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Workflow What's On Next (v1)

Created: 28/08/08 @ 15:23:58 | Updated: 28/08/08 @ 15:27:48

Credits: User Sean Bechhofer

License: Creative Commons Attribution-Share Alike 3.0 License

What_s_on_next_18085_1
Queries the BBC to find out what's on next for a particular channel.

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

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Workflow Unique tags (v1)

Created: 27/08/08 @ 19:43:42 | Updated: 27/08/08 @ 19:43:42

Credits: User hong harper

License: Creative Commons Attribution-Share Alike 3.0 License

Unique_tags_31959_1
This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".

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Workflow missingOutputSplitter (v1)

Created: 27/08/08 @ 10:40:08 | Updated: 27/08/08 @ 10:40:08

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 License

Missingoutputsplitter_17044_1
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Workflow Retrieve Single Molecule from ZINC - structure and figure (v1)

Created: 24/08/08 @ 22:52:25 | Updated: 25/08/08 @ 21:57:16

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieve_single_molecule_from_zinc_-_structure_and_figure_19577_1
The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds. With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data inst...

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Workflow mustang provides structural alignment of two proteins (v3)

Created: 20/08/08 @ 14:41:21 | Updated: 25/08/08 @ 15:40:45

Credits: User Steffen Möller

Attributions: Workflow Fetch PDB flatfile from RCSB server

License: Creative Commons Attribution-Share Alike 3.0 License

Mustang_provides_structural_alignment_of_two_proteins_3114_3
This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Data Set Metadata Generator (v1)

Created: 19/08/08 @ 21:17:14 | Updated: 19/08/08 @ 21:25:53

Credits: User Andrea Wiggins

License: Creative Commons Attribution-Share Alike 3.0 License

Data_set_metadata_generator_24594_1
This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

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Workflow What's On Next (v1)

Created: 28/08/08 @ 15:23:58 | Updated: 28/08/08 @ 15:27:48

Credits: User Sean Bechhofer

License: Creative Commons Attribution-Share Alike 3.0 License

What_s_on_next_18085_1
Queries the BBC to find out what's on next for a particular channel.

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

Viewed: 8 times | Downloaded: 4 times

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Workflow Unique tags (v1)

Created: 27/08/08 @ 19:43:42 | Updated: 27/08/08 @ 19:43:42

Credits: User hong harper

License: Creative Commons Attribution-Share Alike 3.0 License

Unique_tags_31959_1
This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".

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

Viewed: 14 times | Downloaded: 9 times

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Workflow missingOutputSplitter (v1)

Created: 27/08/08 @ 10:40:08 | Updated: 27/08/08 @ 10:40:08

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 License

Missingoutputsplitter_17044_1
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Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Retrieve Single Molecule from ZINC - structure and figure (v1)

Created: 24/08/08 @ 22:52:25 | Updated: 25/08/08 @ 21:57:16

Credits: User Steffen Möller

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieve_single_molecule_from_zinc_-_structure_and_figure_19577_1
The ZINC database (http;//zinc.docking.org) is a collection of substances with known structures and some chemical characterisation that are commercially available. It is freely available and a much respected resource for computational screening for functional compounds. With the ZINC ID at hand, the ZINC web site is contacted and from there the URL parsed the refence to the real data. This workflow does not scale for regular docking applications. One would retrieve a collection of data inst...

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

Viewed: 38 times | Downloaded: 16 times

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Workflow mustang provides structural alignment of two proteins (v3)

Created: 20/08/08 @ 14:41:21 | Updated: 25/08/08 @ 15:40:45

Credits: User Steffen Möller

Attributions: Workflow Fetch PDB flatfile from RCSB server

License: Creative Commons Attribution-Share Alike 3.0 License

Mustang_provides_structural_alignment_of_two_proteins_3114_3
This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 74 times | Downloaded: 36 times

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Workflow Data Set Metadata Generator (v1)

Created: 19/08/08 @ 21:17:14 | Updated: 19/08/08 @ 21:25:53

Credits: User Andrea Wiggins

License: Creative Commons Attribution-Share Alike 3.0 License

Data_set_metadata_generator_24594_1
This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

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

Viewed: 44 times | Downloaded: 17 times

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Workflow Perfrom a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Updated: 02/08/08 @ 14:35:11

License: Creative Commons Attribution-NoDerivs 3.0 License

Perfrom_a_text_based_search_through_pubmed_2447_3
This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Rating: 3.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow BioAID_DiseaseDiscovery (v1)

Created: 12/11/07 @ 22:39:04 | Updated: 15/11/07 @ 09:01:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_28978
This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical) 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned; the AIDA service inside is based on Apache Lucene) 3. Discover proteins: extract proteins ...

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

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Workflow QR code (matrix code) generator (v4)

Created: 07/10/07 @ 17:17:03 | Updated: 16/07/08 @ 01:46:13

License: Creative Commons Attribution-Share Alike 3.0 License

Qr_code__matrix_code__generator_23815_4
The latest (and greatest) version of the QR code generator workflow. This workflow uses the QR code service provided by the ChemTools project.

Rating: 1.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 1

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Workflow Download from ChemSpider using Accurate Mass (v2)

Created: 26/11/07 @ 17:16:29 | Updated: 05/02/08 @ 12:56:12

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 License

Download_from_chemspider_using_accurate_mass_17623_2
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Workflow Add Mesh String to Biological Process (v2)

Created: 03/10/07 @ 18:36:28 | Updated: 03/10/07 @ 18:36:28

License: Creative Commons Attribution-NoDerivs 3.0 License

Add_mesh_string_to_biological_process_12549
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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 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

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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 CountListElements (v5)

Created: 17/10/07 @ 14:44:27 | Updated: 17/10/07 @ 16:13:54

License: Creative Commons Attribution-NoDerivs 3.0 License

Countlistelements_6480
Very simple workflow to count the number of items in a list (top level only in case of nested lists). Does no more than count = list.size();

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

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Workflow Translate Nucleotide sequence into Peptide sequence (v2)

Created: 03/10/07 @ 18:36:27 | Updated: 03/10/07 @ 18:36:27

License: Creative Commons Attribution-NoDerivs 3.0 License

Setp2_12504
Translate Nucleotide sequence into Peptide sequence using EBI Service. 1. Find nucleotide sequence from EBI wsdbfetch(using ref.seq Id NM_005700) 2. Translation nucleotide sequence(from 1) into peptide sequence using EBI EMBOSS4 transeq.

Rating: 2.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Gene annotation pipeline for the Graves disease scenario (v2)

Created: 03/10/07 @ 18:36:09 | Updated: 22/11/07 @ 16:03:15

Credits: User Katy Wolstencroft User Peter Li

License: Creative Commons Attribution-NoDerivs 3.0 License

Gene_annotation_pipeline_for_the_graves_disease_scenario_19721
This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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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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