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Get FlyTED Gene Expression Images for a Ge... (1)

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This is a simple workflow testing running a restful service in Taverna. This restful service http://www.open-biomed.org.uk/service/flyted/records/probe/{probe} is part of the flykit/flyted services http://code.google.com/p/open-biomed/wiki/Flyted, which is built using the Talis Puelia Linked Data API (http://code.google.com/p/puelia-php/). We want to use this simple workflow to test the idea of bridging linked data and scientific workflows using Restful services. A test input gene name can ...

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Junzhao

GetCities2 (1)

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 Get cities by entering a country name

Created: 2012-05-03 | Last updated: 2012-05-03

Credits: Xiaoxiaoshijie

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Presentation - Research on the Web: The Rise of New ...

Created: 2012-04-21 11:26:22 | Last updated: 2012-05-15 09:51:35

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Introduction to Taverna and HELIO presentation

Created: 2012-04-19 09:00:18

Credits: Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 67 times | Downloaded: 59 times

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HELIO Taverna Tutotial

Created: 2012-04-19 08:36:41 | Last updated: 2012-04-19 08:36:42

Credits: Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 67 times | Downloaded: 50 times

SNP Position Information (1)

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This workflow extracts information about the position of SNPs and the genes they are associated with, using BioMart (ENSEMBL Variation 66).

Created: 2012-04-17 | Last updated: 2012-04-17

Credits: Katy Wolstencroft

Match gene lists based on information in l... (7)

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[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics

Attributions: Match concept profiles Explain concept scores

ICDAR 2011 End-to-End Applications contest... (1)

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Full workflow for use with the DAE platform and as used for the ICDAR 2011 "Document Analysis Algorithm Contributions in End-to-End Applications" contest, including contributed algorithms.

Created: 2012-04-14 | Last updated: 2012-04-14

Credits: Bart Lamiroy

Create and execute a simulation on the RIS... (1)

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Create and execute a simulation on the RISE server. This workflow take 3 inputs: the XML to configure the RISE framework, the URL of the ZIP file model (a zipped directory containing the model files), and the new framework name. This workflow produce on the output the simulation LOG file.

Created: 2012-04-09

Unix tool service using string replacement (1)

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The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2012-04-05

Credits: Alan Williams

Spreadsheet Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2012-04-05

Credits: Alan Williams

Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2012-04-05

Credits: Alan Williams

Secure Web service call example (2)

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This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu. You ...

Created: 2012-04-05 | Last updated: 2013-06-11

Credits: Alan Williams

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Render gene via BioGPS (3)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: Alan Williams

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2012-04-05

Credits: Alan Williams

Numerically adding two values. (1)

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2012-04-05

Credits: Alan Williams

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2012-04-05

Credits: Alan Williams

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2012-04-05

Credits: Alan Williams

Example workflow for REST and XPath activi... (1)

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2012-04-05

Credits: Alan Williams

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Example for external tools with zip and unzip (1)

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This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2012-04-05 | Last updated: 2014-04-09

Credits: Alan Williams

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Alan Williams

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Katy Wolstencroft

Get Pathway-Genes and gene description by ... (2)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with.

Created: 2012-03-27 | Last updated: 2012-04-03

Credits: Eleni

Format_transform_RMonto-RSextension (1)

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This workflow provides transformation of an item description attribute set from RMonto operator into a format required by attribute based k-NN operators of the Recommender extension.

Created: 2012-03-26

DemoWorkflow (1)

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 Demo Workflow

Created: 2012-03-22 | Last updated: 2012-03-22

Credits: Jribault

(Updated)Retrieve sequence in EMBL format. (1)

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This workflow retrieves a sequence associated with its features in embl format.

Created: 2012-03-19 | Last updated: 2012-04-02

Credits: Ankit upadhyay

Available instruments through DPAS which a... (1)

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This workflow uses a DPAS servlet to obtain all available intrument keys in the DPAS (Data Provider Access Service) and formats the return as VOTable.

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Anja Le Blanc

Attributions: Available instruments through DPAS Split VOTable into its values

Example of Execute_SQL_Query with parameters (1)

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This workflow connects to a mysql on localhost, queries the "world" database which is one of the test databases on MySQL 5.5, queries it about which countries have Dutch as a language, and emits answers in both Lists and in xml. This workflow is intended as an example to help you see the syntax for the various inputs to this local service beanshell. see: http://www.mygrid.org.uk/dev/wiki/display/taverna/Execute+SQL+Query for instructions on jars, dependencies etc. The jar used he...

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Helen Hulme

localhost Tesseract-Ocrad comparison (3)

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Simple demo workflow, for use with a standalone (localhost) version of the DAE platform. Compares Tesseract and Ocrad OCR results. For demonstration reasons and ease of use, this workflow has hardcoded username/password values. This is, obviously, very bad, but since it relates only to a sandboxed virtual server, potential damage is null.

Created: 2012-03-16 | Last updated: 2012-05-16

Credits: Bart Lamiroy

Simple Tesseract-Ocrad comparison (1)

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Simple demonstration workflow for use with the on-line Lehigh-based DAE server, comparing the results of Tesseract and Ocrad OCR engines on a specific document image.

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Bart Lamiroy

kddcup98 direct marketing (1)

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RapidMiner supports Meta Learning by embedding one or several basic learners as children into a parent meta learning operator. In this example we generate a data set with the ExampleSetGenerator operator and apply an improved version of Stacking on this data set. The Stacking operator contains four inner operators, the first one is the learner which should learn the stacked model from the predictions of the other four child operators (base learners). Other meta learning schemes like Boosting ...

Created: 2012-03-15

Check in UOC which instruments were observ... (2)

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Query of the UOC to find the instrument_observatory keys for instruments which were observing at a given time period and a given location.

Created: 2012-03-15 | Last updated: 2012-03-15

Credits: Anja Le Blanc

Jpylyzer Review Demonstration (1)

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 Review demonstration workflow that compares the jpylyzer tool with the struct checker and jhove.  Runs on British Library JISC 1 content, looking for invalid images.

Created: 2012-03-15 | Last updated: 2012-03-15

Credits: Carl

Jane's Final Workflow (1)

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Example workflow demonstrating the use of the DAE platform's web service capabilities, as published "The Non-Geek's Guide to the DAE Platform", Bart Lamiroy & Daniel Lopresti, DAS - 10th IAPR International Workshop on Document Analysis Systems (2012).

Created: 2012-03-14 | Last updated: 2012-03-14

Credits: Bart Lamiroy

Split VOTable into its values (1)

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This workflow takes a single VOTable and splits it up in a vector for the names of fields, a vector for the UCDs of the fields, a vector for the UTypes of the fields, and a two dimensional vector for the values.

Created: 2012-03-14 | Last updated: 2012-03-14

Credits: Anja Le Blanc

Co-rotating Interaction Regions backwards ... (1)

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Run the cir backwards propagation code on the HELIO processing service. Required inputs: time start of backwards propagation, the object (planet/spacecraft) from where the propagation should start, assumed solar wind speed at the time, assumed error of solar wind speed Output: VOTable with times at different points in solar system

Created: 2012-03-14 | Last updated: 2012-03-14

Credits: Anja Le Blanc

Propagation of the Solar Energetic Particl... (1)

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use of the processing service to calculate time delays to the planets Inputs: time when propagation should start from the hit object hit_object where was the SEP event observed speed of the solar wind error value of solar wind speed beta traveling speed of energetic particals as percentage of the speed of light

Created: 2012-03-13 | Last updated: 2012-03-13

Credits: Anja Le Blanc