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Items tagged with "file" (11)

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Workflows (10)

Taverna 1 Original Uploader Paul Fisher	HUMAN Microarray CEL file to candidate pathways (v4) Created: 03/10/07 @ 18:35:55 \| Last updated: 26/11/09 @ 17:34:24 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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 returned 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 (2 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1216 times \| Downloaded: 359 times Tags (12): affymetrix \| cel \| file \| genotype \| kegg \| microarray \| nbiconworkflows \| pathway-driven \| pathways \| phenotype \| shim	View Download (v4)
Taverna 1 Original Uploader Paul Fisher	Mouse Microarray Analysis (v3) Created: 03/10/07 @ 18:36:05 \| Last updated: 03/12/09 @ 16:20:33 License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. Example ids from the Mouse430_2 affymetrix array are as follows (newline separated): 1447227_at 1440624_at 1436240_at 1454904_at 1435665_at 1418148_at 1429831_at Rating: 5.0 / 5 (1 rating) \| Versions: 3 \| Reviews: 0 \| Comments: 1 \| Citations: 1 Viewed: 490 times \| Downloaded: 127 times Tags (18): affmetrix \| cel \| data-driven \| disease \| expression \| file \| gene \| genotype \| kegg \| microarray \| mouse \| nbiconworkflows \| pathway-driven \| phenotype \| RNA \| shim \| uniprot	View Download (v3)
Taverna 1 Original Uploader Wassinki	AppendToFile (v2) Created: 11/11/08 @ 15:11:38 \| Last updated: 11/11/08 @ 15:14:43 Credits: Wassinki License: Creative Commons Attribution-Share Alike 3.0 Unported License Processor to add content to a (existing) file. The content is added to the end of the file. The inputs: Filename: the file name of a file, if the file does not exists, a new file is added Content: the string to append NewLine [default = true]: if true, a newline is added to the end of the line (useful if you want to add a record each time) The processor supports Multi-Threading since version 2. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 73 times \| Downloaded: 36 times Tags (4): append \| basic \| file \| processors	View Download (v2)
Taverna 1 Original Uploader Jumblej...	fetch_fasta (v1) Created: 20/03/09 @ 11:22:45 \| Last updated: 20/03/09 @ 11:29:16 Credits: Jumblejumble License: Creative Commons Attribution-Share Alike 3.0 Unported License This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 155 times \| Downloaded: 71 times Tags (11): alignment \| beanshell \| blastall \| database \| FASTA \| fetch \| file \| list \| strings \| text \| tree	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Tab Parser (v1) Created: 19/08/09 @ 16:05:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 1 time Tags (12): concept \| file \| gene \| line \| ondex \| ovtk \| oxl \| parser \| protein \| tab \| table \| taxonomy	View
Bioclipse Scripting Language Original Uploader Egon Willighagen	Download CAS numbers and save as SD file (v1) Created: 15/10/09 @ 09:05:39 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 62 times \| Downloaded: 44 times Tags (5): bioclipse \| cas_number \| cheminformatics \| file \| services	View Download (v1)
Taverna 1 Original Uploader trybik	Transform XML with parameters (v1) Created: 29/11/10 @ 11:45:52 \| Last updated: 29/11/10 @ 11:53:46 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Similar to Transform_XML local widget but accepts transformation parameters and skips the part with writing to the output file. The essence, i.e. Transform_XML beanshell works with Strings representing file contents, not with file URLs. The XML transfomation parameters are given as a list of strings in the "param_name = param_value" format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 14 times Tags (6): beanshell \| file \| transform \| xml \| xsl \| xslt	View Download (v1)
Taverna 2 Original Uploader Kalai	Download Structures from PubChem given chemical names (v1) Created: 24/05/11 @ 13:13:52 \| Last updated: 24/05/11 @ 14:19:24 Credits: Kalai Michael Gerlich Attributions: Download Entries from PubChem License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned. The pubchem compound_ID is then used to download structures from PubChem. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 12 times Tags (26): bioinformatics \| cheminformatics \| compound \| data \| download file \| esearch \| eutils \| file \| list \| ncbi \| open science \| open source \| pccompound \| split \| string \| structure \| structure retrieval \| synthetic \| taverna 2 \| taverna2 \| url2list \| workflow \| workflows \| wsdl \| xml \| xpath	View Download (v1)
Taverna 2 Original Uploader Harvey	Convert GML to SVG (v1) Created: 31/08/11 @ 12:06:27 \| Last updated: 31/08/11 @ 12:06:31 Credits: Harvey License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow can convert the GML (Geography Markup Language) file to SVG image. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 13 times Tags (8): convert \| file \| genesi \| gml \| gml2svg \| pywps \| svg \| workflow	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Merge list of errors to string (v2) Created: 13/09/11 @ 14:04:50 \| Last updated: 13/09/11 @ 14:16:05 License: Creative Commons Attribution-Share Alike 3.0 Unported License Based on http://myexperiment.elda.org/workflows/27/ The beanshell scripts collectively builds a temporary file of the merged string (by default using newline as separator). As each item is appended to the file separately by Write_text_append, this means it can handle occassional errors in the list, such as in the output from Sometimes_fails. Such items are not included in the merged string. To use, merge with your workflow and delete "Create_Lots_if_Strings", "Sometimes_Fai... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1 time \| Downloaded: 2 times Tags (5): beanshell \| error \| file \| handling \| list	View Download (v2)