The current work reveals a methodology that provides an adequate basis to portray and model supply chains mathematically and formally as well as to synthesize optimal and alternative supply scenarios algorithmically while taking into account structural redundancy. The proposed methodology is based on the combinatorial foundations of algorithmic process synthesis or more specifically on the P-graph framework. A biodiesel supply network involving blending and transportation serves as an illustrative example. A novel algorithm generates the mathematical model and alternative solutions to increase reliability of supply scenarios. Major steps of the generation are the structure generation and estimation of reliability of a supply scenario.