<s>
Virtual	B-Application
Cell	I-Application
(	O
VCell	B-Application
)	O
is	O
an	O
open-source	B-Application
software	I-Application
platform	O
for	O
modeling	O
and	O
simulation	O
of	O
living	O
organisms	O
,	O
primarily	O
cells	O
.	O
</s>
<s>
Virtual	B-Application
Cell	I-Application
is	O
an	O
advanced	O
software	O
platform	O
for	O
modeling	O
and	O
simulating	O
reaction	O
kinetics	O
,	O
membrane	O
transport	O
and	O
diffusion	O
in	O
the	O
complex	O
geometries	O
of	O
cells	O
and	O
multicellular	O
tissues	O
.	O
</s>
<s>
VCell	B-Application
models	O
have	O
a	O
hierarchical	O
tree	O
structure	O
.	O
</s>
<s>
Given	O
initial	O
concentrations	O
of	O
species	O
,	O
VCell	B-Application
can	O
calculate	O
how	O
these	O
concentrations	O
change	O
over	O
time	O
.	O
</s>
<s>
Each	O
"	O
Application	O
"	O
corresponds	O
to	O
a	O
mathematical	O
description	O
,	O
which	O
is	O
automatically	O
translated	O
into	O
the	O
VCell	B-Application
Math	O
Description	O
Language	O
.	O
</s>
<s>
The	B-Application
Virtual	I-Application
Cell	I-Application
can	O
be	O
used	O
as	O
a	O
distributed	B-Architecture
application	I-Architecture
over	O
the	O
Internet	O
or	O
as	O
a	O
standalone	O
application	O
.	O
</s>
<s>
VCell	B-Application
converts	O
the	O
biological	O
description	O
into	O
an	O
equivalent	O
mathematical	O
system	O
of	O
differential	O
equations	O
.	O
</s>
<s>
VCell	B-Application
allows	O
users	O
a	O
choice	O
of	O
numerical	O
solvers	O
to	O
translate	O
the	O
mathematical	O
description	O
into	O
software	O
code	O
which	O
is	O
executed	O
to	O
perform	O
the	O
simulations	O
.	O
</s>
<s>
The	B-Application
Virtual	I-Application
Cell	I-Application
license	O
allows	O
free	O
access	O
to	O
all	O
members	O
of	O
the	O
scientific	O
community	O
.	O
</s>
<s>
Users	O
may	O
save	O
their	O
models	O
in	O
the	O
VCell	B-Application
DataBase	O
,	O
which	O
is	O
maintained	O
on	O
servers	O
at	O
U	O
.	O
Connecticut	O
.	O
</s>
<s>
The	O
VCell	B-Application
Database	O
uses	O
an	O
access	O
control	O
system	O
with	O
permissions	O
to	O
allow	O
users	O
to	O
maintain	O
their	O
models	O
private	O
,	O
share	O
them	O
with	O
select	O
collaborators	O
or	O
make	O
them	O
public	O
.	O
</s>
<s>
The	O
VCell	B-Application
website	O
maintains	O
a	O
that	O
are	O
public	O
and	O
associated	O
with	O
research	O
publications	O
.	O
</s>
<s>
VCell	B-Application
supports	O
the	O
following	O
features	O
:	O
</s>
<s>
VCell	B-Application
also	O
offers	O
a	O
hybrid	O
deterministic/stochastic	O
spatial	O
solver	O
for	O
situations	O
where	O
some	O
species	O
are	O
present	O
in	O
low	O
copy	O
number	O
and	O
others	O
are	O
present	O
in	O
high	O
copy	O
number	O
.	O
</s>
<s>
Most	O
solvers	O
can	O
be	O
run	O
locally	O
,	O
all	O
solvers	O
can	O
be	O
run	O
remotely	O
on	O
VCell	B-Application
servers	O
.	O
</s>
<s>
These	O
tools	O
are	O
available	O
in	O
VCell	B-Application
.	O
</s>
<s>
Models	O
and	O
simulation	O
setups	O
(	O
so-called	O
Applications	O
)	O
can	O
be	O
stored	O
in	O
local	O
files	O
as	O
Virtual	B-Application
Cell	I-Application
Markup	O
Language	O
(	O
VCML	O
)	O
or	O
stored	O
remotely	O
in	O
the	O
VCell	B-Application
database	O
.	O
</s>
<s>
VCell	B-Application
allows	O
users	O
integrated	O
access	O
to	O
a	O
variety	O
of	O
sources	O
to	O
help	O
build	O
and	O
annotate	O
models	O
:	O
</s>
<s>
Models	O
stored	O
in	O
the	O
VCell	B-Application
database	O
can	O
be	O
made	O
accessible	O
by	O
their	O
authors	O
to	O
some	O
users	O
(	O
shared	O
)	O
or	O
all	O
users	O
(	O
public	O
)	O
.	O
</s>
<s>
VCell	B-Application
can	O
import	O
models	O
from	O
the	O
BioModels	O
Database	O
.	O
</s>
<s>
The	B-Application
Virtual	I-Application
Cell	I-Application
is	O
being	O
developed	O
at	O
the	O
at	O
the	O
University	O
of	O
Connecticut	O
Health	O
Center	O
.	O
</s>
