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MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.4. R-SCRIPTS WITH THE RSHELL PROCESSOR R is a popular scripting language oriented towards statistical computing, and with the addition of the BioConductor module, suitable for biological data analysis. Taverna comes with support executing R-scripts as part of a workflow. The functionality is very similar to how to use the Beanshell processor, so this section will only cover what is special about the RShell processor. 3.3. WORKFLOW DIAGRAM Each solid dark arrow (a data link) has two types. The upper of these is the type of information flowing out of the output of the processor the link is from, the lower that of the input the link is to. TAVERNA 1.7.1 MANUAL. Warning. If you are running a version of Taverna later than version 1.7, for example 2.0, then please visit the Taverna site for up-to-date documentation.4.7. WSDL PROCESSOR
Once the WSDL has been added to the list of services, processors can be added to the workflow just like any other processor. When expanding the list of inputs, or outputs, to the services, those that require a complex data structure will be described as having a mime type of 'text/xml' (or l'(text/xml') if it expects an array of complex datatypes).
1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list.USER MANUAL
User Manual. Taverna Workbench now comes in editions (builds) for several domains - astronomy, biodiversity, bioinformatics and digital preservation. These editions mainly differ in available plugins (e.g. for service types) and default service sets. Taverna Workbench Enterprise is an edition which contains all available plugins. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
RSERVE INSTALLATION AND DEPLOYMENT Installing R and additional modules. To install R on the machine where you want to run the scripts, download the installation from one of the sites linked to at the R Project .. If you have any problems installing or running R, then it is a good idea to consult the R FAQ.. Once you have R installed, you can start it either on the command line with the command R or using the appropriate XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.4. R-SCRIPTS WITH THE RSHELL PROCESSOR R is a popular scripting language oriented towards statistical computing, and with the addition of the BioConductor module, suitable for biological data analysis. Taverna comes with support executing R-scripts as part of a workflow. The functionality is very similar to how to use the Beanshell processor, so this section will only cover what is special about the RShell processor. 3.3. WORKFLOW DIAGRAM Each solid dark arrow (a data link) has two types. The upper of these is the type of information flowing out of the output of the processor the link is from, the lower that of the input the link is to. TAVERNA 1.7.1 MANUAL. Warning. If you are running a version of Taverna later than version 1.7, for example 2.0, then please visit the Taverna site for up-to-date documentation.4.7. WSDL PROCESSOR
Once the WSDL has been added to the list of services, processors can be added to the workflow just like any other processor. When expanding the list of inputs, or outputs, to the services, those that require a complex data structure will be described as having a mime type of 'text/xml' (or l'(text/xml') if it expects an array of complex datatypes).
1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list.USER MANUAL
User Manual. Taverna Workbench now comes in editions (builds) for several domains - astronomy, biodiversity, bioinformatics and digital preservation. These editions mainly differ in available plugins (e.g. for service types) and default service sets. Taverna Workbench Enterprise is an edition which contains all available plugins. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
RSERVE INSTALLATION AND DEPLOYMENT Installing R and additional modules. To install R on the machine where you want to run the scripts, download the installation from one of the sites linked to at the R Project .. If you have any problems installing or running R, then it is a good idea to consult the R FAQ.. Once you have R installed, you can start it either on the command line with the command R or using the appropriate XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
3.3. WORKFLOW DIAGRAM Each solid dark arrow (a data link) has two types. The upper of these is the type of information flowing out of the output of the processor the link is from, the lower that of the input the link is to. 4.4. R-SCRIPTS WITH THE RSHELL PROCESSOR R is a popular scripting language oriented towards statistical computing, and with the addition of the BioConductor module, suitable for biological data analysis. Taverna comes with support executing R-scripts as part of a workflow. The functionality is very similar to how to use the Beanshell processor, so this section will only cover what is special about the RShell processor.MYGRID » FETA
Informatics applications that are available as web services are numerous and are growing in number. More service providers are supplying web service versions of their applications and more ‘legacy’ command-line and web page applications are being made available as web services via SoapLab and GowLab wrapping. Consequently, service discovery is becoming increasingly important. 3.5. ENACTOR LAUNCH PANEL The Enactor Launch Panel (ELP) allows the user to enter input data for a workflow then launch the workflow enactor with that data. It is only shown if the workflow requires some input, if the workflow has no user specified inputs this panel is never shown and the enactment statusdisplay in
CHAPTER 2. DEVELOPERS GUIDE. Maven, version 2.0.4, is a pre-requisite to building Taverna, as of course is Java, but inparticular Java SE 5.0.. Once the pre-requisites have been met, from the root of the Taverna directory run the command: mvn install This installs the artifacts into your local mavenrepository.
