The workflow performs a quality control process on gene expression data sets stored in the Gene Expression Omnibus database. The QC process is performed using Bioconductor R packages. A variety of statistics are produced by the workflow including a diagnostic plot from snm normalisation and nucleotide composition bias.

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BioXSD example workflow (v1)

Created: 12/10/10 @ 09:19:17 | Last updated: 12/10/10 @ 09:21:55

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) Bioinformatics 26:i540-6. The workflow only calls one BioXSD web service (BLAST) since the second service (ClustalW) in the example workflow is currently down :(

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Generate CombiUgi library (v1)

Created: 10/08/10 @ 12:15:37 | Last updated: 10/08/10 @ 12:16:00

Credits: Peter Li Romney

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generates a CombiUgi library using data from a Goolgle spreadsheet containing smiles strings of compounds to undergo virtual Ugi reactions

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Predict Abraham descriptors (v1)

Created: 05/08/10 @ 16:26:19 | Last updated: 05/08/10 @ 16:26:20

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values. The workflow returns all the Abraham descriptors E, S, A, B and V in a HTML file.Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values

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Predict chemical solubility in solvents (v2)

Created: 04/08/10 @ 11:42:55 | Last updated: 04/08/10 @ 11:43:30

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Predicts solubility in molar units for a given chemical compound represented as a SMILES string in a given solvent. Uses a beanshell script to enable the user to select the solvent from a list.

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download (v2)

Created: 16/07/10 @ 10:41:38 | Last updated: 16/07/10 @ 10:53:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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smiles-identity-idlist (v1)

Created: 16/07/10 @ 09:50:50 | Last updated: 16/07/10 @ 09:53:16

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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file-similarity-entrez-url (v2)

Created: 16/07/10 @ 09:34:45 | Last updated: 16/07/10 @ 09:43:39

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

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Simple search (v1)

Created: 13/07/10 @ 15:18:44 | Last updated: 13/07/10 @ 15:18:45

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Performs a lite search on ChemSpider

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Search structures in ChEBI database (v1)

Created: 13/07/10 @ 15:08:20 | Last updated: 13/07/10 @ 15:10:10

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Does a substructure, similarity or identity search using a structure in the Chebi database

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Get ontology children (v1)

Created: 13/07/10 @ 14:51:32 | Last updated: 13/07/10 @ 14:51:33

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves the ontology children of an entity including the relationship type, using the ChEBI identifier.

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Get ontology parents (v1)

Created: 13/07/10 @ 14:48:37 | Last updated: 13/07/10 @ 14:48:38

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

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Get complete entity by list (v1)

Created: 13/07/10 @ 14:44:02 | Last updated: 13/07/10 @ 14:47:57

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information from the chebi database for a list of chebi identifiers

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Get complete chebi entity (v1)

Created: 13/07/10 @ 14:38:12 | Last updated: 13/07/10 @ 14:38:13

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns informations for a given compound represented by its chebi identifier

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Asynchronous chemspider search by formula (v1)

Created: 13/07/10 @ 14:15:41 | Last updated: 13/07/10 @ 14:16:17

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Performs an asynchronous search on ChemSpider by molecular formula

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getLiteEntity (v1)

Created: 13/07/10 @ 14:14:52 | Last updated: 13/07/10 @ 14:14:53

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves a list of "lite" entities containing only the ChEBI ASCII name and ChEBI identifier. The input parameters are a search string and a search category. If the search category is null then it will search under all fields. The search string accepts the wildcard character "*" and also unicode characters. You can get maximum results upto 5000 entries at a time.

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chemspider identifier to MOL format (v1)

Created: 13/07/10 @ 13:52:02

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns the MOL file for a given compound represented by its chemspider identifier

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Get structure synonyms (v1)

Created: 13/07/10 @ 11:38:56 | Last updated: 13/07/10 @ 11:38:57

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns synonyms for a given compound represented by a MOL fileReturns synonyms for a given compound

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Get compound thumbnail (v1)

Created: 13/07/10 @ 11:29:03 | Last updated: 13/07/10 @ 11:29:04

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns a small image of the 2D structure of given chemical compound represented by its chemspider identifier

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Get compound information (v1)

Created: 13/07/10 @ 11:17:08 | Last updated: 13/07/10 @ 11:17:09

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information about a given compound represented by its chemspider id

