02.03.2020 change 02.03.2020

Computer Boffins to Improve Bioinformatics Systems for Understanding Long-term Environmental Effects on Health

Credit: Fotolia Credit: Fotolia

Polish IT specialists have teamed up with scientists from Poland and across Europe to research the long-term impact of the environment on human health.

Beginning with the foetal period and continuing up until death, the field of study known as exposome looks at how environmental factors play a role in the incidence of cancer, cardiovascular diseases, respiratory disorders and civilization diseases.

So far, no systematic research has been undertaken, because science has not yet developed the appropriate methods and tools.

But now the IT experts will provide high-performance, scalable software necessary for analysing genetic data while scientists from the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM) at the University of Warsaw will develop bioinformatics software.

ICM is part of the Human Exposome Assessment Platform (HEAP) project coordinated by Professor Joakim Dillner from Karolinska Instituet (Stockholm, Sweden).

Almost EUR 12 million has so far been allocated to research carried out by 11 European partners and the whole project is worth 100 million euros.

The tools created will enable scientists to analyse data related to incidence and prevention of selected oncological diseases. It will be possible to use them in databases describing consumer habits.

The HEAP project also involves analysing data from wristbands worn by pregnant women. Sensors placed in wristbands cab measure environmental factors such as bacterial flora or pollen. Data from Sweden, Denmark and Finland will be analysed first.

Professor Piotr Bała from ICM said: “Currently, some of the bioinformatics software is not adapted to high-power computing systems, especially those available in supercomputing centres. ICM`s task is to develop or adapt existing software for the latest multiprocessor architectures to fully utilize available computing power, while significantly reducing the time needed to perform analyses.”

He added that in Poland work is already been carried out on a highly efficient version of the NCBI-BLAST software for DNA sequence comparison. More information is available here.

He continued: “The application lets us effectively use supercomputing resources and, compared to a typical workstation, shorten the time of genetic data analysis over 100 times, from weeks to hours. The software developed at ICM UW is faster and much more user friendly than competing solutions.”

ICM at the University of Warsaw is the only Polish member of the European Human Exposome Network.

The network will undertake large-scale research on the exposme, implementing nine projects.

The programme involves 126 institutions, which are mainly academic, from all over Europe.

PAP - Science in Poland, Karolina Duszczyk

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