Entering reactions
Enter the reactions using a standard spreadsheet interface. As you add reations and rate constants, the "Species" and "Constants" lists are updated.
Settings
BioNetS is a hybrid solver, but you might want to use it only for the Gillespie solver. To do that, all species have to be marked as "Discrete". For species that are not marked as discrete the solver will allow reactions that do not produce or degrade discrete species to be handled using chemical Langevin equations. The fifth column in the reaction table gives and indication if a reaction will be handled discretely or not.
Running
The next step is to run the simulation. Open the "Run View"
This is connected to the main window, and allows you to enter in the initial conditions, and settings such as how long to run the simulation and how many time values should be saved for the purposes of plotting.
Note that for each species, the "Hist." button has been checked. This means that the solver will include a histogram collector for each species that is marked.
When you hit the "Run" button, BioNetS will go through the following steps:
- Create source code for the solver, tailored to the particular system, specified in the main window.
- Call on a C++ compiler (you need to install the developer tools, which are free from Apple). If the model hasn't changed, the source hasn't changed so no compilation is necessary.
- Saves the input arguments into a data file
- Launces the executable created in step 2
- Once finished, opens the output file and displays the results.
The program will only rerun when you hit the "Run" button, so selecting different species just involves reading different portion of the output file.
Multiple runs
Once you have run things using all discrete, try switching species that have "large" values over to continuous. Species that stay in the range [0,5] should definitely stay discrete, but species that hover around hundreds might be better represented with a continuous variable + noise. BioNetS allows you to go through those scenarios, and look at the effect this has. Since Langevin is an approximation, the solution might not be accurate enough, but try toggling things on and off and rerunning.
Post Processing
BioNetS is good for initial tests and exploration. For further analysis, it is recommended that you use the output from BioNetS in another tool such as Matlab, or your own numerical harness. To support that, BioNetS can output it's solver as an executable as well as a source code tree (complete with a makefile).
To see the input files needed, read the help document, or see what BioNetS saves by opening the folder /var/tmp/BioNetS-username/Script-**/ where "username" is your login name and "**" is a running counter. This is because BioNetS creates a temporary folder for each script, where it saves the source code, compiles the code and later runs the program. Look at Input.mat to see the input arguments, and Output.mat to see what comes out. The executable is called "runme". Note that the file format that is used is -v4 in matlab, so you need to add that flag to the save statement.
You can also run the executable using ascii input and output. See the built in help for more information.
For further information send mail to David.