<s>
Some	O
tools	O
also	O
support	O
CellML	B-Language
,	O
a	O
standard	O
used	O
for	O
representing	O
physiological	O
processes	O
.	O
</s>
<s>
Name	O
Description/Notability	O
OSLicenseSiteSBML	O
Support	O
iBioSim	O
iBioSim	O
is	O
a	O
computer-aided	O
design	O
(	O
CAD	O
)	O
tool	O
for	O
the	O
modeling	O
,	O
analysis	O
,	O
and	O
design	O
of	O
genetic	O
circuits.multiplatform	O
(	O
Java/C	O
++	O
)	O
Apache	B-Application
Yes	O
CompuCell3D	O
GUI/Scripting	O
tool	O
for	O
building	O
and	O
simulating	O
multicellular	O
models.multiplatform	O
(	O
C++	O
/Python	O
)	O
MIT	O
Yes	O
,	O
but	O
only	O
for	O
reactions	O
.	O
</s>
<s>
COPASI	O
GUI	O
tool	O
for	O
analyzing	O
and	O
simulating	O
SBML	O
models.multiplatform	O
(	O
C++	O
)	O
Artistic	O
License	O
Yes	O
Cytosim	O
Spatial	O
simulator	O
for	O
flexible	O
cytoskeletal	O
filaments	O
and	O
motor	O
proteins	O
Mac	O
,	O
Linux	B-Application
,	O
Cygwin	O
(	O
C++	O
)	O
GPL3	O
Not	O
applicable	O
libroadrunner	O
High-performance	O
software	O
library	O
for	O
simulation	O
and	O
analysis	O
of	O
SBML	O
modelsmultiplatform	O
(	O
C/C	O
++	O
)	O
Apache	B-Application
License	O
Yes	O
massPy	O
Simulation	O
tool	O
that	O
can	O
work	O
with	O
COBRApymultiplatform	O
(	O
Python	O
)	O
MIT	O
Yes	O
MCell	O
GUI	O
tool	O
for	O
particle-based	O
spatial	O
stochastic	O
simulation	O
with	O
individual	O
molecules	O
multiplatform	O
MIT	O
and	O
GPLv2	O
Not	O
applicableOpenCORA	O
cross-platform	O
modelling	O
environment	O
,	O
which	O
is	O
aimed	O
at	O
organizing	O
,	O
editing	O
,	O
simulating	O
,	O
and	O
analysing	O
CellML	B-Language
files	O
on	O
Windows	B-Application
,	O
Linux	B-Application
and	O
macOS.multiplatform	O
(	O
C++	O
/Python	O
)	O
GPLv3Uses	O
CellML	B-Language
PhysiBoSS	O
A	O
specialized	O
form	O
of	O
the	O
PhysiCell	O
agent-based	O
modeling	O
platform	O
that	O
directly	O
integrates	O
Boolean	O
signaling	O
networks	O
into	O
cell	O
Agentsmultiplatform	O
(	O
C++	O
)	O
BSD-3	O
Yes	O
,	O
but	O
only	O
for	O
reactions	O
PhysiCell	O
A	O
agent-based	O
modeling	O
framework	O
for	O
multicellular	O
systems	O
biology.multiplatform	O
(	O
C++	O
)	O
BSD-3	O
Yes	O
,	O
but	O
only	O
for	O
reactions	O
PySCeS	O
Python	O
tool	O
for	O
modeling	O
and	O
analyzing	O
SBML	O
modelsmultiplatform	O
(	O
Python	O
)	O
BSD-3	O
Yes	O
pySB	O
Python-based	O
platform	O
with	O
specialization	O
in	O
rule-based	O
models.multiplatform	O
(	O
Python	O
)	O
BSD-3	O
Partial	O
ReaDDy	O
Particle-based	O
spatial	O
simulator	O
with	O
intermolecular	O
potentials	O
Linux	B-Application
and	O
Mac	O
Custom	O
Not	O
applicable	O
SBSCL	O
Java	O
library	O
with	O
efficient	O
and	O
exhaustive	O
support	O
for	O
