Workflows

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)

Arabidopsis thaliana QTL Analysis (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The 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. ...

Created: 2009-07-08 | Last updated: 2009-12-14

Credits: Paul Fisher

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

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

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

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

Query dbsnp, transform to HTML (1)

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Created: 2009-05-21 | Last updated: 2009-05-21

Credits: PL

LINTUL crop model (1)

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Created: 2009-04-01

Credits: Robert Muetzelfeldt

Search InChI in NCBI eSearch (pccompound) (1)

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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.

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

Credits: Michael Gerlich

Download Entries from PubChem (1)

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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.

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

Credits: Michael Gerlich

Demo of ChemSpider InChi to SMILES webserv... (1)

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Created: 2009-03-28 | Last updated: 2009-03-28

Credits: David De Roure

fetch_fasta (1)

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This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: Jumblejumble

Biomart Protein Sequence Retrieval (1)

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This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

Created: 2009-03-09

Credits: Kieren Lythgow

Sesame triplestore loader from a dereferen... (2)

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Load triples obtained from an URL in N3 or XML format and load them into your local Sesame Triplestore locally installed and available at http://localhost/sesame. The http://localhost/sesame/servlets/uploadURL service of Sesame is used in HTTP POST mode.

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Workflow Pattern - Blocking Discriminator ... (1)

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This workflow is a GWorkflowDL representation of a blocking discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored and the AND transition is blocked. The pattern is resets if both, A and B have been invoked. Then the next token on "begin" can be processed. Please note that the transitions "C", "ignore", and "release" have different priorities (represented by p0, p1, an...

Created: 2009-01-20

Credits: Andreas Hoheisel

Wash and filter molecules (1)

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The Wash and Filter workflow performs some processing on incoming structures to filter out those wildcards or unspecified atom types, standardise stereo and charges, and various other adjustments. This is an advance on the filter used in the paper... Drug Discovery Today Volume 14, Issues 1-2, January 2009, Pages 31-40 ‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries  

Created: 2009-01-20

Credits: Paul Dobson

Author's collaborators according to pubmed (1)

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SELECT distinct ?s2 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "author" .   ?s2 ?p2 ?s1 .   FILTER( regex(?s1, "pubmed") ) } followed by SELECT ?creator, count() FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 .   ?s1 ?p2 ?o2 .   FILTER( regex(?o2, "author"))   ?s1 ?creator . } ORDER BY DESC(count())

Created: 2009-01-20 | Last updated: 2009-01-20

Credits: Francois Belleau

Text search within sparql point (1)

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This workflow make possible full text search within different sparql point made available by the Bio2RDF project.

Created: 2009-01-19

Credits: Francois Belleau

Workflow Pattern - Synchronization (AND-Join) (2)

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This workflow is a GWorkflowDL representation of a synchronization (AND Join) that waits until A and B finish their execution. This workflow is equivalent to the following pseudo code: threadA = new Thread( end_A = A() ); threadB = new Thread( end_B = B() ); threadA.join(); threadB.join();

Created: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Structured Partial Join (1)

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This workflow is a GWorkflowDL representation of a structured partial join (N-out-of-M join) that invokes D after N=2 invocations of A or B or C (M=3). All next (M-N) invocations of A or B or C are ignored. This is only one out of various possibilities to model this workflow pattern.

Created: 2009-01-06

Credits: Andreas Hoheisel

Affimetrix microarray: part two (perm) (1)

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We use a permutation test to infer the significance of the differently expressed genes found by the ANOVA analysis. Permutation tests are computationally intensive, needing at least 1000 permutations per gene to obtain acceptable results. For large experiments, the in-built feature of running R/MAANOVA in a single cluster may not be enough. We are using WS- VLAM workflow management system [2] to create a Grid-enabled R/MAANOVA workflow (Grid-MAANOVA) that will simultaneously run in multiple c...

Created: 2008-12-05

Credits: Zhiming Zhao

Basic eSearch/eFetch cycle (1)

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This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI. It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences. I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am ...

Created: 2008-12-04 | Last updated: 2008-12-04

Credits: Giovanni Dall'Olio

AUGUSTUS Workflow for predicting genes in ... (1)

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AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Currently, it has been trained to predict genes in human, Drosophila melagonaster, Arabidopsis thaliana, Brugia malayi, Aedes aegypti, Coprinus cinereus, Tribolium castaneum, Schistosoma mansoni, Tetrahymena thermophila, Galdieria sulphuraria and Zea mays. In addition the species parameters of the following species are a courtesy of Jason Stajich: Caenorhabditis elegans, Saccharomyces cerevisiae, Ustilago ma...

Created: 2008-11-25 | Last updated: 2008-12-05

Credits: MediGRID

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

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

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

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)

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