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User: Michael Gerlich
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Name: Michael Gerlich Joined: Wednesday 04 June 2008 @ 11:13:51 (GMT) Last seen: Monday 04 May 2009 @ 14:14:12 (GMT) Email (public): mgerlich [at] ipb-halle.de Website: http://www.ipb-halle.de Location: Halle, Germany |
Michael Gerlich has been credited 8 times Michael Gerlich has an average rating of: 0.0 / 5 (0 ratings in total) for their items |
Description/summary not set
Other contact details:
Not specifiedInterests:
Bioinformatics, Databases, web application
Field/Industry: Bioinformatics
Occupation/Role(s): PhD Student
Organisation(s):
Leibniz Institute of Plant Biochemistry
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Workflow
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Original Uploader |
Created: 24/05/11 @ 13:13:52 | Last updated: 24/05/11 @ 14:19:24
Credits:
Attributions:
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: 39 times | Downloaded: 19 times Tags (26): |
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 Download (v1)
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Workflow
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Original Uploader |
Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13
Credits:
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: 198 times | Downloaded: 0 times Tags (21): |
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Workflow
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Original Uploader |
Created: 30/03/09 @ 09:26:25 | Last updated: 30/03/09 @ 09:47:00
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 93 times | Downloaded: 47 times Tags (12): |
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Download (v1)
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Workflow
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Original Uploader |
Created: 30/03/09 @ 09:24:33 | Last updated: 30/03/09 @ 09:43:07
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflows queries ChemSpider for compound information and compound images. Note that a Chemspider security token is needed in order to access some of the ChemSpider services (receive one by registering at ChemSpider).
Possible search terms might be InChI codes, ChemSpider identifiers or names.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 51 times | Downloaded: 24 times Tags (6): |
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Download (v1)
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Workflow
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Original Uploader |
Created: 30/03/09 @ 09:22:36 | Last updated: 30/03/09 @ 09:39:23
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Given a KEGG compound identifier (e.g. cpd:C00905), this workflow queries KEGG DB for pathways and compound information for each of these compounds. As the KEGG pathway service tries to find pathways which contain all input compounds, the input list is split up to circumvent this behaviour and to search for only one compound in a pathway at a time. Compounds identified in pathways are marked as red in the resulting pathway image.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 75 times | Downloaded: 39 times Tags (3): |
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Download (v1)
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Workflow
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Original Uploader |
Created: 30/03/09 @ 09:20:42 | Last updated: 30/03/09 @ 09:34:37
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results.
Adding support for downloading this XML file and writing it to filesystem is planned.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 74 times | Downloaded: 52 times Tags (4): |
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Download (v1)
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Workflow
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Original Uploader |
Created: 11/06/08 @ 12:13:36 | Last updated: 11/06/08 @ 12:15:21
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Attributions:
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: 97 times | Downloaded: 43 times Tags (4): |
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Download (v1)
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Workflow
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Original Uploader |
Created: 05/06/08 @ 16:00:38 | Last updated: 16/06/08 @ 11:40:46
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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: 128 times | Downloaded: 62 times Tags (8): |
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Download (v2)
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