This depends on your application and what you want to do.
If you are a service provider and want to include your services in Taverna, please refer to the documentation for service providers. If you services are not on the list of services that Taverna can invoke out of the box, you may consider developing a plugin for Taverna that will enable it.
If you want to invoke a Taverna workflow from your application (e.g. from a Web site, a portal or a standalone app) – you may consider using the Taverna Server or Command Line Tool to run workflows remotely.
If you have an integration scenario that is not mentioned here, please contact us and together we can figure out a solution.