Transport ecosystems that combine Software Defined Networking (SDN) and Network Function Virtualization (NFV) are characterized by an unprecedented network control and resource dynamicity. Manual optimization is unmanageable. In this context, open systems that manage and orchestrate SDN/NFV-enabled networks offer programming frameworks that abstract the low-level particularities in the data-plane forwarding devices and in the hardware appliances that provide the IT resources. Although these open systems present notable complexity, their programming abstractions promote a client layer where third-party applications can provide different functionalities thus enabling Optimization-as-a-Service (OaaS) business opportunities. In this paper, we cover open-source optimization software initiatives for offline planning and online provisioning and orchestration of SDN/NFV networks. With this goal in mind, we first focus on open software (and framework) initiatives through a set of realistic use cases that require optimization in multi-layer optical transport scenarios and ecosystems that combine transport with IT resources. The importance of a joint optimization of both network and IT domains is emphasized, a new paradigm triggered by SDN/NFV technologies. We discuss the theoretical limits to algorithm performances, and review available open-source frameworks for problem modelling that enable the interaction with solvers. Finally we focus on the Net2Plan open-source network planning tool, a Java-based software that suitably embraces the multiple features required in the optimization of joint transport network and IT resource SDN/NFV ecosystems. Recent works based on Net2Plan are reviewed to illustrate its suitability for rapid algorithm prototyping, and for interaction with SDN/NFV-enabled networks.