SBMLmultiplatform	O
(	O
Java	O
)	O
LGPL	B-Application
Yes	O
SBW	O
(	O
software	O
)	O
A	O
distributed	O
workbench	O
that	O
includes	O
many	O
modeling	O
toolsmultiplatform	O
(	O
C/C	O
++	O
)	O
BSD-3	O
Yes	O
Smoldyn	O
Particle-based	O
simulator	O
for	O
spatial	O
stochastic	O
simulations	O
with	O
individual	O
molecules	O
multiplatform	O
(	O
C/C	O
++	O
/Python	O
)	O
LGPLNot	O
applicable	O
Spatiocyte	O
Spatial	O
modeling	O
software	O
that	O
uses	O
a	O
fine	O
lattice	O
with	O
up	O
to	O
one	O
molecule	O
per	O
site	O
multiplatform	O
Unknown	O
Not	O
applicable	O
SpringSaLaD	O
Particle-based	O
spatial	O
simulator	O
in	O
which	O
molecules	O
are	O
spheres	O
that	O
are	O
linked	O
by	O
springs	O
multiplatform	O
Unknown	O
Not	O
applicable	O
STEPSStochastic	O
reaction-diffusion	O
and	O
membrane	O
potential	O
solver	O
on	O
distributed	O
meshesmultiplatform	O
(	O
C++	O
/Python	O
)	O
GPLv2Partial	O
Tellurium	O
(	O
software	O
)	O
Simulation	O
environment	O
,	O
that	O
packages	O
multiple	O
libraries	O
into	O
one	O
platform.multiplatform	O
(	O
Python	O
)	O
Apache	B-Application
License	O
Yes	O
URDME	O
Stochastic	O
reaction-diffusion	O
simulation	O
on	O
unstructured	O
meshes	O
MatLab	O
on	O
Mac	O
,	O
Linux	B-Application
GPL3	O
Not	O
applicable	O
VCell	B-Application
Comprehensive	O
modeling	O
platform	O
for	O
non-spatial	O
,	O
spatial	O
,	O
deterministic	O
and	O
stochastic	O
simulations	O
,	O
including	O
both	O
reaction	O
networks	O
and	O
reaction	O
rules	O
.	O
</s>
<s>
No	O
No	O
No	O
No	O
SBW	O
Yes	O
No	O
Yes	O
No	O
No	O
No	O
No	O
Smoldyn	O
No	O
No	O
No	O
No	O
No	O
No	O
Yes	O
Spatiocyte	O
SpringSaLaD	O
STEPS	O
Tellurium	O
(	O
software	O
)	O
Uses	O
libroadrunner	O
URDME	O
VCell	B-Application
Yes	O
No	O
?	O
</s>
<s>
Name	O
Stoichiometry	O
matrix	O
Reduced	O
stoich	O
matrix	O
Conserved	O
moiety	O
analysis	O
Jacobian	O
MCA	O
COPASI	O
Yes	O
Yes	O
Yes	O
Yes	O
Yes	O
libroadrunner	O
Yes	O
Yes	O
Yes	O
Yes	O
Yes	O
masspy	O
via	O
libroadrunner	O
PySCeS	O
Yes	O
Yes	O
Yes	O
Yes	O
Yes	O
VCell	B-Application
?	O
</s>
<s>
Name	O
Description/Notability	O
Language	O
Terminus	O
ante	O
quemBased	O
on	O
earliest	O
publication	O
date	O
BIOSIM	O
The	O
first	O
ever	O
recorded	O
digital	O
simulator	O
of	O
biochemical	O
networks	O
(	O
by	O
David	O
Garfinkel	O
)	O
FORTRAN	O
IV	O
1968	O
KDF	B-Device
9	I-Device
First	O
simulator	O
to	O
support	O
MCA	O
.	O
</s>
<s>
Name	O
Description/Notability	O
Language	O
SBML	O
Support	O
Terminus	O
ante	O
quemBased	O
on	O
earliest	O
publication	O
dateCORFirst	O
public	O
CellML-based	O
environment.Object	O
PascalUses	O
CellML2010	O
DBsolve	O
Early	O
GUI	O
based	O
simulation	O
platform	O
.	O
</s>