4.7. WSDL PROCESSOR
Once the WSDL has been added to the list of services, processors can be added to the workflow just like any other processor. When expanding the list of inputs, or outputs, to the services, those that require a complex data structure will be described as having a mime type of 'text/xml' (or l'(text/xml') if it expects an array of complex datatypes).
4.5. BIOMART QUERY INTEGRATION The query is created by dragging a dataset (shown in the panel above) into the advanced model explorer as with any other processor type. Similarly to the Beanshell scripting engine all Biomart processors require configuration before they are of any use within the workflow. 3. RUNTIME CONFIGURATION OF RAVEN WITHIN THE WORKBENCH The raven.properties file also contains configuration for the workbench plugin manager. Specifically it declares a location to go to for a list of available profiles (used by the select workbench versionmenu) as
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
RELEASE NOTES
Bug - Raven does not interpolate maven propertie - Nested workflows with retries fails with "execute() called twice - Max local workers for nested workflows too loRefinement - Retrieving a fasta output from Biomar - Local worker for getting an item or range from a lisEdit/Copy Release Notes. The text area below allows the project release notes to be edited and copied to anotherMYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences MYGRID DEVELOPER BLOG 4. SCUFL LANGUAGE AND WORKBENCH FEATURES The iteration strategy is displayed as a tree. The leaf nodes in the tree correspond to the individual inputs to the processor, in this case ' string1 ' and ' string2 '. Non leaf nodes represent the different ways of combining the input iterators and the 'cross product' node represents the 'all 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
USER MANUAL
User Manual. Taverna Workbench now comes in editions (builds) for several domains - astronomy, biodiversity, bioinformatics and digital preservation. These editions mainly differ in available plugins (e.g. for service types) and default service sets. Taverna Workbench Enterprise is an edition which contains all available plugins. BUILDING AND RUNNING A WORKFLOW 5. Type in a name for this input (e.g. ID) and click OK. 6. Do the same to create a new workflow output. This time select Workflow output port. Call this output Sequence. 7. You n TASK 3.3 - IMPLEMENTATION PLAN - CAGRID - MYGRID DEVELOPER Word doc version of this document can be downloaded here. 1 Introduction. The US National Cancer Institute provides an integrated biomedical informatics infrastructure called the INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196 XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences MYGRID DEVELOPER BLOG 4. SCUFL LANGUAGE AND WORKBENCH FEATURES The iteration strategy is displayed as a tree. The leaf nodes in the tree correspond to the individual inputs to the processor, in this case ' string1 ' and ' string2 '. Non leaf nodes represent the different ways of combining the input iterators and the 'cross product' node represents the 'all 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
USER MANUAL
User Manual. Taverna Workbench now comes in editions (builds) for several domains - astronomy, biodiversity, bioinformatics and digital preservation. These editions mainly differ in available plugins (e.g. for service types) and default service sets. Taverna Workbench Enterprise is an edition which contains all available plugins. BUILDING AND RUNNING A WORKFLOW 5. Type in a name for this input (e.g. ID) and click OK. 6. Do the same to create a new workflow output. This time select Workflow output port. Call this output Sequence. 7. You n TASK 3.3 - IMPLEMENTATION PLAN - CAGRID - MYGRID DEVELOPER Word doc version of this document can be downloaded here. 1 Introduction. The US National Cancer Institute provides an integrated biomedical informatics infrastructure called the INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196 XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
2.2. CONFIGURATION
If you are behind an HTTP proxy, and there's a reasonable chance that you are, you'll need to modify the mygrid.properties.The properties http.proxyHost and http.proxyPort need to be set to the hostname, or IP address, and port. There is also the additional property http.nonProxyHosts which if set lists hosts for which the proxy is not used, separated by a ‘|’. 3.4. AVAILABLE SERVICES Services are shown in a hierarchical view. The exact semantics of this hierarchy vary by service type; soaplab, for example, has some concept of service categories so the view for a soaplab server shows the top level installation, then child nodes corresponding to the various categories and finally leaf nodes corresponding to actual services: BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. BUILDING AND RUNNING A WORKFLOW 5. Type in a name for this input (e.g. ID) and click OK. 6. Do the same to create a new workflow output. This time select Workflow output port. Call this output Sequence. 7. You nIMPLICIT ITERATION
