Frequently Asked Questions

Questions:

1. What units are used in BioNetGen?
2. How do I create a Virtual cell BioModel from the BioNetGen model?
3. I exported an SBML model into Virtual Cell and results of simulations are different. What is wrong?
4. What rate laws are supported by BioNetGen?
5. Can I get the source code for BioNetGen?
6. After about 5-10 minutes of BioNetGen running I still have no messages. What should I do?
7. Why BioNetGen@VCell working from my home computer is so much slower than from my office?
8. What is BioNetGen@VCell and what is BioNetGen@LANL?

Answers:

1. Q: What units are used in BioNetGen? A: In BioNetGen units are not specified, but they are assumed to be consistent. BioNetGen does not check units for consistency. It's a responsibility of a modeler to make sure that all units are consistent. Say, for ODE simulations, if concentrations are in nM, then first order kinetic rate should be 1/s, and the second order is 1/(nM s). For stochastic simulations, concentrations can be in molecules and rate constants in 1/s and 1/(molecules s).
2. Q: How do I create a Virtual cell BioModel from the BioNetGen model? A: Include writeSBML() option into an input (bngl) file. In the output panel, select .xml file and click on "Create Biomodel". Virtual Cell will launch a new window with the model. It is not yet saved in VCell repository. You need to click on File -> Save as and select a new name for the model.
3. Q: I exported an SBML model into Virtual Cell and results of simulations are different. What is wrong? A: Default units in SBML are M (molars). Default units in the Virtual cell are mM (micromolars). As no units are specified in BioNetGen, the Virtual Cell assumes that units are in M, and multiplies them by 10e6 to convert them into mM. Respectively, rate constants (that are assumed to be 1/(M s)) are multiplied by 10e-6. Thus, the simulation results in the Virtual Cell are 10e6 times larger compared to the simulation results in BioNetGen. The issue of units will be resolved in the next release of BioNetGen@VCell.
4. Q: What rate laws are supported by BioNetGen? A: Currently, BioNetGen supports mass-action, Michaelis-Menton and saturation kinetics. More different laws are forthcoming.
5. Q: Can I get the source code for BioNetGen? A: Please contact Los Alamos BioNetGen site for such inquires.
6. Q: After about 5-10 minutes of BioNetGen running I still have no messages. What should I do? A: It makes sense to interrupt BioNetGen running and check messages. Thus you will identify what is the slowest step: it might be the network generation or simulation.
7. Q: Why BioNetGen@VCell working from my home computer is so much slower than from my office? A: Contrary to the Virtual Cell, which send all jobs to the server, BioNetGen@VCell runs on your computer. Thus, the speed of network generation and simulation depends on the computer you are using.
8. Q: What is BioNetGen@VCell and what is BioNetGen@LANL? A: BioNetGen software was developed at Los Alamos National Lab by M.L. Blinov, J.R. Faeder and W.S. Hlavacek as a downloadable and installable application. BioNetGen@VCell is a web version that is fully integrated with the Virtual Cell modeling and simulation framework. It is maintained by M.L.Blinov, who is now at the Center for Cell Analysis and Modeling of the University of Connecticut Health Center, home of the Virtual Cell software.