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Items tagged with "taverna2" (15)
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Created: 04/07/10 @ 18:29:33 | Last updated: 04/07/10 @ 18:29:34
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License: Creative Commons Attribution 3.0 Unported License
Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.
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Created: 04/07/10 @ 18:30:58 | Last updated: 04/07/10 @ 18:31:00
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License: Creative Commons Attribution 3.0 Unported License
Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.
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Created: 04/07/10 @ 18:31:57 | Last updated: 04/07/10 @ 18:31:59
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License: Creative Commons Attribution 3.0 Unported License
A workflow from part of the BioMoby tutorial
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Created: 04/07/10 @ 18:32:58 | Last updated: 04/07/10 @ 18:33:00
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License: Creative Commons Attribution 3.0 Unported License
This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.
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Created: 04/07/10 @ 18:33:54 | Last updated: 04/07/10 @ 18:33:55
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License: Creative Commons Attribution 3.0 Unported License
Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.
InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the sig...
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Created: 04/07/10 @ 18:34:57 | Last updated: 04/07/10 @ 18:34:59
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License: Creative Commons Attribution 3.0 Unported License
Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB
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Created: 04/07/10 @ 18:35:59 | Last updated: 04/07/10 @ 18:36:00
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License: Creative Commons Attribution 3.0 Unported License
Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
Based on the FetchDailyDilbert workflow.
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Created: 04/07/10 @ 18:36:58 | Last updated: 04/07/10 @ 18:37:00
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves nucleotide and protein sequences with the literature and references associated
to them given a protein and a nucleotide id.
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Created: 04/07/10 @ 18:37:58 | Last updated: 04/07/10 @ 18:38:00
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License: Creative Commons Attribution 3.0 Unported License
Perform multiple iterations of services in order to show pipelining
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Created: 04/07/10 @ 18:39:07 | Last updated: 04/07/10 @ 18:39:09
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License: Creative Commons Attribution 3.0 Unported License
This workflow retrieves a sequence associated with its features in embl format
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Created: 13/07/10 @ 12:50:54 | Last updated: 13/07/10 @ 12:50:55
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License: Creative Commons Attribution 3.0 Unported License
Example using the SpreadsheetImport service to import data from an Excel spreadsheet.
The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date.
The source data is from http://data.gov.uk/
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Created: 26/11/10 @ 15:13:46 | Last updated: 26/11/10 @ 15:13:48
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License: Creative Commons Attribution 3.0 Unported License
This workflow uses an R service running on localhost to calculate sin(0.45)
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Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Prerequisite:
CDK -Taverna Plugin 0.5.1
http://www.ts-concepts.de/cdk-taverna2/plugin/
- To run this workflow you need a Score file which is written to text file.
- This could be generated from ScorerActivity.t2flow
http://www.myexperiment.org/workflows/2121/download?version=1
Description of input ports :
score_file: Path to file name that has pre computed scores.
Note:
While passing file as input it could be passed as list of many files or single fi...
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Created: 24/05/11 @ 13:13:52 | Last updated: 24/05/11 @ 14:19:24
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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.
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Created: 13/05/11 @ 19:35:39 | Last updated: 29/08/11 @ 14:25:47
Reference:
Natural Product-likeness Score and Its Application for Prioritization of Compound
Libraries
Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer
Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf
The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...
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