  Biological cells rely on precise spatiotemporal coordination of biochemical
reactions to control their many functions. Such cell signaling networks have
been a common focus for mathematical models, but they remain challenging to
simulate, particularly in realistic cell geometries. Herein, we present our
software, Spatial Modeling Algorithms for Reactions and Transport (SMART), a
package that takes in high-level user specifications about cell signaling
networks and molecular transport, and then assembles and solves the associated
mathematical and computational systems. SMART uses state-of-the-art finite
element analysis, via the FEniCS Project software, to efficiently and
accurately resolve cell signaling events over discretized cellular and
subcellular geometries. We demonstrate its application to several different
biological systems, including YAP/TAZ mechanotransduction, calcium signaling in
neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we
utilize experimentally-derived realistic cellular geometries represented by
well-conditioned tetrahedral meshes. These scenarios demonstrate the
applicability, flexibility, accuracy and efficiency of SMART across a range of
temporal and spatial scales.