Lists to single value. If a service expects a list, but you provide it with a single value (like from the Text Constant), Taverna will simply wrap the value in single-item list(s) for you.Be careful, though, if you later change the workflow to do an implicit iteration over the service outputting a single value, the following service would receive the full iteration output in one go. TASK 3.3 - IMPLEMENTATION PLAN - CAGRID - MYGRID DEVELOPER Word doc version of this document can be downloaded here. 1 Introduction. The US National Cancer Institute provides an integrated biomedical informatics infrastructure called the PROVENANCE EXPORT TO OPM AND JANUS Exporting provenance from the Workbench. From the Taverna workbench, go to the Result perspective, select a finished workflow run (which has been run with provenance enabled), mak INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196 FORMER TAVERNA 3 BUGS (NOW MOVED TO APACHE TAVERNA Key Summary Updated; T3-883: XPath fails with "uses unbound namespace prefix default" 2013-10-11T18-11 2014-07-11: T3-996: Can't get non-nodelist resultsMYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
TAVERNA SERVER
Taverna Server Architecture. Taverna Server is a java web application that runs in a application server such as Apache Tomcat, Jetty, etc. It has a REST interface for running workflows and handling input/output data. There is a web interface for server administration. INDEX OF /OPENJDK/1.7.0-U40-UNOFFICIAL Parent Directory - LICENSE: 16-Jan-2014 11:03 : 19K : README.html: 16-Jan-2014 11:29 : 630 : convert-bundle.sh: 17-Jan-2014 14:13 : 1.5K: openjdk-1.7.0-u40
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
TAVERNA SERVER
Taverna Server Architecture. Taverna Server is a java web application that runs in a application server such as Apache Tomcat, Jetty, etc. It has a REST interface for running workflows and handling input/output data. There is a web interface for server administration. INDEX OF /OPENJDK/1.7.0-U40-UNOFFICIAL Parent Directory - LICENSE: 16-Jan-2014 11:03 : 19K : README.html: 16-Jan-2014 11:29 : 630 : convert-bundle.sh: 17-Jan-2014 14:13 : 1.5K: openjdk-1.7.0-u40
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences CHAPTER 1. USERS GUIDE. Workflow - A set of components and relations between them used to define a complex process from simple building blocks. Relations may be in the form of data links, transferring information from the output of one component to the input of another, or in the form of control links which state some conditions on the execution of a component. MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access.MYGRID BUILD SERVER
myGrid build server. These pages were intended for use for developers of myGrid software. Contact Stian, Alan, Shoaib if you think you should have administrator access. MYGRID DEVELOPER BLOG Life Science Identifiers was an identification scheme for identifying Life Science information, e.g. describing genes, proteins, species.It was created by the bioinformatics community, and standardized in 2004 as an LSID specification through the Object Management Group.As of 2016 it is no longer used, except within the biodiversity community for identifying species. DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list.TAVERNA SERVER
Taverna Server Architecture. Taverna Server is a java web application that runs in a application server such as Apache Tomcat, Jetty, etc. It has a REST interface for running workflows and handling input/output data. There is a web interface for server administration. FORMER TAVERNA 3 BUGS (NOW MOVED TO APACHE TAVERNA Key Summary Updated; T3-883: XPath fails with "uses unbound namespace prefix default" 2013-10-11T18-11 2014-07-11: T3-996: Can't get non-nodelist results INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access. 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access. 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical SciencesMYGRID
]> input and output are different representations of the same thing - syntax translation input and output are different representations of the same thing - syntax translation input is equivalent to output output is part of input input uniquely identifies output The biological sense of the word. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects.COMMAND LINE TOOL
What is the difference between the bundled and standalone executeworkflow? The standalone command line tool has a separate configuration home directory, called taverna-cmdline-2.x.x - while the bundled tool uses the same configuration from taverna-2.x.x as the Taverna Workbench.. Any proxy settings have to be configured manually - copy conf/HttpProxy-B307A902-F292-4D2F-B8E7TAVERNA SERVER
Taverna Server Architecture. Taverna Server is a java web application that runs in a application server such as Apache Tomcat, Jetty, etc. It has a REST interface for running workflows and handling input/output data. There is a web interface for server administration.SERVICE TYPES
Taverna can access a large number of Web services in the fields of bioinformatics, astronomy, chemoinformatics, health informatics andothers.
