<s>
The	O
Nucleic	O
Acid	O
Package	O
(	O
NUPACK	B-Application
)	O
is	O
a	O
growing	O
software	O
suite	O
for	O
the	O
analysis	O
and	O
design	O
of	O
nucleic	O
acid	O
systems	O
.	O
</s>
<s>
Jobs	O
can	O
be	O
run	O
online	O
on	O
the	O
NUPACK	B-Application
webserver	B-Application
or	O
NUPACK	B-Application
source	O
code	O
can	O
be	O
downloaded	O
and	O
compiled	O
locally	O
for	O
non-commercial	O
academic	O
use	O
.	O
</s>
<s>
NUPACK	B-Application
algorithms	O
are	O
formulated	O
in	O
terms	O
of	O
nucleic	O
acid	O
secondary	O
structure	O
.	O
</s>
<s>
For	O
a	O
dilute	O
solution	O
containing	O
multiple	O
strand	O
species	O
interacting	O
to	O
form	O
multiple	O
species	O
of	O
ordered	O
complexes	O
,	O
NUPACK	B-Application
calculates	O
for	O
each	O
ordered	O
complex	O
:	O
</s>
<s>
The	O
page	O
accepts	O
as	O
input	O
either	O
sequence	O
information	O
,	O
structure	O
information	O
,	O
or	O
both	O
,	O
performing	O
diverse	O
functions	O
based	O
on	O
the	O
information	O
provided	O
,	O
including	O
automatic	B-General_Concept
layout	I-General_Concept
and	O
rendering	O
of	O
secondary	O
structures	O
with	O
or	O
without	O
ideal	O
helical	O
geometry	O
.	O
</s>
<s>
The	O
NUPACK	B-Application
web	O
application	O
is	O
programmed	O
within	O
the	O
Ruby	B-Application
on	I-Application
Rails	I-Application
framework	O
,	O
employing	O
Ajax	B-General_Concept
and	O
the	O
Dojo	B-General_Concept
Toolkit	I-General_Concept
to	O
implement	O
dynamic	O
features	O
and	O
interactive	O
graphics	O
.	O
</s>
<s>
Plots	O
and	O
graphics	O
are	O
generated	O
using	O
NumPy	B-Application
and	O
matplotlib	B-Language
.	O
</s>
<s>
The	O
site	O
is	O
supported	O
on	O
current	O
versions	O
of	O
the	O
web	B-Application
browsers	I-Application
Safari	B-Application
,	O
Chrome	B-Application
,	O
and	O
Firefox	B-Application
.	O
</s>
<s>
The	O
NUPACK	B-Application
library	O
of	O
analysis	O
and	O
design	O
algorithms	O
is	O
written	O
in	O
the	O
programming	B-Language
language	I-Language
C	I-Language
.	O
Dynamic	O
programs	O
are	O
parallelized	O
using	O
Message	B-Application
Passing	I-Application
Interface	I-Application
(	O
MPI	O
)	O
.	O
</s>
<s>
The	O
NUPACK	B-Application
web	B-Application
server	I-Application
and	O
NUPACK	B-Application
source	O
code	O
are	O
provided	O
for	O
non-commercial	O
research	O
purposes	O
and	O
is	O
with	O
this	O
restriction	O
not	O
Free	B-Application
and	I-Application
open	I-Application
source	I-Application
software	I-Application
.	O
</s>
<s>
NUPACK	B-Application
development	O
is	O
funded	O
by	O
the	O
National	O
Science	O
Foundation	O
via	O
the	O
Molecular	O
Programming	O
Project	O
and	O
by	O
the	O
Beckman	O
Institute	O
at	O
the	O
California	O
Institute	O
of	O
Technology	O
(	O
Caltech	O
)	O
.	O
</s>
