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User: Pieter Neerincx
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Name: Pieter Neerincx Joined: Monday 25 February 2008 @ 12:55:28 (GMT) Last seen: Friday 18 September 2009 @ 14:07:28 (GMT) Email (public): Not specified Website: Not specified Location: Wageningen, Netherlands |
Pieter Neerincx has been credited 8 times Pieter Neerincx has an average rating of: 5.0 / 5 (1 rating in total) for their items |
I have added my ‘abstract’ for the NBIC workshop ‘NBIC on workflows’ as a blog: http://www.myexperiment.org/blogs/26
Other contact details:
Not specifiedInterests:
BioMoby web services
Taverna
Micro array probe design & annotation
Genome annotation
Text mining & data mining in general
Field/Industry: Biology
Occupation/Role(s): PhD student
Organisation(s):
Wageningen University & Research centre
Laboratory of Bioinformatics
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Workflow
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Original Uploader |
Created: 06/05/09 @ 08:49:59 | Last updated: 06/05/09 @ 08:50:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site
The amount of services used
The amount of local processors used
The amount of scripting tasks
The amount of sub workflows
Furthermore it classifies the local services based on their intended function.
The workflow has two inputs: ...
Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 163 times | Downloaded: 62 times Tags (9): |
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Workflow
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Created: 13/02/09 @ 09:05:35 | Last updated: 13/02/09 @ 09:08:20
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Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Version info
The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our
case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes.
...
Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 556 times | Downloaded: 105 times Tags (7): |
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Workflow
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Original Uploader |
Created: 16/02/09 @ 16:32:36 | Last updated: 16/02/09 @ 16:42:10
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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 linking to CEL files.
The User object contains a user ID, a password and an ...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 211 times | Downloaded: 90 times Tags (6): |
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Workflow
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Original Uploader |
Created: 13/03/08 @ 14:38:03 | Last updated: 16/02/09 @ 16:41:29
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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 linking to CEL files.
The User object contains a u...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 2 | Citations: 0 Viewed: 186 times | Downloaded: 58 times Tags (6): |
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Workflow
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Original Uploader |
Created: 27/02/08 @ 00:43:33 | Last updated: 03/03/08 @ 22:11:50
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 113 times | Downloaded: 38 times Tags (4): |
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Workflow
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Original Uploader |
Created: 27/02/08 @ 00:46:22 | Last updated: 03/03/08 @ 22:11:17
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 68 times | Downloaded: 33 times Tags (4): |
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Workflow
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Original Uploader |
Created: 27/02/08 @ 00:48:39 | Last updated: 03/03/08 @ 22:10:54
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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 ...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 62 times | Downloaded: 33 times Tags (5): |
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Workflow
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Original Uploader |
Created: 27/02/08 @ 00:49:44 | Last updated: 03/03/08 @ 22:08:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported 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...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 89 times | Downloaded: 42 times Tags (5): |
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