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Asynchronous chemspider simple search (v1)

Created: 13/07/10 @ 11:08:34 | Last updated: 13/07/10 @ 11:08:35

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Performs an asynchronous simple search on ChemSpider

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Get spectrum information (v1)

Created: 13/07/10 @ 09:48:50 | Last updated: 13/07/10 @ 09:48:51

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information about a spectrum identified by its chemspider spectrum identifier

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Get compound spectra information (v1)

Created: 13/07/10 @ 09:42:03 | Last updated: 13/07/10 @ 09:42:04

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information about spectra stored in ChemSpider for a given compound represented by its chemspider identifier

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Get spectra information (v1)

Created: 13/07/10 @ 09:32:27 | Last updated: 13/07/10 @ 09:32:28

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information about the spectra stored in ChemSpider

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Get ChemSpider record in MOL format (v1)

Created: 12/07/10 @ 10:47:44 | Last updated: 12/07/10 @ 10:47:46

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns ChemSpider record in MOL format or empty string in case of failure.

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Get extended compound information for a list of chemspider identifiers (v1)

Created: 12/07/10 @ 10:33:31 | Last updated: 12/07/10 @ 10:34:11

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information for a given list of chemspider compound identifiers.

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Get extended compound information (v1)

Created: 12/07/10 @ 10:06:37 | Last updated: 12/07/10 @ 10:06:39

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns information from chemspider for a given chemical represented by its chemspider identifier

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Get list of chemspider databases (v1)

Created: 12/07/10 @ 09:53:38 | Last updated: 12/07/10 @ 09:53:40

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns a list of databases catalogedReturns a list of databases cataloged by ChemSpider

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Convert chemical identifier (v1)

Created: 09/07/10 @ 15:45:53 | Last updated: 09/07/10 @ 15:46:31

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts a chemical compound identifier from one format to another using the open babel web service provided by ChemSpider

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SmilesToInchi (v1)

Created: 09/07/10 @ 15:37:08 | Last updated: 09/07/10 @ 15:37:10

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Convert SMILES to InChI. Result is v1.02s InChI.

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MolToInchiKey (v1)

Created: 09/07/10 @ 12:10:00 | Last updated: 09/07/10 @ 12:10:02

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts a MOL file to an InChIKey. Result is v1.02s InChIKey.

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MolToInchiString (v1)

Created: 09/07/10 @ 12:01:45 | Last updated: 09/07/10 @ 12:01:47

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts a MOL file to InChI. Result is v1.02s InChI.

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isValidInChiKey (v1)

Created: 09/07/10 @ 11:55:56 | Last updated: 09/07/10 @ 11:55:58

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Checks that specified argument is valid InChIKey. Works for v1.02b InChIKey only.

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InchiStringToSmiles (v1)

Created: 09/07/10 @ 11:38:59 | Last updated: 09/07/10 @ 11:39:01

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts an inchi string into SMILES format

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InChIStringToMolFile (v1)

Created: 09/07/10 @ 11:21:23 | Last updated: 09/07/10 @ 11:23:05

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts an InChI string into a MOL file using the Inchi ChemSpider web service

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InChIStringToInChiKey (v1)

Created: 09/07/10 @ 11:12:58 | Last updated: 09/07/10 @ 11:23:55

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts an InChI string to an InChi key

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InChIToCSID (v1)

Created: 09/07/10 @ 11:09:29 | Last updated: 09/07/10 @ 11:09:31

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Convert InChI to ChemSpider ID

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InChi key to MOL file (v1)

Created: 09/07/10 @ 11:05:11 | Last updated: 09/07/10 @ 11:05:13

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns a MOL file for a given InChi key

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InChi key to Inchi string (v1)

Created: 09/07/10 @ 10:58:54 | Last updated: 09/07/10 @ 11:00:16

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Converts an InChI key to an InChI string using the ChemSpider Inchi web service.

