Software 
A
windows executable software can be downloaded here. This software can
perform
the stochastic
simulation algorithm (SSA), the binomial
t-leap and the Poisson t-leap simulations for a well-mixed
reacting system.
EGFR induced MAP kinase cascade input files can be downloaded here. A MATLAB file is
provided here that generates the
necessary
input files for use with the executable software. This makes the
reaction mechanism input relatively format free and automatic, i.e.,
one can bypass most of the SOFTWARE MANUAL explanations and
instructions given below. The reaction system
needs to be specified by the user in readable form. See sample for
reaction formulae to be entered here.
Help for the MATLAB file is provided within the file. Help for binomial t-leap is given below.
SOFTWARE
MANUAL
Input
files required
Main
input file: input.txt
Reaction dynamics:
input_dyna.txt
Reaction stoichiometry:
input_stoic.txt
Reaction connectivity matrix: input_connectiv.txt
Initial population size: input_population.txt
Species
for which probability
distribution function is to be generated: input_species.txt
Output
files generated
Single
trajectory: out_traj.txt
Probability
distribution function: out_pdf.txt
End
configuration of the phase space: out_population.txt
Description
of the input files
input.txt (sample): Information
regarding the type of calculation to be
performed is specified. Here is an example of the input
2 Total number of species in the reaction
network
2
Total number of reactions in
the reaction
network
1
Simulation algorithm : (1)
SSA (2) binomial t-leap
(3) Poisson t-leap
1
Simulation type : (1) single
trajectory (2) ensemble average
10000 Number of trajectories
for
generating the probability distribution function
10.5 Maximum real time to be
simulated (time units)
1000 Maximum
number of
100 Frequency of
output—10
snapshots will be generated (=1000/100)
0.2 Coarse-graining
factor, r
(note 0<r<1)
131 Random
number generator seed
(enter an non-zero integer)
2 Number
of species for
generating the probability distribution function
input_connectivity.txt (sample): The
participating species in reactions
are represented as a graph. The connectivity is specified in the
following
format:
Reaction_number Connectivity_1 Connectivity_2 Connectivity_3
Connectivity_4
Example:
If the thirty third reaction is S1+S2->2S4,
specify it as
33 1 2 4
0
A
maximum of four species is allowed in each reaction.
input_stoic.txt (sample): The
stoichiometry of participating
species in reactions are specified in the following format:
Reaction_number Stoich_1 Stoich_2
Stoich_3 Stoich_4
Example:
If the thirty third reaction is S1+S2->2S4
specify it as
33 -1 -1
2
0
Note
that only integer values are allowed for stoichiometric coefficients.
input_dyna.txt
(sample): The reaction
rate constants are specified in the
following format:
Reaction_number rate_constant
Example:
If the thirty third reaction is S1+S2->2S4,
its transition probability is k33X1X2
—
assuming k33=39.4, specify it as
33 39.4
Of
course k33 should be a non-negative number.
input_population.txt (sample): The initial
species populations of all
species Si, i=1,…,N are specified in the following format:
Species_number Population
If the
populations of S1, S2 S3 and S4
are
100, 10000, 0, 12 molecules, respectively, specify the input as
1 1000
2 10000
3 0
4 12
Note
that only integer values are allowed.
The
executable file itself has several checks to ensure correct input. The
input
files for the EGFR activated MAP kinase cascade can be downloaded here.
Species_number
Description
of the output files
out_traj.txt: Snapshots of
the species populations generated at
the frequency specified by the user in comma separated variable format;
first
column is time, following by columns of species populations ordered
indexwise.
out_population.txt: Final
population snapshot for the last
trajectory attempted.
out_pdf.txt: For the number
of trajectories specified by the
user in input.txt, the corresponding number of trajectories are
generated. Each
trajectory stops at the maximum real time specified by the user. When a
trajectory calculation stops, the population of the species specified
by the
user in input_species.txt is recorded. This way a probability
distribution for
species population at the user specified maximum time can be obtained.
The file
out_pdf.txt contains the number of hits for a specific population size.
For
example on the right 10000 trajectories were used. Note if the maximum
number
of
Prof. Dion
G. Vlachos
Department of Chemical Engineering
University of Delaware
Newark DE 19711 USA
Fax: 302-831-1048
Email: vlachos@che.udel.edu
Created and designed by Abhijit Chatterjee