Getting Started
What You Need to Run MCell
To start using MCell, two things are required:
- First you should have the MCell simulator installed on your computer. You
could download the MCell binary file from the
MCell homepage;
The MCell simulator is available for a variety of platforms. The user can
run it on a single processor machine, a cluster, or a parallel computer. The
MCell team supports the following platforms:
- AIX IBM Power
- ALPHA
- FREEBSD i686
- LINUX i686
- Mac OSX G4/5
- SGI
- SPARC
- WIN32
- Second, you should create a simulation input file. The input file
is written in the MCell Model Description Language. It should include all the information
for the simulator to complete a given simulation, such as the description of the
simulation object, the distribution of the molecules, the chemical reaction
mechanisms, as well as the output specifications.
How to Run MCell
After installing the correct MCell binary file for your machine,
and creating a simulation input file, file.mdl, using the MCell Model Description Language, the user can initiate
a MCell simulation by simply typing:
mcell [options] file.mdl
in the command line.
A list of the available [options] and their functions are given in the table below:
Options
[-help] |
print help message
|
[-info] |
print MCell info message
|
[-seed n] |
choose random sequence number (default:
1), n is an integer between 1 and 3000 |
[-iteration n] |
override iterations in the MDL
file (file.mdl) |
[-logfile log_file_name] |
send the output log to file (default:stderr)
|
[-logfreq n] |
output log frequency (default:100)
|
By default, the output of the simulation will go to your screen
directly. Alternatively, you can redirect the output of the simulation by running the simulation
in the background and defining the output log file. If you have a long simulation
or large number of simulations, the best approach is to create a script file to
manage the simulation(s) and the output.
The simulator will parse the simulation input file in a top-down order. It
will need to initialize the simulation before the actual start of the simulation iteration.
Therefore, the content of the input MDL file for a simulation should follow a specific order,
the annatomy of the MDL
file will be given in the next section.
The basic steps for creating a MCell simulation is given in the following flow chart.
What is the MCell Model Description Language (MDL)
A MDL file is a MCell Model Description Language(MDL) format file. The MCell
Model Description Language is a high level, biology-oriented computer language
designed particularly for the MCell simulator. It is easy for biological researchers and scientists
to understand and grasp. All MDL commands, keywords
and functions are written in upper case, so it is easy to distinguish them from the user-defined
variables.
Since the MDL file is order-dependent, it is important to keep your MDL file in the
right order. Most of the MDL keywords and functions are optional, defined
only as needed to complete a particular simulation; However, two MDL
commands are required by the simulator: the temporal length of each simulation iteration (TIME_STEP)
and the total number of iterations (ITERATION_NUMBER)of the simulation. The general anatomy of a MDL
file is given in the following list. For detailed instructions on creating MDL files, please refer to the User Manual.
Anatomy of the MCell Model Description Language
Include other MDL files into the current MDL file. |
INCLUDE_FILE = "file.name"
|
| Necessary parameters
for the MCell simulation |
Simulation
time step |
TIME_STEP = c
|
Total number of iterations
of the simulation |
ITERATION_NUMBER
= n |
|
| Parameters needed for initializing a
MCell simulation |
Number of divisions
along the radial directions in the unit length |
RADIAL_SUBDIVISIONS
= n |
Number of radial
directions in a single octant of an unit sphere |
RADIAL_DIRECTIONS
= n |
Number of effector
grids over an unit surface area |
EFFECTOR_GRID_DENSITY
= n |
|
| Spatial partitioning
of the simulation object |
- PARTITION_X = [ coordinates of the partitioning points along
the x direction]
- PARTITION_Y = [ coordinates of the partitioning points along
the y direction]
- PARTITION_Z = [ coordinates of the partitioning points along
the z direction]
|
| Specification of the
checkpointing method |
Definition
of the checkpoint |
CHECKPOINT_ITERATIONS
= n |
Output simulation
results after checkpoint |
CHECKPOINT_OUTFILE
= "outfile.name" |
Input file
to continue the simulation after the break of the checkpoint |
CHECKPOINT_INFILE
= "input.name" |
|
| Definition of the logical
objects |
- Ligand
- The ligand release pattern
- Chemical reaction
|
| Definition of the physical
objects and object modifier |
|
| Specification of the
simulation output |
- Visaulization output of the simulation
- Chemical reaction data of the simulation
- General "C" language output
|
How to Visualize the MCell
Simulation Results
To visualize your simulation results, you should define the format
of the visualization output as the format of the visualization tool which
will be used. The MCell simulator supports the following data formats for 3D rendering:
If you choose the visualization output format as the IBM's DataExplore,
you can also visualize the simulation results with the MCell rendering tool DReAMM(
Design, Render, Animate the MCell Model). DReAMM is designed as a module
of the IBM's DataExplore, it can be used to handle both 3D visualizations and
2D plots. It is very easy to use DReAmm to animate MCell simulation results, detailed instructions can be found in the DReAMM website.
DReAMM is available for download at the MCell home page.
|
