Workflows

XSTAR (3)

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This is a simple workflow designed to run XSTAR with an user selected input. XSTAR is a computer program for calculating the physical conditions and emission spectra of photoionized gases. More information can be found here: - XSTAR home page: http://heasarc.nasa.gov/lheasoft/xstar/xstar.html - XSTAR on the Spinet client (Soaplab2): http://caoba.ivic.ve:8180/soaplab2-axis/

Created: 2010-04-02 | Last updated: 2011-02-27

myFirstLinearDataflow (1)

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No description

Created: 2010-04-12

Credits: Paolo

Entrez Gene to KEGG Pathway (2)

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Created: 2010-04-15 | Last updated: 2010-04-15

Credits: Paul Fisher

Available instruments through DPAS (5)

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This workflow uses a DPAS servlet to obtain all available intrument keys in the DPAS (Data Provider Access Service) and formats the return as VOTable.

Created: 2010-04-15 | Last updated: 2012-03-16

Retrieve all data for all instruments for ... (3)

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This workflow looks up all instruments known to have worked during the requested periode of time (ICS), restructures results to make them fit instruments.xsd and requests data for this periode from DPAS. Result: VOTable with list of URLs to data.

Created: 2010-04-15 | Last updated: 2010-08-09

Credits: Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query

DPAS simpel query workflow (1)

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call of the simpleQuery web service; all inputs are requested from the user; xml list as output file format

Created: 2010-04-16

HEC standard query (1)

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calls the HEC web service; inputs are start and stop time, which table should be queried and an optional where clause, as in an SQL statement output is of VOTable format

Created: 2010-04-16

DPAS general query (1)

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general query to DPAS; it gets a list of instruments and lists for start and stop times; for a query hessiEC, phoenix2; start times 2001-01-01 00:00:00, 2005-04-01 00:00:00; stop times 2001-01-05 00:00:00, 2005-05-1 00:00:00 it would perform to queries: hessiEC from 2001-01-01 00:00:00 to 2001-01-05 00:00:00 and phoenix2 from 2005-04-01 00:00:00 to 2005-05-1 00:00:00 There is only one output file with the results from both queries.

Created: 2010-04-19 | Last updated: 2010-04-19

Credits: Anja Le Blanc

DPAS general query with sorted field (1)

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same as DPAS general query. Calling the DPAS sortedQuery web service. additional input: partialSorting input boolean true or false false all result entries are sorted by start measurementTime true each request is sorted by measurement time; no overall time order, but queries stay in the order they there asked.

Created: 2010-04-19 | Last updated: 2010-04-19

Credits: Anja Le Blanc

retrieve data for all instruments for even... (1)

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This workflow uses the HEC to retrieve events for a time spane given by the user from a HEC table given by the user as well. It uses all instruments available in the DPAS to retrieve data for the events Output: XML as returned by the DPASThis workflow uses the HEC to retrieve events for a time spane given by the user from a HEC table given by the user as well. It uses all instruments available in the DPAS to retrieve data for the events; empty results are filtered out, the data is combind wi...

Created: 2010-04-21

Credits: Anja Le Blanc

Attributions: DPAS general query HEC standard query Retrieve all data for all instruments for a given periode of time

Census data and PRM services integration (1)

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This workflow combines services that provide census data with PRM (Population Reconstruction Model) services.

Created: 2010-04-21 | Last updated: 2010-04-21

Credits: Alex Nenadic

Census data service (1)

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Census data services, invoked with a fixed SQL query

Created: 2010-04-21 | Last updated: 2010-04-21

Credits: Alex Nenadic

PRM (People Reconstruction Model) service (2)

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No description

Created: 2010-04-21 | Last updated: 2010-09-15

Credits: Alex Nenadic

DataBiNS with Kegg ID (3)

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Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

Created: 2009-07-09 | Last updated: 2010-11-22

Credits: Mark Wilkinson Fong Chun Chan

KEGG Gene IDs to KEGG Pathways (1)

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this is a simplified version of Paul's workflow (linked?) that is designed to be provenance-friendly

Created: 2009-06-04 | Last updated: 2010-01-07

Credits: Paolo

Attributions: Pathways and Gene annotations for QTL region

myWorkflow (2)

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asdasdasd

Created: 2009-06-09

Credits: Rob

G-language Genome Analysis Environment - B... (2)

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Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta...