INDEX OF /OPENJDK/1.7.0-U40-UNOFFICIAL Parent Directory - LICENSE: 16-Jan-2014 11:03 : 19K : README.html: 16-Jan-2014 11:29 : 630 : convert-bundle.sh: 17-Jan-2014 14:13 : 1.5K: openjdk-1.7.0-u40
FORMER TAVERNA 3 BUGS (NOW MOVED TO APACHE TAVERNA Key Summary Updated; T3-883: XPath fails with "uses unbound namespace prefix default" 2013-10-11T18-11 2014-07-11: T3-996: Can't get non-nodelist results INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access. 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access. 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical SciencesMYGRID
]> input and output are different representations of the same thing - syntax translation input and output are different representations of the same thing - syntax translation input is equivalent to output output is part of input input uniquely identifies output The biological sense of the word. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects.COMMAND LINE TOOL
What is the difference between the bundled and standalone executeworkflow? The standalone command line tool has a separate configuration home directory, called taverna-cmdline-2.x.x - while the bundled tool uses the same configuration from taverna-2.x.x as the Taverna Workbench.. Any proxy settings have to be configured manually - copy conf/HttpProxy-B307A902-F292-4D2F-B8E7TAVERNA SERVER
Taverna Server Architecture. Taverna Server is a java web application that runs in a application server such as Apache Tomcat, Jetty, etc. It has a REST interface for running workflows and handling input/output data. There is a web interface for server administration.SERVICE TYPES
Taverna can access a large number of Web services in the fields of bioinformatics, astronomy, chemoinformatics, health informatics andothers.
INDEX OF /OPENJDK/1.7.0-U40-UNOFFICIAL Parent Directory - LICENSE: 16-Jan-2014 11:03 : 19K : README.html: 16-Jan-2014 11:29 : 630 : convert-bundle.sh: 17-Jan-2014 14:13 : 1.5K: openjdk-1.7.0-u40
FORMER TAVERNA 3 BUGS (NOW MOVED TO APACHE TAVERNA Key Summary Updated; T3-883: XPath fails with "uses unbound namespace prefix default" 2013-10-11T18-11 2014-07-11: T3-996: Can't get non-nodelist results INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access. 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical Sciences 4.2. CONDITIONAL BRANCHING Conditional branching is the term used to describe the set of operations such as ' if do else do ' and the various case and switch statements in conventional imperative languages such as C, PERL and Java. Taverna's language representation differs in some crucial ways from these languages so the representation of conditionals isdifferent, the
MYGRID DEVELOPER AREA myGrid developer area. These pages are intended for internal use for the developers of the myGrid team. Contact Stian, Ian or David if you think you should have access. 4. USING THE TAVERNA API TO PROGRAMMATICALLY EXECUTE A To avoid needing to use a bootstrapped approach, the solution is to initialise the Raven repository programmatically. This is achieved by using the LocalRepository method introduced with Taverna 1.5.2:. public Repository getRepository(File base, ClassLoader loader, SetsystemArtifacts);
DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. BEANSHELL - TAVERNA 2.5 - MYGRID DEVELOPER WIKI To add an input port: Select the Input ports tab from the Beanshell configuration dialog. Click Add port button. Enter the name of the input port. Specify the input port depth. If the input is a list or a list of lists select its depth accordingly. For simple values leave it as 0 which is the default value. SCUFL2 - DEVELOPER DOCUMENTATION - MYGRID DEVELOPER WIKI Scufl2 has moved to Apache (incubator) Information in this section is out of date! SCUFL2 is the proposed new mechanism for specifying Taverna workflows. SCUFL2 defines a model, a workflow bundle file format (.wfbundle), and a Java API for working with workflowstructures.
