Taverna 1.x is unfortunately not very good at dealing with large data. You have two options – first is to redesign your services such that you pass references to data held elsewhere. This will generally benefit all your users as the efficiency hit you take when running large (>1MB) files through a SOAP service is pretty severe compared to the hundred or so bytes used by a reference to a data file (i.e. a HTTP URL).
Alternatively, you can use the Web service Data Proxy to dynamically rewrite the SOAP messages. It overcomes the problem of Web services that return large items of data causing Taverna 1.7.x to struggle or fail due to memory constraints. It solves this problem by allowing the user to select specific data elements for referencing, leading to the data to be stored on the proxy and the Web service SOAP response is rewritten to replace the data itself with a URL to the actual data. The Web service Data Proxy is available for download.
Many of the issues that make the Web service Data Proxy necessary for Taverna 1.7.x are overcome in Taverna 2.x. Taverna 2.x uses a more efficient mechanism for storing data and so can handle larger data sets.
