myExperiment - Tags - metabolomics

Workflows (11)

Taverna 1 Original Uploader Egon Willighagen	Download from ChemSpider using Accurate Mass (v2) Created: 26/11/07 @ 17:16:29 \| Last updated: 05/02/08 @ 12:56:12 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 215 times \| Downloaded: 95 times Tags (5): accurate mass \| cheminformatics \| chemspider \| mass spectrometry \| metabolomics	View Download (v2)
Taverna 1 Original Uploader Michael Gerlich	getInchIfromMassBankPeaklist_ChemSpider_workflow_withImage (v2) Created: 05/06/08 @ 16:00:38 \| Last updated: 16/06/08 @ 11:40:46 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 123 times \| Downloaded: 54 times Tags (8): accurate mass \| bioinformatics \| chemspider \| compound info + image \| mass spectrometry \| massbank \| metabolomics \| systems biology	View Download (v2)
Taverna 1 Original Uploader Michael Gerlich	Download from ChemSpider using Accurate Mass revised (v1) Created: 11/06/08 @ 12:13:36 \| Last updated: 11/06/08 @ 12:15:21 Credits: Michael Gerlich Egon Willighagen Attributions: Download from ChemSpider using Accurate Mass License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 94 times \| Downloaded: 42 times Tags (4): accurate mass \| chemspider \| mass spectrometry \| metabolomics	View Download (v1)
Taverna 1 Original Uploader Markf	simple_xcms_pipeline (v1) Created: 14/07/08 @ 15:17:25 \| Last updated: 14/07/08 @ 15:19:02 Credits: Markf License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 73 times \| Downloaded: 39 times Tags (3): metabolomics \| metware \| NBIC	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	MassBank to KEGG (v1) Created: 30/03/09 @ 09:30:32 \| Last updated: 30/03/09 @ 09:49:13 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 193 times \| Downloaded: 0 times Tags (21): bget \| bioinformatics \| chemspider \| compound \| compound info + image \| database \| eutils \| image \| inchi \| information \| mass spectrometry \| massbank \| metabolomics \| ncbi \| pathway \| pccompound \| pubchem \| pug \| search \| summary \| xml	View
Taverna 2 Original Uploader http://...	getTimololFromMassBank (v1) Created: 10/11/09 @ 08:58:05 \| Last updated: 10/11/09 @ 08:59:56 Credits: http://sneumann.pip.verisignlabs.com/ License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 33 times \| Downloaded: 28 times Tags (3): mass spectrometry \| massbank \| metabolomics	View Download (v1)
Bioclipse Scripting Language Original Uploader http://...	In-silico Fragmentation of Naringenin (v2) Created: 08/02/10 @ 12:19:23 Credits: 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: 246 times \| Downloaded: 50 times Tags (3): identification \| mass spectrometry \| metabolomics	View Download (v2)
Taverna 2 Original Uploader Ishtiaq AHMAD	Warp2D - 2D Time Alignment Workflow (v3) Created: 20/05/10 @ 18:46:07 \| Last updated: 22/11/10 @ 10:32:03 Credits: Ishtiaq AHMAD License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 31 times \| Downloaded: 9 times Tags (19): 2d time alignment \| daf \| data \| data analysis framework \| download file \| metabolomics \| nbpp \| nbpp.nl \| netherlands bioinformatics \| netherlands bioinformatics for proteomics \| netherlands bioinformatics for proteomics platform (nbpp) \| peak list \| peaklist \| peaks \| proteomics \| proteomics platform \| time alignment \| upload file \| warp2d	View Download (v3)
Taverna 2 Original Uploader Kalai	Generate Atom Signatures of molecules given SDF as input (v1) Created: 13/05/11 @ 17:14:06 \| Last updated: 13/05/11 @ 19:47:24 Credits: Kalai License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 28 times \| Downloaded: 9 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| synthetic \| taverna 2 \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Scoring small molecules for metabolite likeness/ Natural product likeness (v1) Created: 13/05/11 @ 17:22:28 \| Last updated: 13/05/11 @ 17:26:17 Credits: Kalai 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 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 structural data SM_file:... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 8 times Tags (22): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| re-use \| structure \| synthetic \| workflow \| workflows	View Download (v1)
Taverna 2 Original Uploader Kalai	Plotting distribution of natural product likeness scores (v1) Created: 13/05/11 @ 17:34:58 \| Last updated: 13/05/11 @ 17:35:08 Credits: Kalai 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 8 times Tags (24): bioinformatics \| cdk \| cdk-taverna \| chemoinformatics \| compound \| curation \| drug \| ebi \| example \| filter \| filtering \| metabolism \| metabolite-likeness \| metabolomics \| natural \| open science \| open source \| plot \| re-use \| structure \| synthetic \| taverna2 \| workflow \| workflows	View Download (v1)

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Creator:

Kalai

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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Uploader:

Marie Brown

Automated Workflows for Accurate Mass-based Putative Metabolite Identification in LC/MS-derived Metabolomic Datasets

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

Credits: 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...

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Items tagged with "metabolomics" (13)