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InChi key to ChemSpider identifier (v1)

Created: 09/07/10 @ 10:54:07 | Last updated: 09/07/10 @ 10:54:08

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Returns Converts an InChIKey to a ChemSpider ID

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Generate InChi key (v1)

Created: 09/07/10 @ 10:45:09 | Last updated: 09/07/10 @ 10:45:11

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generates an inchi key for a given compound using the inchi web service provided by ChemSpider

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Generate inChi information (v1)

Created: 09/07/10 @ 10:22:29 | Last updated: 09/07/10 @ 10:23:47

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Uses the GenerateInchiInfo web service operation from ChemSpider to generate information relating to the InChi string for a given chemical compound

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Generate inChi (v1)

Created: 09/07/10 @ 10:06:35 | Last updated: 09/07/10 @ 10:08:37

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Generates an inChi string for a given chemical represented by its SMILES string, SDF or MOL file using the inchi web service provided by ChemSpider

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AlitoraKDAInputModule test workflow (v1)

Created: 07/07/10 @ 11:14:19 | Last updated: 07/07/10 @ 11:16:04

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow calls the AlitoraKDAInputModule service from the test GenePattern server.

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Select items from list (v1)

Created: 30/03/10 @ 14:04:45

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow pops up a window containing an input list of strings. The user is invited to select one or more strings for downstream processing.

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Copasi time simulation of SBML model (v1)

Created: 26/03/10 @ 17:23:25

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Uses the synchronous Copasi time simulation web service to predict the concentrations of species over a time period. The results from Copasi are provided in SBRML format which is visualised as a graph using an R script.

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SBML model optimisation (v1)

Created: 26/03/10 @ 17:21:53

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow modifies reaction kinetic parameters against experimental data stored in the MCISB key results database

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SBML model parameterisation (v1)

Created: 26/03/10 @ 17:20:14

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow

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Taverna 2

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Peter Li

Construction of skeleton SBML model using subsystem term (v1)

Created: 26/03/10 @ 17:11:26 | Last updated: 26/03/10 @ 17:12:06

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term.

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Taverna 2

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Peter Li

Construction of skeleton SBML model using a list of yeast ORF numbers (v1)

Created: 26/03/10 @ 17:08:13 | Last updated: 26/03/10 @ 17:13:15

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers

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graph
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model
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ORF
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pathways
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yeast

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Taverna 2

Original Uploader

Peter Li

Invocation of Gene Pattern modules using R (v1)

Created: 19/03/10 @ 10:26:34 | Last updated: 19/03/10 @ 10:29:08

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A workflow to invoke a Gene Pattern module using an R script. Note that a FTP URL for the data to be analysed is required, not the data itself!

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Taverna 1

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Paul Fisher

Pathways and Gene annotations for Arabidopsis affy data (v2)

Created: 06/03/09 @ 17:18:13 | Last updated: 03/12/09 @ 16:59:11

Credits: Paul Fisher Peter Li

Attributions: Pathways and Gene annotations for QTL region

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

This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

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Taverna 1

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Antoon Goderis

AffyidToGeneAnnotationnoGOIDandPepstats.xml (v1)

Created: 12/07/08 @ 21:14:58 | Last updated: 12/07/08 @ 21:16:01

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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benchmarks

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Taverna 1

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Peter Li

Identification of differential genes using the LIMMA Bioconductor package within R (v1)

Created: 02/07/08 @ 11:24:12 | Last updated: 02/07/08 @ 11:28:21

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

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Taverna 1

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Peter Li

Identification of differential genes using t-tests by R (v2)

Created: 15/04/08 @ 15:37:42 | Last updated: 01/07/08 @ 17:21:18

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

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Taverna 1

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Peter Li

selectworker (v1)

Created: 25/03/08 @ 10:01:38 | Last updated: 25/03/08 @ 10:23:34

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow shows how the selectData beanshell script can be used to select items from a given list for analysis by downstream processors. Use Control and left mouse click to select multiple items.

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Taverna 1

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Katy Wolstencroft

Gene annotation pipeline for the Graves disease scenario (v2)

Created: 03/10/07 @ 18:36:09 | Last updated: 22/11/07 @ 16:03:15

Credits: Katy Wolstencroft Peter Li

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

This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

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Taverna 1

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Peter Li

Query Maxd microarray database (v1)

Created: 14/11/07 @ 16:01:50 | Last updated: 22/11/07 @ 12:06:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieves data from the maxd database given name of data set

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Taverna 1

Original Uploader

Peter Li

Mapping microarray data onto metabolic pathways (v1)

Created: 14/11/07 @ 16:51:26 | Last updated: 22/11/07 @ 10:39:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

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