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Items tagged with "filter" (36)

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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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Workflows (34)
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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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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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Original Uploader

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 Split text/string into its lines and filte... (1)

Created: 19/08/09 @ 17:23:13

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 Unported License

When retrieving a URL or soemthing alike, one can often identify the region of interest as a single line. Besides the expected output, also some interim values, like the lines split are forwarded, to allow some straight-forward cascading of filters with reduced redundancy.

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Workflow find events in xray and radio (7)

Created: 16/03/10 @ 15:07:39 | Last updated: 16/03/10 @ 15:19:30

Credits: User Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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instruments: hessiEC, phoenix2 attention: hessi name has changed!

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Workflow Extracting data from VOTable format by usi... (1)

Created: 01/07/10 @ 14:01:03 | Last updated: 01/07/10 @ 14:01:04

Credits: User Anja Le Blanc User Donal Fellows

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Input VOTable and 'name' of a Output corrosponding data of that field in an arrayInput VOTable and 'name' of a Field

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Workflow Change Class Distribution of Your Training... (1)

Created: 21/01/11 @ 14:57:11 | Last updated: 21/01/11 @ 14:57:12

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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This example process shows how to change the class distribution of your training data set (in this case the training data is what ever comes out of the "myData reader"). The given training set has a distribution of 10 "Iris-setosa" examples, 40 "Iris-versicolor" examples and 50 "Iris-virginica" examples. The aim is to get a data set which has the class distribution for the label, lets say 10 "Iris-setosa", 20 "Iris-versicolor" and 20 "Iris-virginica. Beware that this may change some propert...

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Workflow Extract content of columns from VOTables (3)

Created: 24/02/11 @ 10:19:41 | Last updated: 20/08/12 @ 12:51:13

Credits: User Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Extracts all values from all columns which are passed from the input ColumnNames

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Generate Atom Signatures of molecules give... (1)

Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

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Workflow Scoring small molecules for metabolite lik... (2)

Created: 13/05/11 @ 17:22:28 | Last updated: 18/03/12 @ 16:41:39

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

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Workflow Plotting distribution of natural product l... (1)

Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

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Workflow date filter for ice Class Map service (NERSC) (1)

Created: 02/11/11 @ 10:05:35 | Last updated: 04/11/11 @ 10:27:00

Credits: User Jorgejesus

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Workflow to filter available dates with ice classification images. Service provided by NERCS. Dates are filtered using a simple regular expression

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Workflow Find periods of time where two ILS objects... (2)

Created: 04/11/11 @ 15:47:11 | Last updated: 18/11/11 @ 14:58:19

Credits: User Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Inputs: name of target_obj of ILS of two objects and a number of degrees which these obejcts are allowed to be appart in hci longitude coordinates. Output VOTable of time periods where these two objects are closer than +/- input angle together.

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

Created: 16/03/12 @ 15:45:57 | Last updated: 16/03/12 @ 15:55:59

Credits: User Anja Le Blanc

Attributions: Workflow Available instruments through DPAS Workflow Split VOTable into its values

License: BSD License

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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.

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Pack Natural product likeness filter


Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

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