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - B... (2)

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Given a numerical vector (array), this workflow calculates the maximum value (max) and its index (maxdex), minumum value (min) and its index (mindex), mean, sum, median, and standard deviation. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew of a given genome sequence. Use this as a template for using more than 100 analysis programs implemented in G-language Genome Analysis Environment, which can be used in a similar manner. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew (by default, for keto bases, with window size of 1000) of a given genome sequence identifier. Here the genome sequence in Fasta format is downloaded through the Togo Web Service with RefSeq identifier. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - B... (2)

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This workflow shows simple sequence manipulation functions of G-language GAE, such as random shuffling, obtaining a reverse complement, and translation of nucleotide sequences, and showing basic composition statistics for nucleotide and amino acid sequences. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew of a given genome sequence (for the entire genome, for only the coding sequences, for only the intergenic regions, and for only the third codon positions), as well as the GC content with sliding windows. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (3)

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This workflow calculates and graphs the AT skew of a given genome sequence, using options of gcskew program. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05 | Last updated: 2011-01-09

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - S... (2)

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This workflow calculates the Student's T-test and Pearson/Spearman correlations. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - R... (2)

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This workflow displays a documentation of G-language GAE programs. If you input the "keywords", this workflow searches for the keyword through the documentations. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-03-30 | Last updated: 2010-03-30

Credits: cory (Kazuki Oshita)

Execute GWorkflowDL workflow using Taverna 2 (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench.

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Andreas Hoheisel

EBI InterproScan T2 (1)

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This T2 version of the Interpro scan workflow is an example of the while loop in action. This is used to poll the async EBI service for the result (busy waiting)

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

Execute GWorkflowDL workflow using Taverna... (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench. This workflow contains all the input parameters as string constants, so it can be started right away without user inputs.

Created: 2009-06-30

Credits: Andreas Hoheisel

Attributions: Execute GWorkflowDL workflow using Taverna 2

EBI_InterProScan for Taverna 2 (2)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-01-26 | Last updated: 2010-01-26

Credits: Stian Soiland-Reyes Paolo Katy Wolstencroft Hamish McWilliam

Attributions: EBI InterproScan T2 EBI_InterProScan

EBI_InterProScan for Taverna 2 (2)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to t...

Created: 2010-01-26 | Last updated: 2010-11-24

Credits: Stian Soiland-Reyes Katy Wolstencroft Paolo Hamish McWilliam

Attributions: EBI_InterProScan for Taverna 2 EBI InterproScan T2 EBI_InterProScan EBI InterProScan

Biomart and EMBOSS analysis (1)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes Tomoinn

Attributions: Demonstration of configurable iteration

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch PDB flatfile from RCSB server Fetch PDB flatfile from RCSB server

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: GBSeq test

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Retrieve sequence in EMBL format

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: A workflow version of the EMBOSS tutorial

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: Stian Soiland-Reyes Ian Dunlop

getGoTermsFromUniprotId (1)

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This service is invoking UniprotAPI to retrive GOTerms associated with the list of UniprotIds provided in the input. It is using Axis2 webservice created using UniprotAPI and published with wsdl. Example uniprotIds for input: "A2ABK7", "A2ABK8", "A2ABK9"

Created: 2009-07-09 | Last updated: 2009-07-09

Credits: Jelena (Obradovic) Dreskai

getPubMedIdsFromUniprotIds (1)

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This service is invoking UniprotAPI to retrive PubMedIds for articles associated with the list of UniprotIds provided in the input. It is using Axis2 webservice created using UniprotAPI and published with wsdl. Example uniprotIds for input: "Q5VWZ2"

Created: 2009-07-09

Credits: Jelena (Obradovic) Dreskai

Tutorial Workflow (2)

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No description

Created: 2009-07-18

Credits: Nima

Term Extraction with NaCTeM's TerMine Tool (2)

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Pass in text and retrieve a list of terms discovered ranked by their importance within the text.

Created: 2009-07-23

Credits: Brian Rea National Centre for Text Mining (NaCTeM)

An example workflow with WSRF service (1)

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An example workflow with WSRF service The service used is http://sidgrid.ci.uchicago.edu:8100/wsrf/services/CounterService The service is included in Globus toolkit installation (ws-core). If the it is down you can host your own and modify the workflow definition file to point to your own. The workflow first creates a counter instance and adds the value 10 for two times to the same counter. Therefore the result should be 20.

