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EU Research Group Awarded $1.7M to Develop Informatics Infrastructure for Infectious Disease Diagnostics

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A research group led by scientists from the Cork Institute of Technology has received a €1.3 million ($1.7 million) grant from the European Commission for a four-year project, dubbed ClouDx-i, that will focus on the development of cloud computing techniques for large-scale bacterial genome sequencing and infectious disease diagnostics.

Besides CIT, researchers from CIT spinout NSilico and the University of Edinburgh’s division of pathway medicine will also work on ClouDx-i.

The team intends to develop “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,” NSilico’s founder and CEO Paul Walsh explained in a statement.

Roy Sleator, NSilico’s co-founder, will coordinate research efforts around bacterial genomics and large-scale next-generation sequencing of bacterial pathogens; Walsh will handle software development efforts focused on using high-performance computing techniques to speed up patients’ treatment; and Aisling O'Driscoll, a professor in CIT's computing department, will lead efforts to develop a cloud computing platform technology on which biological algorithms can run.

The partners intend to develop techniques that would make it possible to identify disease-causing bacteria in hospital samples much faster than current culture-based approaches can, Sleator told BioInform.

As part of that effort, the researchers hope to identify genes in human hosts that are up- or down-regulated in response to infection as well as genetic markers that could be used to identify the infecting bacteria, he explained.

This provides “two very powerful molecular markers, which will allow us, in the first instance, to diagnose the infection … and then, in the second instance, to see how the patient will respond,” he said.

During the first two years of the project, the partners will work on collecting contaminated blood specimens and sequencing the genomes of all the bacteria found in the samples, Sleator said.

Additionally, researchers at the University of Edinburgh will also analyze transcriptomic data from the project participants’ samples, he said.

Meanwhile, the bioinformatics team will use cloud computing and big data technologies to create a system to manage the sequencing datasets produced by the project as well as to parallelize algorithms that will be used to process the genomic data, CIT’s O'Driscoll told BioInform.

She added that the team will create an easy-to-use software interface that biologists will use to interact with the ClouDx-i system.

The system would allow a biologist to, for example, compare biomarkers identified in patient samples to information in public resources such as PubMed and “within a couple of hours diagnose what the infection is, [and] what is the likely outcome" of a particular treatment, Sleator said.

NSilico will consider commercializing the fruits of ClouDx-i, he said, though he noted that the primary goal of the project is to "develop something which will be of benefit to clinicians and ultimately to patients and will help better improve our treatments and reduce our medical bills.”

NSilico, which opened its doors two years ago, has developed and intends to market commercial cloud-based software known as BioMapper — a bioinformatics management system that lets non-bioinformaticians analyze genomic sequence data.

BioMapper uses a "mashup" approach to automatically connect a number of open source bioinformatics algorithms, enabling users to move their data between various tools within the same environment, Sleator explained.

Users can build their own genomics and metagenomics workflows within the system and reuse them as needed, he said. They can also add new algorithms that currently aren’t available through BioMapper if needed, he said.

BioMapper’s bioinformatics list includes programs for gene identification programs and motif analysis searches as well as tools for protein visualization and analysis, Sleator said.

BioMapper is offered as a software-as-a-service solution. Sleator said that pricing for the software is still being determined. The company is mulling an annual subscription where customers would pay a monthly fee for a basic set of features and an additional fee for more specialized capabilities.

For now, the software is being used in collaborations at several institutions including the University of Chicago, University College Cork, and the University of Edinburgh, Sleator said.

While BioMapper won’t be used directly in ClouDx-i, Sleator said that the project will benefit from lessons NSilico learned while developing its software.

For example, the firm will use its software development expertise to build a “similar framework” for ClouDx-i and it will repeat “a lot of case studies we have done with biologists … with our clinicians,” he said.

Funding for the ClouDx-i project comes from the EC’s Marie Curie Industry-Academia Partnerships and Pathways program.

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