Workflows

Automatic Protein-Ligand Docking (1)

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Nimrod harnesses grid-based high-performance computing resources to evaluate a n umber of protein-ligand interaction algorithms. Different computational chemistry approaches are combined with non-linear optimization algorithms. This work is explained in Abramson, D. A., Amoreira, C., Baldridge, K. K., Berstis, L., Kondrick, C., Peachey, T. C., 2006, "A flexible grid framework for automatic protein-ligand docking", Proceedings of the Second IEEE International Conference on e-Science...

Created: 2009-05-15 | Last updated: 2009-05-16

Credits: Jeffersontan

snpNeighbours (1)

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My first Taverna workflow:  the input is the SNP "rs25". The Web Services invoked finds its position on the human genome and find its neighbours at 100bp. The XML result is then saved to a local file. The web services used here are under developpement and might be turned off in a near future.

Created: 2009-05-14 | Last updated: 2009-05-14

Credits: Pierre Lindenbaum

group difference pseudopotential (1)

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This is a Nimrod plan file for a parameter scan of a group difference pseudopotential (GDP). This is the initial step in "paremeterization of a capping atom for hybrid quantum mechanics-molecule mechanics (QM/MM) calculations." Based on paper by Sudholt, W., Baldridge, K., Abramson, D., Enticott, C. and Garic, S., “Application of Grid computing to parameter sweeps and optimizations in molecular modeling”, Future Generation Computer Systems, 21 (2005), 27-35. Also appeare...

Created: 2009-05-14 | Last updated: 2009-05-16

Taverna rendering of the PAN-STARRS workfl... (1)

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Example inputs: CSVRootPath = /Users/paolo/Documents/myGRID/OPM/PC3/SampleData/J062941 JobID:J062941  

Created: 2009-04-30

Credits: Paolo

Search InChI in ChemSpider (1)

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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.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

Retrieve Pathways and Compound information... (1)

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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.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: Michael Gerlich

MiscanMod (1)

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Created: 2009-03-27 | Last updated: 2009-04-23

Credits: Robert Muetzelfeldt

Kegg_DrugID (1)

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 This workflow accepts looks up drug identifiers from KEGG given a pathway identifier. You can enter a pathway ID in the form path:map07026

Created: 2009-03-18 | Last updated: 2009-03-18

Credits: Rory

Get Graphs of Name (1)

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This workflow gets the Ondex graphs relating to a specified name

Created: 2009-02-27

Credits: Paul Fisher

Get Concepts (1)

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This workflow gets all the concepts in an Ondex graph, using a given graph id

Created: 2009-02-27

Credits: Paul Fisher