About Taverna workbench core
Using the Taverna version of the wsdl-generic artifact and the corresponding BIFI version.Figure 10Comparison of WUIs of example Workflow 1 automatically built using wsdl-artifact provided by the Taverna Workbench and the BIFI Plugin. BIFI generated workflow user interface for setting input data for Example Workflow 1 (left) using Taverna wsdl-generic artifact and (right) using the extended BIFI wsdl-generic artifact.Full size imageUnlike the WSDL processor, the R processor has no description file to parse. But workflow developers may set the following built-in data types for R processor input ports: Logical, Numeric, Integer, String, Logical Vector, Numeric Vector, Integer Vector, String Vector, Text-File. The R predictor uses this information for determining which user interface to use.Furthermore, BIFI provides the required extension points over service provider interfaces [15] by which developers can add their own Workflow Port Component (WPC) implementations as well as data type to WPC generator mappings. Given the properties (like simple type restrictions in XSD), generators create appropriate WPC objects to be shown in the workflow user interface.ResultsThe XworX BIFI plugin brings great simplicity in the usage of the Taverna Workbench. To demonstrate these advantages, the differences between WSDL and R are highlighted using two workflows.The first workflow consumes SOAP based web services from NCBI PubChem [16] and given a list key, prepares a file containing those records in the selected format for download [17]. The second workflow demonstrates usage of an R package for quality control and primary analysis of Illumina Infinium methylation data [18].When using Taverna without BIFI, users must enter the workflow inputs for Example Workflow 1 using the pop-up dialog as shown in Figure 2. The same workflow opened with BIFI enabled Taverna will display a user interface as shown in Figure 10. All available input ports are directly accessible through the BIFI generated GUI.For the
Key features of the Taverna workbench core that are enabled through these drivers include:
- Releases taverna/taverna-workbench-product - GitHub
- [TAVERNA-810] Taverna workbench plugin to allow
- taverna / taverna-workbench-product / Compare - Bitbucket
- incubator-taverna-workbench-common-activities/taverna
- Maven Repository: net.sf.taverna.t2.taverna-workbench taverna
- Taverna dialog for WIP. A screenshot of the Taverna workbench
- taverna workbench core full version activation code (updated
The actual logic and an output port collecting the resulting analysis data. See Figure 1 for a simple workflow graph.Figure 1A simple Taverna workflow. The Graph of a simple workflow from The Taverna Workbench consisting of two workflow input ports, one processor and one workflow output port.Full size imageThe creation (design) and the execution of the workflow are two independent steps. After designing a workflow, users specify data for the WIPs, which are then routed to the next processor during the execution time.WIPs carry no metadata in a computer interpretable form, however, except information about the data dimension. But this information is apparently not sufficient to provide the advanced, self-describing user interfaces, which give a sense of the type and format of the data to be entered for analysis. Figure 2 shows the Taverna dialog for setting input values of WIPs generated for the Example Workflow 1 as supplied as Additional file 1. This dialog provides users only with text areas to enter the input data in text form. This limitation is due partly to a shortage of remote services provided by autonomous third parties around the world having insufficient or non-existent metadata. Examining SOAP based web services, which constitute the majority of remote services listed in Taverna, the metadata are often as simple as data type definitions like ‘string’ which have no information about complex file formats [2]. This shortcoming may make the data type so unpredictable that users should basically execute the service using some data and see what happens. Erroneous results can be expected which could easily lead to disappointment and deter users from using the system [11].Figure 2Taverna dialog for WIP. A screenshot of the Taverna workbench shows the input dialog to enter the data for WIPs. It provides only a text area to enter the
