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Protein Identification through String Matching Algoritm
Gea Bianchi –Fabiola Casasopra
{gea.bianchi, fabiola.casasopra}@mail.polimi.it
NECSTLab,
March 2016
2
PrISMA has two main goals:
 Improving the efficiency of the
proteomic biomarkers recognition
 Mantain the versatility of the
application:
different databases and different
protein biomarkers
“A goal is a dream with a
deadline”
-N. Hill
3
ASIC
HW only implementation
FPGA
HW/SW co-design
GPP
SW only implementation
Max versatility Max energy efficiency
FPGAs are:
 They are between GPPs and ASICs in terms of versatility and energy
efficiency
 Reprogrammable and less time-demanding then ASICs
GPP = General Purpose Processor; FPGA = Field Programmable Gate Array;
ASIC = Application-specific Integrated Circuit.
MAX EASE OF PROGRAMMING
4
 Define the ideal number of HW cores
(in terms of parallelization and energy efficiency)
 Handle the complete human protein database
and share it among the devices
 Optimize the comunication
 Optimize the results collection
Implement the comunication between more AVNET ZedBoardsTM
Next steps to give life to PrISMA …
Protein Identification through String Matching Algoritm
Thanks for your
attention!
Gea Bianchi –Fabiola Casasopra
{gea.bianchi, fabiola.casasopra}@mail.polimi.it
facebook.com/PrISMA2016
twitter.com/PrISMA_NECSTLab
Channel: NECST@XOHW16

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2. PrISMA: FPGAs central role

  • 1. Protein Identification through String Matching Algoritm Gea Bianchi –Fabiola Casasopra {gea.bianchi, fabiola.casasopra}@mail.polimi.it NECSTLab, March 2016
  • 2. 2 PrISMA has two main goals:  Improving the efficiency of the proteomic biomarkers recognition  Mantain the versatility of the application: different databases and different protein biomarkers “A goal is a dream with a deadline” -N. Hill
  • 3. 3 ASIC HW only implementation FPGA HW/SW co-design GPP SW only implementation Max versatility Max energy efficiency FPGAs are:  They are between GPPs and ASICs in terms of versatility and energy efficiency  Reprogrammable and less time-demanding then ASICs GPP = General Purpose Processor; FPGA = Field Programmable Gate Array; ASIC = Application-specific Integrated Circuit. MAX EASE OF PROGRAMMING
  • 4. 4  Define the ideal number of HW cores (in terms of parallelization and energy efficiency)  Handle the complete human protein database and share it among the devices  Optimize the comunication  Optimize the results collection Implement the comunication between more AVNET ZedBoardsTM Next steps to give life to PrISMA …
  • 5. Protein Identification through String Matching Algoritm Thanks for your attention! Gea Bianchi –Fabiola Casasopra {gea.bianchi, fabiola.casasopra}@mail.polimi.it facebook.com/PrISMA2016 twitter.com/PrISMA_NECSTLab Channel: NECST@XOHW16