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Make 28 CPUh load on the Grid (1)

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This workflow makes 28 CPU hours load on a Grid. Therefore it calls 100 times (represented by 100 input tokens) the program "makeload", which makes 1000 Seconds load each. The processing is done recurrent, so you can use this workflow to benchmark the speedup of your Grid environment, or just to heat up your computer center... This workflow also serves as an example of a typical parameter study modeled with GWorkflowDL. Of cause this workflow can only be invoked with a X509 certif...

Created: 2008-11-25 | Last updated: 2008-12-17

Credits: Andreas Hoheisel

GWorkflowDL: Generic execution of programs (1)

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This workflow is an example of the execution of an arbitrary command line program. This workflow transfers a tar.gz package containing the linux program "date" to a free Grid resource, unpacks, and executes it. After execution the URL to the file with the standard output is available on "stdout", the standard error on "stderr".

Created: 2008-11-25 | Last updated: 2008-11-25

Credits: Andreas Hoheisel

Calculation of molecular descriptors for m... (1)

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This workflow loads iteratively molecules from a database. For each molecule the atom typse are perceived before the hydrogens are added and the aromaticity is detected. Than the QSAR worker calculates the selected descriptors. The result of this calculation is stored in database table.

Created: 2008-11-15

Credits: Thomasku

Write pathway to disk (2)

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Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

Created: 2008-11-14 | Last updated: 2008-11-14

Credits: Thomaskelder

Topological Substructure Search Workflow (1)

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This workflow performs a topological substructure search. The molecules to be searched are loaded from a MDL SD file. The substructure is loaded from a SMILES (workflow input). The matched molecules are converted to CML and for the molecules which do not contain the substructure the InChI is generated.

Created: 2008-11-06

Credits: Thomasku

Sample makefile workflow (1)

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Created: 2008-10-30 | Last updated: 2008-10-30

Credits: Giovanni Dall'Olio

While Sample (1)

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This WF shows how to use while constructs in workflows. The condition block generates a true or false condition. The while loop is executed once, each time the condition is true.

Created: 2008-10-21

Credits: Trident

Extract lists from a tab-delimited spreads... (1)

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This workflow takes a spreadsheet exported as a tab delimited file, such as an Excel spreadsheet. The style is expected as a matrix of data with the first row containing the column names and the first column containing the row names (see below). The top left cell is discarded. The workflow outputs three lists. A list of column names, a list of row names, and a two deep list of data points. The first list is a list of the rows and the sublist is a list of values of the cells from the columns....

Created: 2008-10-17 | Last updated: 2008-10-18

Credits: Andrew Gibson

Genetic Analysis parallel processing example (1)

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This workflow shows both parallel and sequential elements. Input files are read in parallel and the resulting output shared with later activities.

Created: 2008-10-13

Credits: Trident

get_enzymes_by_gene (1)

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Retrieve all the EC numbers which are assigned to a given gene Input example: eco:b0002

Created: 2008-10-08

Credits: Franck Tanoh

runFunCUT (1)

MOBY Web Services (synchronous and asynchronous) that describe the FunCUT method. Is recommended use asynchronous MOBY services because the method needs huge range of time.   FunCUT Method Short Description: Annotates homologous sequences and includes new features related to the specific identification of protein subfamilies (orthologous groups) FunCUT (Abascal and Valencia, 2003. PROTEINS: Structure, Function, and Genetics 53:683– 692 (2003)) is application based on the study...

Created: 2008-10-03 | Last updated: 2008-10-03

Credits: José Manuel Rodríguez

bconv (1)

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Converts external IDs to KEGG IDs.External database:  NCBI GI, NCBI GeneID, GenBank , UniGene , OMIM. Database prefix: ncbi-gi:, ncbi-geneid:, genbank: ,unigene: , uniprot: , omim: Example of input parameter: ncbi-gi:10047090 ncbi-geneid:14751

Created: 2008-09-29 | Last updated: 2008-09-29

Credits: Franck Tanoh

Execute cmd line app - unix - /bin/ls -R o... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the create_and_populate_list beanshell which creates a list of '-R' and the path. The resultant list is passed to the args port of the Execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls -R command on the temporary ...

Created: 2008-09-27

Credits: Alan Williams

Execute cmd line app - unix - /bin/ls of t... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

Created: 2008-09-27

Credits: Alan Williams

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Example XSLT file

Created: 2008-09-26 12:13:31

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Binary data

Comments: 0 | Viewed: 179 times | Downloaded: 282 times

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Example XML file

Created: 2008-09-26 12:12:41

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 220 times | Downloaded: 377 times

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Insert Molecules into Database (1)

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This workflow reads the molecules form the an MDL SD File and stores them into a database. The database used here is a Postgres SQL database which uses the PGChem::Tigress chemoinformtic extension. To run this workflow you have to install the CDK-Taverna Plug-in for Taverna 1.7.1.0 from http://cdk-taverna.de/plugin

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

EBI_IntAct (1)

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Find protein binary interactions using the EBI's IntAct service. See http://www.ebi.ac.uk/intact/ for further details.

Created: 2008-07-09

Credits: Hamish McWilliam

EBI_OLS_TermInfo (1)

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Get details of an ontology term given its identifer. This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information.

Created: 2008-07-09

Credits: Hamish McWilliam

EBI_Whatizit (1)

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Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf). Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.

