SimThyr is a free continuous dynamic simulation program for the pituitary-thyroid feedback control system.

SimThyr provides a GUI, which allows for visualising time series, modifying constant structure parameters of the feedback loop (e.g. for simulation of certain diseases), storing parameter sets as XML files (referred to as "scenarios" in the software) and exporting results of simulations in various formats that are suitable for statistical software.

[9] Later and expanded versions of the software were used to develop the hypothesis of the TSH-T3 shunt in the hypothalamus-pituitary-thyroid axis,[10] to assess the validity of calculated parameters of thyroid homeostasis (including SPINA-GT and SPINA-GD)[11][12] and to study allostatic mechanisms leading to non-thyroidal illness syndrome.

[13][14] SimThyr was also used to show that the release rate of thyrotropin is controlled by multiple factors other than T4 and that the relation between free T4 and TSH may be different in euthyroidism, hypothyroidism and thyrotoxicosis.

On the other hand, the complexity of the user interface and the lack of the ability to model treatment effects have been criticized.