This paper presents results of a research in the field of software development, design methods, as well as training and synthesis of binary neural networks. The research is based on the model of a biomorphic neuron proposed by A.A. Zhdanov, which features noise immunity and is capable of forgetting and additional training. Software tools for designing and visualizing the modeling of binary neural structures are described. Use cases and features of a formal markup language for neural network models, as well as principles of generating deep learning structures, are discussed. A neural network markup language interpreter can automatically generate source code in Verilog with the description of the neural-like implementation of intelligent systems for software and hardware solutions on programmable logic devices (PLDs).