User: Pieter Neerincx

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Wassinki

Mapping OligoNucleotides to an assembly (v3)

Created: 11/12/08 @ 12:11:59 | Last updated: 19/12/08 @ 09:41:14

Credits: Wassinki Pieter Neerincx

Attributions: Blat against ENSEMBLE Danio_rerio_Genome Blat or Blast against ENSEMBLE Danio_rerio_Genome Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly

License: Creative Commons Attribution-Share Alike 3.0 License

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Pieter Neerincx

AffyArrayNormalization (v1)

Created: 13/03/08 @ 14:47:40

Credits: Pieter Neerincx Philipg

License: Creative Commons Attribution-Share Alike 3.0 License

The AffyArrayNormalization web services normalise raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's normalization R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayNormalization services. The flow is as follows: * A client executes the AffyArrayNormalization_submit service with two inputs: a User object and a collection of URLs to CEL files. * The User object contains a user ID, a password and an e-mail address....

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Pieter Neerincx

AffyArrayQualityAnalysis (v2)

Created: 13/03/08 @ 14:38:03 | Last updated: 13/03/08 @ 14:40:37

Credits: Pieter Neerincx Philipg

License: Creative Commons Attribution-Share Alike 3.0 License

The AffyArrayQualityAnalysis web services provide quality control for raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's quality control R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayQualityAnalysis services. The flow is as follows: * A client executes the AffyArrayQualityAnalysis_submit service with two inputs: a User object and a collection of URLs to CEL files. * The User object contains a user ID, a passw...

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Pieter Neerincx

GeneIlluminator_Disambiguate (v2)

Created: 27/02/08 @ 00:43:33 | Last updated: 03/03/08 @ 22:11:52

Credits: Pieter Neerincx Alako

License: Creative Commons Attribution-Share Alike 3.0 License

Example workflow demonstrating how to use GeneIlluminator_Disambiguate, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (This is the same output as the one from the GeneIlluminator_GetClusters service.) In addition this service takes an Organi...

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Pieter Neerincx

GeneIlluminator_GetClusters (v2)

Created: 27/02/08 @ 00:46:22 | Last updated: 03/03/08 @ 22:11:18

Credits: Pieter Neerincx Alako

License: Creative Commons Attribution-Share Alike 3.0 License

Example workflow demonstrating how to use GeneIlluminator_GetClusters, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (Use GeneIlluminator_GetGraph for a graphical representation of the clusters or GeneIlluminator_Disambiguate to get the mos...

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Pieter Neerincx

GeneIlluminator_GetGraph (v2)

Created: 27/02/08 @ 00:48:40 | Last updated: 03/03/08 @ 22:10:55

Credits: Pieter Neerincx Alako

License: Creative Commons Attribution-Share Alike 3.0 License

Example workflow demonstrating how to use GeneIlluminator_GetGraph, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, a graphical overview of the clusters and gene symbols is created in SVG format and returned to ...

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Pieter Neerincx

GeneIlluminator_GetPubMedQuery (v2)

Created: 27/02/08 @ 00:49:45 | Last updated: 03/03/08 @ 22:08:42

Credits: Pieter Neerincx Alako

License: Creative Commons Attribution-Share Alike 3.0 License

Example workflow demonstrating how to use GeneIlluminator_GetPubMedQuery, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, using the cluster characteristics it creates a boolean PubMed query that could be used to...

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