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Items tagged with "metabolomics" (13)

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Blob Automated Workflows for Accurate Mass-based Putative...

Created: 03/03/11 @ 15:27:04 | Last updated: 03/03/11 @ 15:27:07

Credits: User Marie Brown

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Three workflows, together defined as PUTMEDID-LCMS, have been developed using the open source Taverna environment to perform putative metabolite identification based on accurate mass data acquired from liquid chromatography-electrospray mass spectrometry instruments. Three workflows perform the following steps. (Step 1) Generation of a list of pairwise peak correlations required for input to workflow 2 (workflow 1) (Step 2) Annotation of features to group different ion types of the same metab...

File type: application/x-zip-compressed

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 45 times | Downloaded: 24 times

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Workflows (11)
Original Uploader

Workflow getInchIfromMassBankPeaklist_ChemSpider_wo... (2)

Created: 05/06/08 @ 16:00:38 | Last updated: 16/06/08 @ 11:40:46

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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uses InChI's retrieved from a MassBank peaklist query to get compound information about those compounds via querying ChemSpider for information and displaying those results with image

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

Viewed: 137 times | Downloaded: 80 times

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Original Uploader

Workflow Download from ChemSpider using Accurate Ma... (1)

Created: 11/06/08 @ 12:13:36 | Last updated: 11/06/08 @ 12:15:21

Credits: User Michael Gerlich User Egon Willighagen

Attributions: Workflow Download from ChemSpider using Accurate Mass

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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updated version of Download from ChemSpider using Accurate Mass to make use of the new ChemSpider services

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

Viewed: 105 times | Downloaded: 46 times

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Original Uploader

Workflow simple_xcms_pipeline (1)

Created: 14/07/08 @ 15:17:25 | Last updated: 14/07/08 @ 15:19:02

Credits: User Markf

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A (very) simple demo pipeline that takes an experiment ID, gets the data from the (currently in beta) metware metabolomics datawarehouse and runs XCMS.

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

Viewed: 94 times | Downloaded: 51 times

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Original Uploader

Workflow MassBank to KEGG (1)

Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

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

Viewed: 215 times | Downloaded: 0 times

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Original Uploader

Workflow getTimololFromMassBank (1)

Created: 10/11/09 @ 08:58:05 | Last updated: 10/11/09 @ 08:59:56

Credits: User http://sneumann.pip.verisignlabs.com/

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow will retrieve a peaklist from a fixed entry (Timolol) from the MassBank spectral library. Note, the API is still in alpha, as of 10.11.2009.  

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

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Workflow In-silico Fragmentation of Naringenin (2)

Created: 08/02/10 @ 12:19:23

Credits: User http://sneumann.pip.verisignlabs.com/

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the equivalent of the MetFrag Interface found on http://msbi.ipb-halle.de/MetFrag/ It takes a Speclipse Spectrum and a Bioclipse Molecule and runs MetFrag.  

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 288 times | Downloaded: 64 times

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Original Uploader

Workflow Warp2D - 2D Time Alignment Workflow (3)

Created: 20/05/10 @ 18:46:07 | Last updated: 22/11/10 @ 10:32:03

Credits: User Ishtiaq AHMAD

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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2D Time Alignment We describe a new time alignment method that takes advantage of both dimensions of LC-MS data to resolve ambiguities in peak matching while remaining computationally efficient. This approach, Warp2D, combines peak extraction with a two-dimensional correlation function to provide a reliable alignment scoring function that is insensitive to spurious peaks and background noise. One-dimensional alignment methods are often based on the total-ion-current eluti...

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

Viewed: 56 times | Downloaded: 17 times

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Original Uploader

Workflow Generate Atom Signatures of molecules give... (1)

Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 is re...

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

Viewed: 65 times | Downloaded: 26 times

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Original Uploader

Workflow Scoring small molecules for metabolite lik... (2)

Created: 13/05/11 @ 17:22:28 | Last updated: 18/03/12 @ 16:41:39

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

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

Viewed: 85 times | Downloaded: 23 times

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Original Uploader

Workflow Plotting distribution of natural product l... (1)

Created: 13/05/11 @ 17:34:58 | Last updated: 13/05/11 @ 17:35:08

Credits: User Kalai

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 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...

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

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Pack Natural product likeness filter


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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