Hardware Reference
In-Depth Information
Tabl e 6. 8
Execution time of bioassays mapped to an 8
8 (10
10) electrode
array
Bioassay
Multiplexed
PCR
Protein
Biochip
Direct-addressing biochip
72 s (72 s)
20 s (20 s)
160 s (142 s)
Cross-referencing biochip [ 6 ]
72 s (72 s)
20 s (20 s)
215 s (142 s)
Proposed general-purpose biochip
72 s (72 s)
24 s (20 s)
179 s (157 s)
Tabl e 6. 9
Comparison between lower bound, ILP model, and heuristic
solution
Array
No. pins
No. pins
No. pins
size
(lower bound)
(ILP model)
(heuristic method)
3
3
9
9
9
5
7
18
21
23
7
8
24
29
30
8
8
26
32
32
9
9
30
Computationally impractical
40
However, cross-referencing biochips require special electrode structures (two
electrodes per unit cell), which introduce fabrication challenges and additional
processing steps [ 4 ]. As a result, the fabrication cost for cross-referencing biochip is
likely to be higher than biochips without two electrodes per unit cell. For low-cost
disposable chips, it is arguable whether cross-referencing design is always the right
solution due to higher fabrication cost.
Finally, we present a comparison between the lower bound on the number of pins
predicted by Theorem 6.1 , the exact optimization results obtained using ILP model,
and the results obtained using the heuristic procedure. Note that the lower bound
on the number of pins may not always be achievable in practice and correspond to
an actual pin-assignment configuration. On the other hand, the ILP model and the
heuristic procedure can produce the configurations of the layouts. Hence the actual
minimum number of required pins that we obtain by the ILP model is either equal
to or larger than the theoretical lower bound.
Without loss of generality, we use various rectangular layouts as test cases. The
results are shown in Table 6.9 . The ILP model is solved using Xpress-MP [ 24 ],
which is a widely used commercial ILP solver. The tool runs on a server with 64/,GB
of memory and two quad-core 2.53/,GHz Intel Xeon processors. The computing
time for the 8 8 array is about 5 h while for a 9 9 array, and the solver runs out
of memory. The heuristic method is run on a 2.27 GHz Intel i3 Dual core processor
with 2 GB of memory. The CPU times are less than 5 min. for all cases.
 
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