Created: 2008-07-09

Credits: Hamish McWilliam

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Everything You Need To Know About myExperiment...

Created: 2008-07-02 22:31:12 | Last updated: 2008-07-02 23:12:37

9 items in this pack

Comments: 0 | Viewed: 320 times | Downloaded: 81 times

countryExample_working (1)

This Workflow allows you to find a list of the cities in a particular country, the time zone that country is in, the conversion rate of the currency in that country and yours and the international dialling code for that country

Created: 2008-06-16

Credits: Katy Wolstencroft

EBI_DaliLite (1)

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Pairwise structure comparison using the DaliLite tool. The EBI's WSDaliLite web service (see http://www.ebi.ac.uk/Tools/webservices/services/dalilite) is used to access the tool.

Created: 2008-06-07

Credits: Hamish McWilliam

EBI_MAFFT (1)

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Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement MAFFT services (REST or SOAP) should be used instead.

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_MPsrch (1)

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Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch). Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_Kalign (1)

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Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi...

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: Hamish McWilliam

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The Data Playground: An Intuitive Workflow Specifica...

Created: 2008-06-02 14:46:40

Credits: Katy Wolstencroft Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 235 times | Downloaded: 242 times

EBI_blastpgp_PSI-BLAST (1)

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Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.

Created: 2008-05-31

Credits: Hamish McWilliam

Termine Webservice (1)

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Termine is a service provided by the National Centre for Text Mining (NaCTeM) to assist in the discovery of terms in text. More information on the Termine service can be found here. This workflow represents the simplest method of using Termine. The input represents a text string with the output being an string containing a representation of the list of terms, with their C-Value scores (representing significance in the text), in a simple xml format. Other variations of this tools will be adde...

Created: 2008-05-19 | Last updated: 2008-05-19

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

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Using Taverna and webservices as tools to revive a d...

Created: 2008-04-20 17:04:40

Credits: Bas Vroling

License: Creative Commons Attribution 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 168 times | Downloaded: 146 times

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Taverna tutorial

Created: 2008-03-03 11:15:00 | Last updated: 2008-03-03 11:16:11

Credits: Franck Tanoh Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 227 times | Downloaded: 300 times

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Output from FLOSS Communication Centralization Workflow

Created: 2008-02-10 01:56:29 | Last updated: 2008-06-09 21:53:03

Credits: Andrea Wiggins Crowston James Howison

Attributions: FLOSS Communication Centralization Plot, Exponentially Weighted

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PNG image

Comments: 0 | Viewed: 257 times | Downloaded: 126 times

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Introduction to NCeSS Data Mining Pilot Project

Created: 2007-11-22 15:51:42

Credits: Yuwei Lin

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 1 | Viewed: 196 times | Downloaded: 0 times

couple (1)

My Girl Friend and me ^o^/

Created: 2007-11-16 | Last updated: 2007-11-16

Credits: Hong Chang Bum

getFragWithClosure2 (2)

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with parameters

Created: 2007-10-03

Microarray CEL file to candidate pathways (2)

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This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Created: 2007-10-03

querySWS_minimalQuery (2)

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SRS by WS (SWS) is a set of Web Services allowing to retrieve database entries from libraries included in public SRS sites. The querySWS service implement a search on the basis of the database name (lib) and the term to be searched (query). It automatically identifies the best site to query. Additional parameters include in_fields (in which part of the record the terms are searched), out_fields (which information is returned) and site (the SRS site). This workflow is just a demonstration ...

Created: 2007-10-03

Fetch Dragon images from BioMoby v2 (2)

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demonstration to ISSGC07

Created: 2007-10-03

Python script for face and smile detection (1)

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Created: 2019-05-16 | Last updated: 2019-09-27

Credits: George Kargas

Integrated workflow for MSA, Similarity sc... (3)

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Integrated workflow for MSA, Similarity score estimation, and gaps trimming using Clustal Omega and web services at http://bioservices.sci.psu.ac.th/ We demonstrate the workflow using example fasta seqs.

Created: 2016-02-28 | Last updated: 2017-08-16

Credits: Kasikrit Damkliang

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Functional annotation of SNPs using next-generation ...

Created: 2012-06-26 10:41:38 | Last updated: 2015-09-01 14:31:18

12 items in this pack

Comments: 0 | Viewed: 206 times | Downloaded: 31 times

Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

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Who Wants to be a Data Miner?

Created: 2011-11-02 17:54:07 | Last updated: 2013-09-09 16:22:11

12 items in this pack

Comments: 0 | Viewed: 260 times | Downloaded: 142 times

RDKit-pains-parallel (2)

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains, and Indigo-pains.*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ****** This version contains Parallel processing nodes to take advantage of mutil-core processors ***Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the S...

Created: 2011-10-13 | Last updated: 2015-12-01

Credits: sauberns

Attributions: RDKit-pains

EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

caDSR Data service query in caGrid (3)

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This workflow is used as an example in this wiki article: https://wiki.cagrid.org/display/knowledgebase/How+to+Create+CaGrid+Workflow+Using+Taverna+2   Tested with Taverna 2.1.2 as of 6/10/2010

Created: 2010-05-25 | Last updated: 2010-06-11

Credits: Wei Tan

Support-Vector-Machine (SVM) based data cl... (2)

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Support-Vector-Machine based data classificationSupport-Vector-Machine based data classification using genePattern SVM service, the input should be in genePattern STATML format.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: Wei Tan

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)