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Items tagged with "graph" (42)

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Network-member ONDEX Graphs

Unique name: ONDEX
Created: Tuesday 10 February 2009 @ 10:45:09 (GMT)

A group for sharing ONDEX graphs in oxl format http://ondex.sourceforge.net/ http://www.ondex.org/  

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Files (2)
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Blob Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

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Blob Ondex Workflows

Created: 01/09/11 @ 17:17:57 | Last updated: 01/09/11 @ 17:18:05

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains a large number of Taverna 2 workflows that utilise the Ondex Web Service, for manipulating Ondex graphs.

File type: ZIP archive

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Workflows (39)
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Workflow Get Concepts (1)

Created: 27/02/09 @ 16:33:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets all the concepts in an Ondex graph, using a given graph id

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Workflow Get CVs (1)

Created: 27/02/09 @ 16:38:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow lets users retrive all controlled vocabularies for a given Ondex graph

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Workflow Get Evidence Types (1)

Created: 27/02/09 @ 16:40:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets all the evidence types within a specified Ondex graph

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Workflow Get graphs (2)

Created: 05/11/09 @ 12:38:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)

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Workflow Get Graphs of Name (1)

Created: 27/02/09 @ 16:42:35

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets the Ondex graphs relating to a specified name

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Workflow Get relations (1)

Created: 27/02/09 @ 16:45:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets all the realtions from a given Ondex graph

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Viewed: 19 times | Downloaded: 14 times

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Workflow All Pairs Filter (1)

Created: 19/08/09 @ 16:06:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph based on the occurrence of directed edges within the graph. Only those concepts that have directional edges are returned to the user, in the form of a new graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. GdsWeight - The name of the GDS type to ...

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Workflow Clean GO Filter (1)

Created: 19/08/09 @ 16:07:27

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph.

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Workflow Clean UniProt Filter (1)

Created: 19/08/09 @ 16:08:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph, removing any erroneous UniProt data. The result is a new Ondex graph that conatains only connected UniProt data. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph.

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Workflow Concept Class Filter (1)

Created: 19/08/09 @ 16:10:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a Ondex graph based on a specific concept class. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to filter out. RefactorTrinaries - Where the qualifier of a trinary relation is out of scope create a bina...

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Workflow Concept Class Neighbours Filter (1)

Created: 19/08/09 @ 16:11:56

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph based on a user defined concept class. The neighbours of the concept class are returned as a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to. ConceptClass - The Conce...

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Workflow Context Consensus Filter (1)

Created: 19/08/09 @ 16:13:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to a consensus with regards to a specific context (concept list). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Threshold - Double value representing the share of contexts that qualify a graph element for ...

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Workflow Context Filter (1)

Created: 19/08/09 @ 16:14:13

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters an Ondex graph according to a given context. The result is a new Ondex graph with only selected contexts. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context that starts the path. ContextBoolean - Defines two ContextIDs and a boolean operati...

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Workflow CV Filter (1)

Created: 19/08/09 @ 16:15:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to a controlled vocabulary specified by the user. The result is a new Ondex graph with only those concepts that passed the filter. The parameters that can be used with this service graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. CV - A CV to include/exclude Concepts and Relations of (see Exclude param). R...

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Workflow Evidence Type Filter (1)

Created: 19/08/09 @ 16:16:15

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to some user defined evidence values. The result is a new Ondex graph. The parameters that can be used with this web service are given below: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. EvidenceType - EvidenceType to be taken into consideration. RefactorTrinaries - Where the qualifier of a trinary rel...

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Workflow GDS Value Filter (1)

Created: 19/08/09 @ 16:17:27

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph based on a given GDS value supplied by the user. The result is a new Ondex graph with filtered content. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. AttributeName - AttributeName to filter out. GDSValue - A value which will be matched against the ...

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Workflow Genomic Filter (1)

Created: 19/08/09 @ 16:19:01

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

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Workflow Graph Cloner (1)

Created: 19/08/09 @ 16:22:13

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow clones a given Ondex Graph, based on an Ondex Graph identifier.

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Workflow Isolate Clusters Filter (1)

Created: 19/08/09 @ 16:23:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph, isolating clusters within the graph and returning only those clusters as a new graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to be contained in clusters.

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Workflow One Pair Shortest Path Filter (1)

Created: 19/08/09 @ 16:24:41

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a pre-existing Ondex graph using the shortest path algorithm on the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path EndConceptID - The Concept ID that ends the path UseWeights -...

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Viewed: 16 times | Downloaded: 1 time

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Workflow Optimal Paths Filter (1)

Created: 19/08/09 @ 16:25:49

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph based on the optimal path between one or more concepts. The result is a new Ondex graph. The parameters that can be used with service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. PathwayDefinition - pathway definition file. StatisticsOutputDir - The directory to output statistics (Optional). Incl...