Created: 2009-07-28

Credits: Wei Tan Stian Soiland-Reyes

Retrieve details on genetic marker by UniS... (3)

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The workflow retrieves the marker's primers and the organism name - if available. The organism name may not be unique for a given marker. The primers should be. It would be nice if some good soul could investigate how to retrieve the various mappings from the site. The retrieval of the primers is thought to prepare for a manual mapping of the marker's chromosomal location.

Created: 2009-08-19

Credits: Steffen Möller

Retrieve UniSTS numerical UID from name of... (2)

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No description

Created: 2009-08-19

Credits: Steffen Möller

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn Stian Soiland-Reyes

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Ian Dunlop Stian Soiland-Reyes

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Perfrom a text based search through PubMed (1)

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This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Created: 2010-07-05 | Last updated: 2010-07-05

Credits: Paul Fisher

Gene to Pubmed (3)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: Paul Fisher

Phenotype to pubmed (3)

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: Paul Fisher

A template example workflow using U-Compar... (2)

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An example workflow using the U-Compare text mining system inside embedded. Users can easily make their own workflow with U-Compare reusing this workflow. This workflow retrieves abstract texts from Pubmed with user specified query, inputs the texts to U-Compare, interprets the output of U-Compare. You have to download and store the UIMA CPE XML descriptor file (StdinPPIExtraction-CPE-EventMine.xml) to run the default setting, which runs a event extraction text mining workflow by U-Compare. S...

Created: 2010-07-05 | Last updated: 2010-09-02

Credits: Yoshinobu Kano

CTF - MEG Event Averager (1)

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This workflow applies parametrs in a user-specified processing.cfg file to a set of MEG data files. The datasets must be in CTF-format, such as those produced by Omega275 systems. The processing.cfg file and datasets are selected at the initialization of the workflow.  processing.cfg can be created by the data inspection tool DataEditor, and contains desired filter settings etc. This file can also be edited easily with a text editor to tweak settings. The workflow identifies all the trig...

Created: 2010-07-06 | Last updated: 2010-07-06

Credits: Lakelander

AlitoraKDAInputModule test workflow (1)

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

Created: 2010-07-07 | Last updated: 2010-07-07

Credits: Peter Li

Who is Dr Labrie according to Pubmed publi... (2)

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To use this wokflow you need to import services from To use this wokflow you need to import services from http://proxy.bio2rdf.org/bio2rdf/services.txt you can explore the loaded data at http://proxy.bio2rdf.org/fct

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Francois Belleau

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Benb

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Benb

Generate inChi (1)

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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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Generate inChi information (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Generate InChi key (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to ChemSpider identifier (1)

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Returns Converts an InChIKey to a ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to Inchi string (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to MOL file (1)

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Returns a MOL file for a given InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIToCSID (1)

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Convert InChI to ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIStringToInChiKey (1)

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Converts an InChI string to an InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIStringToMolFile (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InchiStringToSmiles (1)

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Converts an inchi string into SMILES format

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

isValidInChiKey (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

MolToInchiString (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

MolToInchiKey (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

SmilesToInchi (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Convert chemical identifier (1)

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

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Get list of chemspider databases (1)

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

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get extended compound information (1)

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

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get extended compound information for a li... (1)

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 Returns information for a given list of chemspider compound identifiers.

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get ChemSpider record in MOL format (1)

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

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get spectra information (1)

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Returns information about the spectra stored in ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound spectra information (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get spectrum information (1)

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Returns information about a spectrum identified by its chemspider spectrum identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Asynchronous chemspider simple search (1)

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Performs an asynchronous simple search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound information (1)

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Returns information about a given compound represented by its chemspider id

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Spreadsheet Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2010-07-13 | Last updated: 2010-07-13

Get compound thumbnail (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get structure synonyms (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Spreadsheed Data Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: David Withers

chemspider identifier to MOL format (1)

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

Created: 2010-07-13

Credits: Peter Li

getLiteEntity (1)

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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.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Asynchronous chemspider search by formula (1)

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Performs an asynchronous search on ChemSpider by molecular formula

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get complete chebi entity (1)

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Returns informations for a given compound represented by its chebi identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get complete entity by list (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get ontology parents (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get ontology children (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Search structures in ChEBI database (1)

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

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Simple search (1)

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Performs a lite search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

CTF - MEG SAM Analysis (1)

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Uses a user-defined text protocol file containing SAM analysis parameters and applies them to a set of MEG datasets. The dataset must be in CTF MEG system format.

Created: 2010-07-15 | Last updated: 2010-07-15

Credits: Lakelander

file-similarity-entrez-url (2)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

smiles-identity-idlist (1)

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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/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li