Taverna workbench core

Author: d | 2025-04-24

Taverna Taverna 2.5 › Taverna Workbench Core › Taverna Workbench Astronomy › Taverna Workbench Bioinformatics › Taverna Workbench Biodiversity › Taverna Workbench Digital Preservation › Taverna Workbench Enterprise Taverna 2.5 Astronomy Edition includes: › VAMDC (Virtual Atomic and Molecular Data Centre) plugin.

taverna-workbench-product: Taverna Workbench Core 2.5.0

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

taverna-workbench-product: Taverna Workbench Core 2.5.0 - Zenodo

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

Taverna Workbench Core 2.5.0 - CORE

What you’ll learnCompTIA CertMaster Labs for A+ Core 1 & Core 2 (220-1101 & 220-1102) enable hands-on practice and skills development using real equipment and software accessed through a remote, browser-based lab environment. Aligned with Official CompTIA courseware and the CompTIA A+ Core 1 & Core 2 ( 220-1101 & 220-1102) exam objectives, CertMaster Labs make it easy for learners to practice and apply their skills in real workplace scenarios in preparation for the certification exam. All lab activities use real equipment and software, offer feedback and hints, and provide a score based on learner inputs, ultimately guiding learners to the most correct and efficient path through job tasks. There are two types of labs in this course:Virtual Workbench Labs which provide learners with valuable hands-on practice in an immersive 3D environment. Each scenario features a Tutorial Mode guides the learner through step-by-step instruction, allowing learners to understand and practice 3D controls, an Explore Mode that enables learners to identify and manipulate hardware components in a sandbox environment, and an Assisted Mode that takes learners step by step through a procedure, offering help when needed.Virtual Machine Labs which utilize virtual machines built to simulate a server network so a learner can gain real-world, hands-on experience with tools, applications, and operating systems they would utilize in a job environment.Virtual machine labs are also available in different modes:Assisted Labs guide the learner step-by-step through tasks, offering assessment and feedback throughout a 10-15 minute experience, allowing the learner to correct any misunderstandings as they proceed through the activity.Applied Labs present a series of goal-oriented scenarios in a 20-30 minute experience covering multiple topics, scoring the student at the end of the activity based on their ability to successfully complete each scenario. As a result, learners are forced to think critically about how to approach problems without a prescribed set of steps.Labs Available:Assisted Lab: Exploring the Lab EnvironmentVirtual Workbench Lab: Installing a MotherboardVirtual Workbench Lab: Installing Power SuppliesVirtual Workbench Lab: Installing and Configuring System MemoryVirtual Workbench Lab: Installing RAMVirtual Workbench Lab: Installing CPU and CoolerVirtual Workbench Lab: Upgrading and Installing GPU and Daisy-Chain MonitorsAssisted. Taverna Taverna 2.5 › Taverna Workbench Core › Taverna Workbench Astronomy › Taverna Workbench Bioinformatics › Taverna Workbench Biodiversity › Taverna Workbench Digital Preservation › Taverna Workbench Enterprise Taverna 2.5 Astronomy Edition includes: › VAMDC (Virtual Atomic and Molecular Data Centre) plugin. DOWNLOAD; Taverna Workbench CoreTaverna Workbench Core is an edition of Taverna that includes support for DOWNLOAD; Perfectly Clear WorkbenchPerfectly Clear Workbench is

Taverna Workbench Core - reviewpoint.org

Technical Note Open access Published: 20 October 2014 Erkan Dilaveroglu1, Ilhami Visne1, Bilal Günay1, Emrah Sefer1, Andreas Weinhausel1, Frank Rattay2, Carole A Goble3, Ram Vinay Pandey4 & …Albert Kriegner1 BMC Research Notes volume 7, Article number: 740 (2014) Cite this article 1917 Accesses 5 Altmetric Metrics details AbstractBackgroundHeterogeneity in the features, input-output behaviour and user interface for available bioinformatics tools and services is still a bottleneck for both expert and non-expert users. Advancement in providing common interfaces over such tools and services are gaining interest among researchers. However, the lack of (meta-) information about input-output data and parameter prevents to provide automated and standardized solutions, which can assist users in setting the appropriate parameters. These limitations must be resolved especially in the workflow-based solution in order to ease the integration of software.FindingsWe report a Taverna Workbench plugin: the XworX BIFI (Beautiful Interfaces for Inputs) implemented as a solution for the aforementioned issues. BIFI provides a Graphical User Interface (GUI) definition language used to layout the user interface and to define parameter options for Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF) directly or discover appropriate instances from a configured repository. In the absence of a GDF, BIFI generates a default interface.ConclusionThe Taverna Workbench is an open source software providing the ability to combine various services within a workflow. Nevertheless, users can supply input data to the workflow via a simple user interface providing only a text area to enter the input in text form. The workflow may contain meta-information in human readable form such as description text for the port and an example value. However, not all workflow ports are documented so well or have all the required information.BIFI uses custom user interface components for ports which give users feedback on the parameter data type or