FREQUENTLY ASKED QUESTIONS Frequently Asked Questions. This section contains some frequently asked questions that are not answered elsewhere in the User Manual. Can I invoke secure services from workflows? Can I run my workflow as a Web service? Can I run Taverna on another machine or from thecommand line?
XPATH FAILS WITH "USES UNBOUND NAMESPACE PREFIX Running the example REST/XPath workflow attached (from 2.4 starterpack)
MYGRID » ABOUT US
The myGrid team is a multi-institutional, multi-disciplinary internationally leading reasearch group focussing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories. The myGrid team has guaranteed funding until 2016. Sponsors The myGrid team gratefully acknowledge the funding support of their Sponsors: Microsoft the Engineering and Physical SciencesMYGRID
]> input and output are different representations of the same thing - syntax translation input and output are different representations of the same thing - syntax translation input is equivalent to output output is part of input input uniquely identifies output The biological sense of the word. 1. CREATE PROJECT FROM ARCHETYPE Create the plugin from the archetype using the Maven command line tool mvn, then use Import existing maven project to add the generated project to Eclipse. For details, see the workaround of the Failed to create warning box below. Click OK in the "Preferences" dialogue. Now you should be able to find myGrid in the Catalog dropdown list. DASHBOARD - MYGRID DEVELOPER WIKI Welcome to Confluence . Confluence is where your team collaborates and shares knowledge — create, share and discuss your files, ideas, minutes, specs, mockups, diagrams, and projects.COMMAND LINE TOOL
What is the difference between the bundled and standalone executeworkflow? The standalone command line tool has a separate configuration home directory, called taverna-cmdline-2.x.x - while the bundled tool uses the same configuration from taverna-2.x.x as the Taverna Workbench.. Any proxy settings have to be configured manually - copy conf/HttpProxy-B307A902-F292-4D2F-B8E7TAVERNA SERVER
Taverna Server Architecture. Taverna Server is a java web application that runs in a application server such as Apache Tomcat, Jetty, etc. It has a REST interface for running workflows and handling input/output data. There is a web interface for server administration.SERVICE TYPES
Taverna can access a large number of Web services in the fields of bioinformatics, astronomy, chemoinformatics, health informatics andothers.
INDEX OF /OPENJDK/1.7.0-U40-UNOFFICIAL Parent Directory - LICENSE: 16-Jan-2014 11:03 : 19K : README.html: 16-Jan-2014 11:29 : 630 : convert-bundle.sh: 17-Jan-2014 14:13 : 1.5K: openjdk-1.7.0-u40
FORMER TAVERNA 3 BUGS (NOW MOVED TO APACHE TAVERNA Key Summary Updated; T3-883: XPath fails with "uses unbound namespace prefix default" 2013-10-11T18-11 2014-07-11: T3-996: Can't get non-nodelist results INABILITY TO ESTABLISH R CONNECTION CAUSES Running Paul's http://www.myexperiment.org/workflows/10 causes:. WARN 2009-11-22 15:46:02,544 (net.sf.taverna.t2.workflowmodel.processor.dispat h.layers.Invoke:196Got it!
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ESCIENCE LAB
The eScience Lab research group is led by Professor CaroleGoble . The group
is based at the Department of Computer Science , University of Manchester . It’s affiliated with the wider Information Management Group . The eScience Lab team are focused on research and development around a set of tools designed for data driven and computational research. The tools support the coming together of people, data and methods in a particular research area; this is also know as an _e-laboratory_. These e-Laboratories or _e-Labs_ support domains as diverse as systems biology, social science, music, astronomy, multimedia and chemistry. The tools have been adopted by a large number of projects and institutions. Our research and projects span a wide array of topics, including eScience, bioinformatics, biodiversity, scholarly communication, reproducible science, linked data, provenance, community building and knowledge representation.* 2020-10-30
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* Contact eScience Lab: * info@esciencelab.org.uk 2020 University of Manchester. This work is licensed under a Creative Commons Attribution 4.0 International License.
The eScience Lab team is a multi-disciplinary internationally leading research group focusing on the challenges of eScience. We specialise in data and knowledge-intensive e-Laboratories.Details
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