Workflows

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

Associate SEP events at Earth with flare, ... (1)

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This is the implementation of a use case worked on during CDAW3 of the HELIO project. SEP events propagated backward from Earth to the Sun. We allow for +- 30 min around the predicted time to search for flare events. The timing of the flare event informs the search time for Type III radio event (time_start to time_peak) and for the CME event (time_start to time_start+1h). Results are presented in a mulitlayered VOTable.

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

Credits: Anja Le Blanc Rositsa

Attributions: Propagation of the Solar Energetic Particles to the Sun Extract content of columns from VOTables

BayesAss+ estiamtion of populations migrat... (1)

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BayesAss+ is a program that estimates recent migration rates between populations using MCMC. It also estimates each individual’s immigrant ancestry, the generation in which immigration occurred (i.e. the individual can be assigned as an immigrant from a specific population, a non-immigrant, or the offspring of an immigrant and a non-immigrant), the population (as opposed to the sample) allele frequencies, inbreeding (F) values within each population, and genotypes at any locus wit...

Created: 2012-03-08

Credits: Pipeline

Fdist2 Simulation Pipeline Workflow (1)

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Fdist2 is a simulation program to detect loci that might be under selection in samples from structured populations.   Workflow Usage & Specifications The workflow reads an input file "fdist_params2.dat", which consists of 6 lines. This file must only contain numbers in the format described: Total number of demes (100 max). No of populations sampled (must be less than or equal to total number of demes). Expected Fst for infinite allele, infinite island model. Sample si...

Created: 2012-03-08 | Last updated: 2012-03-08

Credits: Pipeline

Migrate Pipeline Workflow (1)

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Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.     Workflow Usage & Specifications Migrate can use the following data types: •Sequence data using Felsenstein's 84 model with or without site rate variation, •Single nucleotide poly...

Created: 2012-03-08

Credits: Pipeline

Get Pathway-Genes by Entrez gene id (4)

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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 are associated with. The workflow outputs also a KEGG pathway map and the objects are colored according to the input color values.

Created: 2012-03-08 | Last updated: 2012-04-14

Credits: Eleni

VAMDC Query to Two Nodes using HTML Consum... (2)

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Workflow to two TAP-XSAMS Node and see results in a HTML view using a Consumer Service. This workflow queries the BaseCol and CDMS Node for MoleculeStoichiometricForumua of 'CO' VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide **NOTE an update to the plugin will need to be released later to handle prefixes on certain query nodes and their restrictables. For instance BaseCol expects 'Target.MoleculeStoichiometricFormula' instead of just 'MoleculeSto...

Created: 2012-03-07 | Last updated: 2012-09-12

Credits: Stormshadow Virtual Atomic and Molecular Data Centre - VAMDC

VAMDC SpectCol tool using Full VAMDC-Tap Q... (2)

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Runs the SpectCol tool bundled with the plugin and can handle a list of URLS. This version asks for the full vamdc URL. SpectCol information: SPECTCOL is a tool that implements VAMDC standards, r etrieve relevant information from different databases such as CDMS, HITRAN, BASECOL, and can upload local files. All transfer of data between the client and the databases use the VAMDC-XSAMS schema. The spectroscopic and collisional information is combined and useful outputs (ascii or xsams) are ...

Created: 2012-03-07 | Last updated: 2012-09-12

Credits: Stormshadow

VAMDC Query to Two Nodes using HTML Consum... (2)

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Workflow to two TAP-XSAMS Node and see results in a HTML view using a Consumer Service. This workflow queries the Hitran and CDMS Node for MoleculeStoichiometricForumua of 'CO' VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide

Created: 2012-03-07 | Last updated: 2012-09-12

Credits: Stormshadow Virtual Atomic and Molecular Data Centre - VAMDC

VAMDC to query on ChemicalName 'OR' Stoich... (4)

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Workflow to query just one TAP-XSAMS Node. This workflow queries the Hitran Node for MoleculeChemicalName of 'HF' and StoichimetricFormula of 'HV' Demonstrates building a query for two Restrictables. VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide

Created: 2012-03-07 | Last updated: 2012-09-12

Credits: Stormshadow Virtual Atomic and Molecular Data Centre - VAMDC

Workflow to Query TAP-XSAMS node. (3)

