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Processing-in-memory architectures and programming libraries for bioinformatics algorithms

Objective

Low cost, high throughput DNA and RNA sequencing (HTS) data is now the main workforce for various genomics and transcriptomics applications. HTS technologies have already started to impact a broad range of research and clinical use for the life sciences. These include, but are not limited to 1) large-scale sequencing studies for population genomics and disease-causing mutation discovery including cancer, 2) metagenomics, 3) comparative genomics, 5) transcriptome profiling, and 6) outbreak detection and tracking including COVID-19, Ebola, and Zika. HTS also impacts the whole health care system in several directions. Although there is still much room for improvement, sequencing of personal genomes is now becoming a part of preventive and personalized medicine as HTS technologies make it possible to 1) identify genetic mutations that enable rare disease diagnosis, 2) determine cancer subtypes therefore guiding treatment options, and 3) characterize infections and antibiotic resistance. Currently all genomics data are processed in energy-hungry computer clusters and data centers, which also necessitate the transfer of data via the internet, which also consumes substantial amounts of energy and wastes valuable time. Therefore there is a need for fast, energy-efficient, and cost-efficient technologies that enable all forms of genomics research without requiring data centers and cloud platforms. In this project we aim to leverage the emerging processing-in-memory (PIM) technologies to enable such powerful edge computing. We will focus on co-designing algorithms and data structures commonly used in bioinformatics together with several types of PIM architectures to obtain the highest benefit in cost, energy, and time savings. BioPIM will also impact other fields that employ similar algorithms. Our designs and algorithms will not be limited to cheap hardware, and they will impact computation efficiency on all forms of computing environments including cloud platforms.

Coordinator

BILKENT UNIVERSITESI VAKIF
Net EU contribution
€ 380 000,00
Address
Eskisehir Yolu 8 Km
06800 Bilkent Ankara
Turkey

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Region
Batı Anadolu Ankara Ankara
Activity type
Higher or Secondary Education Establishments
Non-EU contribution
€ 0,00

Participants (4)

INSTITUT PASTEUR
France
Net EU contribution
€ 390 375,00
Address
Rue Du Docteur Roux 25-28
75724 Paris Cedex 15

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Region
Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Non-EU contribution
€ 0,00
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France
Net EU contribution
€ 338 000,00
Address
Rue Michel Ange 3
75794 Paris

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Region
Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Non-EU contribution
€ 0,00
TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Israel
Net EU contribution
€ 375 915,00
Address
Senate Building Technion City
32000 Haifa

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Activity type
Higher or Secondary Education Establishments
Non-EU contribution
€ 0,00
SAS UPMEM
France
Net EU contribution
€ 482 375,00
Address
6 Place Robert Schuman
38000 Grenoble

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SME

The organization defined itself as SME (small and medium-sized enterprise) at the time the Grant Agreement was signed.

Yes
Region
Auvergne-Rhône-Alpes Rhône-Alpes Isère
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Non-EU contribution
€ 0,00