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Peptide computing is a novel way of computing that uses the interaction between peptides and antibodies as a computational model. Since several copies of peptides and antibodies can interact at the same time, this computing model is massively parallel and highly non-deterministic in nature. Due to these advantages this computational model helps us to solve some of the very hard combinatorial problems quite efficiently. Peptide computing involves preparation of peptide sequences and antibodies with respect to the given problem and it also requires the interactions between various peptide sequences and antibodies. To carry out these various operations there is a need for automation. In this paper we enumerate automation issues in peptide computing with respect to several models defined in the literature. We study and address some of the issues and propose some solution to overcome the same.