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Workflow Pfam Based Ortholog Filter (1)

Created: 19/08/09 @ 16:26:55

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

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Workflow Relation Neighbours Filter (1)

Created: 19/08/09 @ 16:28:09

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph based on some neighbour parameters supplied by the user. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to ConceptID - The Concept ID to seed th...

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Workflow Relation Type Filter (1)

Created: 19/08/09 @ 16:29:10

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a pre-existing ONdex graph based on a some paramters provided by the user. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional) parameter. If no output graph is specified filtered items will be removed from the input graph. TargetRelationType - Target RelationType to filter out. ConceptClassRestriction - Concept Class Restriction as ordered pair representing from/to C...

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Workflow Shortest Path (1)

Created: 19/08/09 @ 16:30:35

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to the shortest path (graph) algorithm. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path. Valid value range is 1 to 2147483647. UseWeights - Use gds values as edge ...

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Workflow Significance Filter (1)

Created: 19/08/09 @ 16:31:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph according to a level of significance set by the user. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetAttributeName - Target AttributeName to filter for significance. Significance - A significance value to filter relatio...

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Workflow SubGraph Filter (2)

Created: 19/08/09 @ 16:38:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters a given Ondex graph to return a new ondex sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. ConceptID - The root concept to start at. Valid value range is 1 to 2147483647. FirstRelationType - RelationType limitation for depth 1 (Optional). FirstConceptClass - C...

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Workflow Tranitive Filter (1)

Created: 19/08/09 @ 16:34:16

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters an Ondex graph to extract a sub-graph. The result is a new Ondex graph containing only the transitive sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. CV - Seed cv that will be used to extract the subgraph (Optional). AttributeName - Seed attribute name that will be us...

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Workflow Unconnected Filter (1)

Created: 19/08/09 @ 16:35:08

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow removes any unconnected nodes from a given Ondex graph through filtering, and returns a new Ondex Graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. RemoveContextDependencies - Set true to remove context dependencies, otherwise unconnected concepts will still remain in the ...

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Workflow Construction of skeleton SBML model using ... (1)

Created: 26/03/10 @ 17:08:13 | Last updated: 26/03/10 @ 17:13:15

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers

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Workflow Construction of skeleton SBML model using ... (1)

Created: 26/03/10 @ 17:11:26 | Last updated: 26/03/10 @ 17:12:06

Credits: User Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term.

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Workflow mathPlot Web service (1)

Created: 26/01/11 @ 22:03:56 | Last updated: 26/01/11 @ 22:04:31

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Plotting operation which uses Mathematica (http://www.wolfram.com/mathematica/) software.

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Workflow [deprecated] Simulate SBML-derived ODEs (1)

Created: 26/01/11 @ 22:10:31 | Last updated: 20/07/11 @ 14:05:59

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2264.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.

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Workflow [deprecated] Probabilistic Model Checking ... (1)

Created: 26/01/11 @ 22:17:00 | Last updated: 20/07/11 @ 14:23:03

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2267 . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/1790).

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Workflow Simulate SBML-derived ODEs (2)

Created: 20/07/11 @ 13:57:19 | Last updated: 20/07/11 @ 14:02:43

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.

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Workflow Probabilistic Model Checking (PMC): plot r... (1)

Created: 20/07/11 @ 14:18:19 | Last updated: 20/07/11 @ 14:21:27

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/2266).

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Viewed: 19 times | Downloaded: 6 times

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Workflow Fertilzer Use Ist 600 (1)

Created: 21/09/11 @ 08:52:43 | Last updated: 21/09/11 @ 08:52:41

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilzerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment.org/files/568/download/FertilizerUse.xls. Based on the water use workflow by David Withers

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Workflow Broccoli production comparisons in NY and ... (1)

Created: 21/09/11 @ 15:23:11 | Last updated: 21/09/11 @ 15:23:08

Credits: User Gstalloch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilzerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment.org/files/568/download/FertilizerUse.xls. Based on the water use workflow by David Withers

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Workflow [untitled] (2)

Created: 27/11/11 @ 23:05:31 | Last updated: 27/11/11 @ 23:10:52

Credits: User Kayleigh Ayn Bohémier

Attributions: Workflow Spreadsheet Import Example Workflow Broccoli: A State Comparison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is a workflow for a Cyberinfrastructure class (Fall 2011) at Syracuse University. It takes information from GapMinder and runs it through a workflow to produce a graph. The original data sets can be found here: https://spreadsheets.google.com/pub?key=pyj6tScZqmEdrsBnj2ROXAg&gid=0 (Literacy rate, adult total) https://spreadsheets.google.com/pub?key=pyj6tScZqmEdIyrBS31XAaw&gid=0 (Income share of poorest 20%)

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