessing the data processing power available in cloud computing platforms.” said NSilico CEO Dr Paul Walsh “By computerising many aspects of the medical process we hope to dramatically cut the time needed to treat patients during hospital stays, getting people back on their feet sooner, thereby cutting medical costs and leading to a better outcome for all.”

Ms O’Driscoll said: “Given the unprecedented scale and rate at which low cost genomics data is being generated, future medical discoveries will largely depend on the ability to interpret vast, multi-dimensional data sets. To realise this, it is vital to harness the power of cloud computing and big data technologies, enabling large biological data sets to be analysed rapidly, without sacrificing accuracy, thereby expediting and improving patient care.”

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