COMSOL is a multi-physics package which is primarily designed for problems requiring solution of PDEs using finite element methods. While Magnolia can be applied to simple PDE problems using finite-difference approaches, it’s not designed to be a full-features PDE solver.
MATLAB and R are general-purpose technical computing environments. ODE problems can be solved in these tools with a little effort, but the language are not specifically designed for modeling systems of ODEs.
Simulink is specifically designed for modeling systems based on ODE in a mostly graphical approach. For some kinds of problems, this is appropriate. For others, and equation-based approach is much easier.
Maple and Mathematica are predominately designed for symbolic solution of mathematical problems. Both contain additional capabilities for numerical solution of certain kinds of problems, but neither is designed from the ground up for modeling ODE-based problems.
ACSL/acslX and Berkeley Madonna are, in a sense, the closest analogs to Magnolia. The primary difference between Magnolia and these tools involve the specifics of the supported modeling and scripting languages, and the overall modeling workflow user interface design.