This book describes numerical methods for partial differential equations (PDEs) coupling advection, diffusion and reaction terms, encompassing methods for hyperbolic, parabolic and stiff and nonstiff ordinary differential equations (ODEs). The emphasis is on time-dependent transport-chemistry problems. Many of the theoretical aspects are illustrated by numerical experiments on models from biology, chemistry and physics. A unified approach is followed by emphasizing the method of lines or semi-discretization. This book treats integration methods suitable for both classes of problems and thus is of interest to PDE researchers unfamiliar with advanced numerical ODE methods, as well as to ODE researchers unaware of the vast amount of interesting results on numerical PDEs.