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Network-member myExperimentBeanshellCollection

Unique name: myExperimentBeanshellCollection Created: Thursday 06 March 2008 @ 11:41:29 (GMT)

Group for development, curation and maintenance of collections of generic Beanshell processors. Join this group if you have some cool Beanshells that you want to share! Please add your Beanshells to the myExperimentBeanshellCollection workflow and don't create new workflows for this purpose. (It's not fun to load dozens of workflows manually to load a fragmented collection of Beanshells.) If t...

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Workflow HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Updated: 04/04/08 @ 12:14:20

License: Creative Commons Attribution-NoDerivs 3.0 License

Microarray_cel_file_to_candidate_pathways_17032_4
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Rating: 5.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1365 times | Downloaded: 1293 times

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Workflow Mouse Pathways and Gene annotations for QTL Phenotype (v3)

Created: 03/10/07 @ 18:36:02 | Updated: 20/02/08 @ 16:05:44

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_and_gene_annotations_for_qtl_phenotype_28303_3
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Rating: 4.5 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 1

Viewed: 1133 times | Downloaded: 1161 times

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Workflow Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_from_diff_expressed_genes_22895_3
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

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

Viewed: 874 times | Downloaded: 799 times

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Workflow Entrez Gene to KEGG Pathway (v2)

Created: 03/10/07 @ 18:36:00 | Updated: 13/11/07 @ 16:16:10

License: Creative Commons Attribution 3.0 License

Entrez_gene_to_kegg_pathway_7493
This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Rating: 4.7 / 5 (3 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1260 times | Downloaded: 756 times

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Workflow Remove null values (v2)

Created: 03/10/07 @ 18:36:05 | Updated: 13/11/07 @ 16:20:42

License: Creative Commons Attribution-NoDerivs 3.0 License

Remove_null_values_27982
This workflow removes any null values from a list of strings

Rating: 4.0 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 571 times | Downloaded: 455 times

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Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Updated: 14/05/08 @ 15:43:16

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

Microarray_cel_file_to_candidate_pathways_1844_2
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 598 times | Downloaded: 1 time

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Workflow Human Pathways from Diff Expressed Genes (v1)

Created: 08/02/08 @ 14:30:17 | Updated: 08/02/08 @ 14:30:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Human_pathways_from_diff_expressed_genes_4391_1
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 433 times | Downloaded: 5 times

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Workflow GBSeq test (v2)

Created: 05/03/08 @ 14:15:35 | Updated: 31/03/08 @ 15:55:09

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 License

Gbseq_test_23328_2
This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 461 times | Downloaded: 314 times

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Workflow myExperimentBeanshellCollection (v2)

Created: 06/03/08 @ 11:46:11 | Updated: 25/03/08 @ 16:23:24

Credits: Network-member myExperimentBeanshellCollection

License: Creative Commons Attribution-Share Alike 3.0 License

Myexperimentbeanshellcollection_24448_2
Public collection of generic Beanshells curated by the myExperimentBeanshellCollection group on myExperiment. Visit http://www.myexperiment.org for details and updates. To use this collection of beanshells in Taverna: * Right click "Available Processors" in the "Design Perspective" * Choose "Add new Workflow scavenger..." * Provide the URL to this beanshell collection on www.myExperiment.org or if you downloaded this to your hard disk, provide a "file" URL to the absolute path of this file ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 400 times | Downloaded: 355 times

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