BranchKB is the software package that runs each Branch. It creates a data store for that Branches knowledge of identified neurons that allows a) customization of the ontology (data model), b) read/write access to the knowledge base through an expressive query language, and c) interaction with the Meta-Server that binds together the Branches into a cooperative entity. BranchKB is being built on top of Protege, an established knowledge-base system. We have developed a core ontology (data model) for representing identified neurons that includes an extensible branch which enables extensive customization. We are wrapping the Protege system into a Java-based set of webservices that will enable diverse clients to interact with read/write knowledge from the system.