In the coming years, genome research will likely transform medical and agricultural practices. The unique genetic profile of a species is leading to the development of customized treatments, from personalized medicine to agrigenomics, but the exponential growth of available genomic data requires a computational effort that may limit the progress of these fields. Within this context, we propose the development of a novel hardware and software advanced support for genomics research, named HUGenomics. The framework aims at facilitating genome assembly process by means of both hardware accelerated algorithms and scientific data visualization tools. Indeed, the system raises the level of abstraction allowing users to easily integrate custom algorithms into the hardware pipeline without any knowledge of the underneath architecture.

1. 05/29/2018
Stanford OTL, Da Vinci Conference Room
Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano
giulia.guidi@mail.polimi.it
An integrated system
to save the world population by 2050
Lorenzo Di Tucci, Giulia Guidi, Sara Notargiacomo, Marco D. Santambrogio

2. An overcrowded future
By 2050 the world population will likely increase by more than 35 percent
1 billion people
35%
https://www.nationalgeographic.com/foodfeatures/feeding-9-billion/
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3. A hungry future
To feed such a population, crop production will need to double
1 billion tons
100%
https://www.nationalgeographic.com/foodfeatures/feeding-9-billion/
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4. The green revolution
Fertilizers and chemicals rely on finite resources and are often unsustainable
Recent advances in genomics promise sustainable intensification of agriculture and
heightened resilience of crops to climate change
Scheben, Armin, Yuxuan Yuan, and David Edwards. "Advances in genomics for
adapting crops to climate change." Current Plant Biology 6 (2016): 2-10.
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5. The challenge
It is fundamental to keep-up with development of biological research
Each DNA provides huge amount of data
to be processed with compute-intensive and fast-changing algorithms
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6. Our solution
HUG is an integrated hardware and software system performing genome assembly
that aims at enhancing the genomic research
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7. !7A view on HUG
FAST
PROTOTYPING
CUSTOM HARDWARE
ALGORITHM
PIPELINE CREATION
OR INTEGRATION DATA
UPLOAD
PROCESSING DATA
VISUALIZATION
YESLINE
NOLINE
Is the algorithm
available on HUG?

8. Performance !8
The algorithms in HUG are the current state-of-the-art:
speedup ranges from 78x to over 2000x with highest available power efficiency

9. Thanks for your attention
Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano
05/29/2018
giulia.guidi@mail.polimi.it
Stanford OTL, Da Vinci Conference Room
Lorenzo Di Tucci, Giulia Guidi, Sara Notargiacomo, Marco D. Santambrogio
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