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