[Bioclusters] FPGA in bioinformatics clusters (again?)

Joe Landman landman at scalableinformatics.com
Mon Jan 16 08:59:33 EST 2006

Hi Farul:

Farul Mohd. Ghazali wrote:

> advantage of the FPGA accelerator. I've been asked to see if the
> accelerators can be used with general purpose apps first and for
> custom algorithms when the group needs it.

If by general purpose apps you mean Smith Waterman or pairwise sequence 
alignment, multiple sequence alignment, HMM, SVM, etc, then yes, you can 
use such units out of the box with such "software", though you would 
need to chose the accelerator carefully, as bitfiles (the "software") 
are not generally compatible between various accelerators.

If you want to know whether or not you can program them, I would refer 
you to http://www.openfpga.org .  You can see a discussion of all the 
aspects (positive and negative).  If you want to program them in C, then 
look at vendors like Celoxica, Impulse (http://www.impulsec.com/), 
Mentor Graphics 
(http://www.mentor.com/products/c-based_design/index.cfm), and others.

C-based design seems to be the rage these days.  Take your C program and 
turn it (the expensive portions) into logic gates.


> TIA again
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Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615

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