Taverna Workbench Core 2.5.0

Centric approach that complements Taverna Workflow System where users interactively build and exchange information about user interfaces of workflows.GUI descriptions may include meta information about what kind of data the service is waiting as input or parameter, restrictions and default/example values. A workflow with GDF is therefore perfectly suitable for ready-to-run sample workflow arrangements (see Figure 5). Please see Additional file 2 for the full GDF syntax.Figure 5A simple workflow user interface by BIFI. A simple workflow user interface generated by BIFI. The GUI description file contains the default values and details about the workflow. With example values already set, the workflow is ready to run with a simple click.Full size imageIn absence of a GDF instance, we have implemented an algorithm to pick the most appropriate GUI for the port depending on the available meta-information on service descriptions.MethodsWe have developed a BIFI plugin in Java 1.6 for the Taverna Workbench 2.4. Due to the diversity of the resources and especially because these resources are usually provided by autonomous third parties, it is hardly possible to implement a solution directly in the resource descriptions. We therefore map input ports to specific, pre-installed GUI-components using the graphical user interface description language we have defined.A workflow in Taverna may have only one GDF instance in the configured GDF repository. In this system we assume that a workflow – GDF pair represents a tool. The workflow and the user interface definition file are linked together using workflow identifiers. Each workflow created in Taverna is automatically assigned a universally unique identifier (UUID [14]) which will be kept unique even throughout the modifications.The Workflow User Interface (WUI) for the workflow will be initiated immediately after the workflow is opened in the Taverna environment. BIFI searches for the appropriate GDF in the configured repository and renders

Taverna Workbench Core 2.5.0 - Zenodo

Even about the type of the data that should be fed to a certain processor.Availability and requirementsProject name: The XworX BIFI Plugin for TavernaProject home page: system(s): All major platforms, such as Linux, Windows and Mac OS XProgramming language: JavaOther requirements: Taverna 2.4, Java 1.6License: LGPLRestrictions to use by non-academics: None AbbreviationsBIFI: Beautiful interfaces for inputs WUI: Workflow user interface GDF: Graphical user interface definition file WIP: Workflow input port UI: User interface WPC: Workflow port component WDSL: Web Services Description Language. ReferencesLi P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, Withers D, Oinn T, Pocock MR, Goble C, Oliver SG, Kell DB: Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data. BMC Bioinformatics. 2008, 9: 334-10.1186/1471-2105-9-334.Article PubMed PubMed Central Google Scholar Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T: Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 2006, 34: 729-732. 10.1093/nar/gkl320.Article Google Scholar Web Services Activity Statement. [ Services Description Language (WSDL) Version 2.0 Part 1: Core Language. MD, Links M: BioMOBY: an open source biological web services proposal. Brief Bioinformatics. 2002, 3: 331-341. 10.1093/bib/3.4.331.Article PubMed Google Scholar Senger M, Rice P, Oinn T: Soaplab - A Unified Sesame Door To Analysis Tools. All Hands Meeting. 2003 Google Scholar BeanShell - Lightweight Scripting for Java. [ I, Rauwerda H, Neerincx PB, Vet PE, Breit TM, Leunissen JA, Nijholt A: Using R in Taverna: RShell v1.2. BMC Res Notes. 2009, 2: 138-10.1186/1756-0500-2-138.Article PubMed PubMed Central Google Scholar myGrid » Home. [ - open source and domain independent Workflow Management System. M: Challenges in Developing User-Adaptive Intelligent User Interfaces. Proceedings of the 17th Workshop on Adaptivity and User Modeling in Interactive Systems at Lernen. Taverna Taverna 2.5 › Taverna Workbench Core › Taverna Workbench Astronomy › Taverna Workbench Bioinformatics › Taverna Workbench Biodiversity › Taverna Workbench Digital Preservation › Taverna Workbench Enterprise Taverna 2.5 Astronomy Edition includes: › VAMDC (Virtual Atomic and Molecular Data Centre) plugin.