<s>
CellML	B-Language
is	O
an	O
XML	B-Protocol
based	O
markup	O
language	O
for	O
describing	O
mathematical	O
models	O
.	O
</s>
<s>
This	O
is	O
reflected	O
in	O
its	O
name	O
CellML	B-Language
,	O
although	O
this	O
is	O
simply	O
a	O
name	O
,	O
not	O
an	O
abbreviation	O
.	O
</s>
<s>
CellML	B-Language
is	O
growing	O
in	O
popularity	O
as	O
a	O
portable	O
description	O
format	O
for	O
computational	O
models	O
,	O
and	O
groups	O
throughout	O
the	O
world	O
are	O
using	O
CellML	B-Language
for	O
modelling	O
or	O
developing	O
software	O
tools	O
based	O
on	O
CellML	B-Language
.	O
</s>
<s>
CellML	B-Language
is	O
similar	O
to	O
Systems	O
Biology	O
Markup	O
Language	O
SBML	O
but	O
provides	O
greater	O
scope	O
for	O
model	O
modularity	O
and	O
reuse	O
,	O
and	O
is	O
not	O
specific	O
to	O
descriptions	O
of	O
biochemistry	O
.	O
</s>
<s>
The	O
CellML	B-Language
language	O
grew	O
from	O
a	O
need	O
to	O
share	O
models	O
of	O
cardiac	O
cell	O
dynamics	O
among	O
researchers	O
at	O
a	O
number	O
of	O
sites	O
across	O
the	O
world	O
.	O
</s>
<s>
The	O
language	O
was	O
an	O
application	O
of	O
the	O
XML	B-Protocol
specification	I-Protocol
developed	O
by	O
the	O
World	O
Wide	O
Web	O
Consortium	O
–	O
the	O
decision	O
to	O
use	O
XML	B-Protocol
was	O
based	O
on	O
late	O
1998	O
recommendations	O
from	O
Warren	O
Hedley	O
and	O
André	O
(	O
David	O
)	O
Nickerson	O
.	O
</s>
<s>
Existing	O
XML-based	O
languages	O
were	O
leveraged	O
to	O
describe	O
the	O
mathematics	O
(	O
content	O
MathML	B-Language
)	O
,	O
metadata	O
(	O
RDF	O
)	O
,	O
and	O
links	O
between	O
resources	O
(	O
XLink	O
)	O
.	O
</s>
<s>
The	O
CellML	B-Language
working	O
group	O
first	O
became	O
aware	O
of	O
the	O
SBML	O
effort	O
in	O
late	O
2000	O
,	O
when	O
Warren	O
Hedley	O
attended	O
the	O
2nd	O
workshop	O
on	O
Software	O
Platforms	O
for	O
Systems	O
Biology	O
in	O
Tokyo	O
.	O
</s>
<s>
The	O
working	O
group	O
collaborated	O
with	O
a	O
number	O
of	O
researchers	O
at	O
Physiome	O
Sciences	O
Inc	O
.	O
(	O
particularly	O
Melanie	O
Nelson	O
,	O
Scott	O
Lett	O
,	O
Mark	O
Grehlinger	O
,	O
Prasad	O
Ramakrishna	O
,	O
Jeremy	O
Rice	O
,	O
Adam	O
Muzikant	O
,	O
and	O
Kam-Chuen	O
Jim	O
)	O
to	O
draft	O
the	O
initial	O
CellML	B-Language
1.0	O
specification	O
,	O
which	O
was	O
published	O
on	O
the	O
11th	O
of	O
August	O
2001	O
.	O
</s>
<s>
This	O
first	O
draft	O
was	O
followed	O
by	O
specifications	O
for	O
CellML	B-Language
Metadata	O
and	O
an	O
update	O
to	O
CellML	B-Language
to	O
accommodate	O
structured	O
nesting	O
of	O
models	O
with	O
the	O
addition	O
of	O
the	O
<import>	O
element	O
.	O
</s>
<s>
Physiome	O
Sciences	O
Inc	O
.	O
also	O
produced	O
the	O
first	O
CellML	B-Language
capable	O
software	O
.	O
</s>
<s>
The	O
at	O
the	O
University	O
of	O
Connecticut	O
Health	O
Center	O
also	O
produced	O
early	O
CellML	B-Language
capable	O
software	O
called	O
Virtual	B-Application
Cell	I-Application
.	O
</s>
<s>
In	O
2002	O
the	O
CellML	B-Language
1.1	O
specification	O
was	O
written	O
,	O
