We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space that may make statistical exploration difficult in practice; instead, we propose to solve a convex optimization problem. Seven criteria based on ecological network indices have been selected to be used as convex goal functions. Numerical results show that the method is fast and can be used for large systems. Minimum flow solutions are analyzed using flow decomposition in paths and circuits. Their consistency is also tested by introducing a system of differential equations for the biomasses and examining the stability of the biomass fixed point. The method is illustrated and explained throughout the text on an ecosystem toy model. It is also applied to realistic food models.
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