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Workflow to just one TAP-XSAMS Node. This workflow queries the Hitran Node for MoleculeChemicalName of 'HF' VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide

Created: 2012-03-07 | Last updated: 2012-09-12

Credits: Stormshadow

VAMDC VALD query with SME processing (4)

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VAMDC workflow that queries the VALD Atomic database in Moscow and runs SME (Spectroscopy Made Easy) VAMDC Taverna Plugin: http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide

Created: 2012-03-07 | Last updated: 2012-11-29

Credits: Stormshadow Virtual Atomic and Molecular Data Centre - VAMDC

RISE UI: Select ZIP file (1)

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 This workflow ask the user to select a ZIP file on his own computer.

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

Credits: Jribault

RISE UI: Select XML file (1)

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 This workflow ask the user to select an existing XML file on his own computer.

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

Credits: Jribault

RISE UI: Create a Framework XML File (1)

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This workflow create a framework configuration XML file based on user interaction.

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

Credits: Jribault

RISE UI: Choose User Workspace (1)

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This workflow ask the user to select a user workspace among those present on the RISE server.

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

Credits: Jribault

RISE UI: Choose Service Type (1)

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This workflow ask the user to select a service type among those present on the RISE server.

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

Credits: Jribault

RISE UI: Choose Framework (1)

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This workflow ask the user to choose a framework among those present on the RISE server.

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

Credits: Jribault

RISE UI: Ask Framework Name (2)

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  This workflow ask the user to enter a new framework name.

Created: 2012-03-05 | Last updated: 2012-03-22

Credits: Jribault

RISE Atomic Service: Upload ZIP Model File (1)

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 This workflow upload a ZIP file of the simulation model on the RISE server.

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

Credits: Jribault

RISE Atomic Service: Get Simulation Result (1)

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 This workflow get the simulation result of an existing simulation on the RISE server.

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

Credits: Jribault

RISE Atomic Service: Execute Simulation (1)

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 This workflow execute a simulation on the RISE server, and wait for its completion.

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

Credits: Jribault

RISE Atomic Service: Delete Framework (1)

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 This workflow delete an existing framework on the RISE Server.

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

Credits: Jribault

RISE Atomic Service: Create Framework (1)

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 This workflow create a new framework on the RISE Server

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

Credits: Jribault

Meta-mining workflow that performs crossva... (1)

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Performs a crossvalidation on a data set composed of baseline RapidMiner workflows described with dataset characteristics used by the given workflow and the learning algorithm used in the given workflow.

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

RISE Atomic Service: Create Account (1)

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 This workflow create an new user account on the RISE server

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

Credits: Jribault

Semantic meta-mining workflow that perform... (1)

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Performs a crossvalidation on a data set composed of meta-data of baseline RapidMiner workflows expressed in RDF with the DMOP's ontology terminology for representing processes. Includes discovery of a set of semantic features (patterns) by the Fr-ONT-Qu algorithm (‘workflow patterns’). Through propositionalisation approach those features may be used in an arbitrary (propositional) RapidMiner classification operator.

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

Filter CME events to events which could ha... (1)

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This workflow uses the initial time period to search for time periods where Earth and Mars are not further appart than 80 degrees. These time periods are used to find Halo CME events. The CME events are forward propagated to Earth and Sun. Only events were the propagation model predicts that both planets are on the propagation path will be included in the final VOTable

Created: 2012-02-29 | Last updated: 2012-02-29

Credits: Anja Le Blanc

Disability estimates by year (1)

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Uses census and health survey for england together with R to estimate disability for districts in the UK

Created: 2012-02-28

Credits: Ian Dunlop

Planning Overview (Scp, Migration, Charact... (1)

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Copies an image from a remote path using scp. Then starts a migration action on the image and extracts properties from the original and migrated image. The properties are compared and on the image data itself, QA algorithms are started.

Created: 2012-02-28

Credits: Markus Plangg

Image Characterisation - Fits (Simple) (1)

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Extracts metadata from images.

Created: 2012-02-27 | Last updated: 2012-02-27

Credits: Markus Plangg