in	O
which	O
imports	O
were	O
added	O
.	O
</s>
<s>
In	O
July	O
2009	O
the	O
CellML	B-Language
website	O
was	O
completely	O
revamped	O
,	O
and	O
an	O
initial	O
version	O
of	O
the	O
new	O
CellML	B-Language
repository	O
software	O
(	O
PMR2	O
)	O
was	O
released	O
.	O
</s>
<s>
A	O
CellML	B-Language
model	O
consists	O
of	O
a	O
number	O
of	O
components	O
,	O
each	O
described	O
in	O
their	O
own	O
component	O
element	O
.	O
</s>
<s>
Mathematical	O
relationships	O
between	O
variables	O
are	O
expressed	O
within	O
components	O
,	O
using	O
MathML	B-Language
.	O
</s>
<s>
MathML	B-Language
is	O
used	O
to	O
make	O
declarative	O
expressions	O
(	O
as	O
opposed	O
to	O
procedural	B-Application
statements	I-Application
as	O
in	O
a	O
computer	O
programming	O
language	O
)	O
.	O
</s>
<s>
However	O
,	O
most	O
CellML	B-Language
processing	O
software	O
will	O
only	O
accept	O
a	O
limited	O
of	O
range	O
of	O
mathematics	O
(	O
for	O
example	O
,	O
some	O
processing	O
software	O
requires	O
equations	O
with	O
a	O
single	O
variable	O
on	O
one	O
side	O
of	O
an	O
equality	O
)	O
.	O
</s>
<s>
The	O
choice	O
of	O
MathML	B-Language
makes	O
CellML	B-Language
particularly	O
suited	O
for	O
describing	O
models	O
containing	O
differential	O
equations	O
.	O
</s>
<s>
CellML	B-Language
models	O
also	O
allow	O
relationships	O
between	O
components	O
to	O
be	O
expressed	O
.	O
</s>
<s>
The	O
CellML	B-Language
specification	O
defines	O
two	O
types	O
of	O
relationship	O
,	O
encapsulation	O
and	O
containment	O
,	O
however	O
more	O
can	O
be	O
defined	O
by	O
the	O
user	O
.	O
</s>
<s>
CellML	B-Language
is	O
defined	O
by	O
core	O
specifications	O
as	O
well	O
as	O
additional	O
specifications	O
for	O
metadata	O
,	O
used	O
to	O
annotate	O
models	O
and	O
specify	O
simulations	O
.	O
</s>
<s>
CellML	B-Language
1.0	O
has	O
some	O
biochemistry	O
specific	O
elements	O
for	O
describing	O
the	O
role	O
of	O
variables	O
in	O
a	O
reaction	O
model	O
.	O
</s>
<s>
In	O
order	O
to	O
fully	O
support	O
this	O
feature	O
,	O
variables	O
in	O
CellML	B-Language
1.1	O
accept	O
variable	O
names	O
as	O
initial	O
values	O
.	O
</s>
<s>
CellML	B-Language
has	O
several	O
metadata	O
specifications	O
,	O
used	O
to	O
annotate	O
models	O
or	O
provide	O
information	O
for	O
running	O
and/or	O
visualizing	O
simulations	O
of	O
models	O
.	O
</s>
<s>
provides	O
the	O
information	O
required	O
to	O
reproduce	O
specific	O
simulations	O
using	O
a	O
CellML	B-Language
model	O
.	O
</s>
<s>
aims	O
to	O
provide	O
a	O
focal	O
point	O
for	O
the	O
CellML	B-Language
community	O
.	O
</s>
<s>
A	O
CellML	B-Language
discussion	O
mailing	O
list	O
can	O
be	O
found	O
at	O
.	O
</s>
<s>
The	O
scope	O
of	O
this	O
mailing	O
list	O
includes	O
everything	O
related	O
to	O
the	O
development	O
and	O
use	O
of	O
CellML	B-Language
.	O
</s>
<s>
A	O
repository	O
of	O
several	O
hundred	O
biological	O
models	O
encoded	O
into	O
CellML	B-Language
can	O
be	O
found	O
on	O
the	O
CellML	B-Language
community	O
website	O
at	O
.	O
</s>
