Discover why and how FPGAs can improve protein identification within the serum proteomics field !

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