8. Appendix: Acronyms

CI
continuous integration
CPU
central processing unit
DES
discrete event simulation
FBA
flux balance analysis
GPU
graphical processing unit
hESC
human embryonic stem cell
InChI
IUPAC International Chemical Identifier
MIASE
Minimum Information About a Simulation Experiment
ODE
ordinary differential equations
PDE
partial differential equations
PDES
parallel discrete event simulation
PGDB
pathway genome database
ROSS
Rensselaer’s Optimistic Simulation System
SBML
Systems Biology Markup Language
SED-ML
Simulation Experiment Description Markup Language
SESSL
Simulation Experiment Specification via a Scala Layer
SI
International System of Units
SMILES
simplified molecular-input line-entry system
SSA
Stochastic Simulation Algorithm
SVG
Scalable Vector Graphics
VCS
version control system
WC
whole-cell