Workflows

InterProScan (SOAP) (1)

• Download

Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

Created: 2010-12-03 | Last updated: 2013-03-28

Attributions: EBI_InterProScan

HTTP Basic authentication example workflow (1)

• Download

This workflow shows an example access to a resource protected by HTTP Basic authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

HTTP Basic authentication + HTTPS example ... (1)

• Download

This workflow shows an example access to a resource protected by HTTP Basic authentication and HTTPS. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

HTTP Digest authentication example workflow (1)

• Download

This workflow shows an example access to a resource protected by HTTP Digest  authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.  

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

Credits: Alex Nenadic

HTTP Digest authentication + HTTPS example... (1)

• Download

This workflow shows an example access to a resource protected by HTTP Digest  authentication and HTTPS. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

WS-Security example workflow (1)

• Download

This workflow shows an example access to various secure Web services protected by WS-Security authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

WS-Security + HTTPS example workflow (1)

• Download

This workflow shows an example access to various secure Web services protected by WS-Security authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

EMBL-EBI ClustalW2 (SOAP) (1)

• Download

Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

Created: 2010-12-06 | Last updated: 2013-03-28

Attributions: EBI_ClustalW2

Cosine vector space (2)

• Download

This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Cosine vector space

Rank Phenotype Terms (2)

• Download

This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Rank Phenotype Terms

Pathway to Pubmed (2)

• Download

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

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Extract Scientific Terms (2)

• Download

This workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Merge QSAR descriptor CSV files (3)

• Download

This workflow merges QSAR descriptor CSV files into a single CSV file. The workflow loads the CSV files from hard disk and builds a single QSAR descriptor vector. Afterwards the vector is converted in one single CSV file and saved to hard disk.

Created: 2010-12-09 | Last updated: 2011-07-21

Curate QSAR descriptor CSV file (2)

• Download

This workflow erases descriptor entries which were not calculated. The QSAR data is loaded from a CSV file and afterwards processed by the Curate_QSAR_Vector worker. At the end the curated CSV file is written to hard disk.

Created: 2010-12-09 | Last updated: 2011-07-21

ART-2a Classification Result As PDF (2)

• Download

This workflow classifies a given CSV file with the ART-2a algorithm. The results are visualized in a PDF file. The QSAR data is loaded from a CSV file and converted into a fingerprint items list which is the suitable data type for the ART-2a algorithm.

Created: 2010-12-09 | Last updated: 2011-07-21

ART-2a Classification Considering Differen... (2)

• Download

This workflow classifies the given CSV files with the ART-2a algorithm. The results are visualized in a PDF file. The QSAR dara is loaded from CSV files and merged together by the Merge_QSAR_Vectors worker. Afterwards they are converted into a fingerprint items list which is the suitable data type for the ART-2a algorithm.

Created: 2010-12-13 | Last updated: 2011-07-21

Biomart and Blast (1)

• Download

Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service

Biomart and Blast with concatinated gene id (1)

• Download

Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service Biomart and Blast

Biomart and 2x BLAST (1)

• Download

Perform Roden and Invertebrates BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). blast_ddbj_invertebrates and blast_ddbj_rodents should execute in parallel as they don't depend on each other.

Created: 2010-12-13 | Last updated: 2010-12-13

Compound Library Screen For Reaction Enume... (2)

• Download

This workflow performs a compound library screen for molecules which match the given template reaction. The reaction is loaded from a RXN file and the Reaction_Reactant_Splitter splits the reaction into its reactants. The compound library is loaded iteratively from a SD file. Afterwards a substructure search is performed for each reactant and the results are saved as SD files.

Created: 2010-12-14 | Last updated: 2011-07-21

Get Molecular Weight Distribution From QSA... (2)

• Download

This workflow calculates a molecular weight distribution from given QSAR vector. The QSAR data containing the molecular weight values is read from a CSV file and converted into a QSAR vector. Finally, the Get_molecular_Weight_Distribution_From_QSAR_vector extracts the weight data and saves it as CSV files.

Created: 2010-12-15 | Last updated: 2011-07-21

Lemmatization (3)

• Download

The workflow lemmatizes the text in the input port. Takes text as input and returns (language dependent) lemmatized text as output. All the words in the resulting text are in the same order as in the original text, but they are transformed to their dictionary form. The workflow asks for the language of lemmatization. Currently, 12 languages are supported: en,sl,ge,bg,cs,et,fr,hu,ro,sr,it,sp.

Created: 2010-12-17 | Last updated: 2010-12-23

Credits: Petra Kralj Novak

Attributions: Select from a list of possible web service parameter values

Multiple choice quiz (1)

• Download

A fun example workflow showing user-interaction and service looping

Created: 2010-09-06

Credits: George

Attributions: Multiple Choice Quiz

Principle Component Analysis (PCA) over mi... (1)

• Download

Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.

Created: 2010-09-10 | Last updated: 2010-09-10

Credits: Wei Tan

Example workflow for REST and XPath activi... (1)

• Download

Note that this workflow depends upon the REST and XPath plugins. This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch d...

Created: 2010-09-13 | Last updated: 2010-09-13

Credits: Sergejs Aleksejevs

retrive dpas data for all ics instruments ... (1)

• Download

This workflow demonstrates the standard query there events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS.

Created: 2010-09-14 | Last updated: 2010-09-14

Credits: Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query Retrieve all data for all instruments for a given periode of time

retrive dpas data for all ics instruments ... (1)

• Download

This workflow demonstrates the standard query where events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS. In this version data from only 3 random events (out of the HEC list) will be requested from the DPAS.

Created: 2010-09-14 | Last updated: 2010-09-14

Credits: Anja Le Blanc

Attributions: retrive dpas data for all ics instruments for HEC event data

From PDF to lemmatized text (1)

• Download

This workflow uses the web service stationed in JSI (IJS Slovenia), which is based on Matjaž Juršič's LemmaGen - lemmatization engine. The workflow accepts a PDF file as an input an uses James Eales's wrokflows to preprocess the data. The workflow interactively asks the user of which language is the text, since the lemmatization process is language based. The output is a string in Taverna Workbench.

Created: 2010-09-16 | Last updated: 2012-01-18

Credits: Netr James Eales

Attributions: PDF to plain text Clean plain text

BowtieToPileup (1)

• Download

This example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. By analysing an actual data set (SNP detection in N. vitripennis) and translating this analysis pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and some of the SAMtools. Instead of ...

Created: 2010-09-16

Population projection transport simulation (1)

• Download

Neiss Transport Sim Demo. Runs a population reconstruction model (PRM) from census data, then projects the simulation through time. Also runs a transport simulation before and after the projection.

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Nick Malleson

Maptube mapper (2)

• Download

Takes a URL of some spatially-aggregated data and a field/column name to map and generates a MapTube url to an online map of the data.

Created: 2010-09-22 | Last updated: 2011-01-10

Credits: Nick Malleson

BioXSD example workflow (1)

• Download

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 :(

Created: 2010-10-12 | Last updated: 2010-10-12

Credits: Peter Li

Polygon buffer - Using pyWPS (1)

• Download

Basic example on how to integrate a Web Processing Service (WPS) using  PyWPS's WSDL/SOAP The workflow will accept a GML file with featureCollection where polyon is described using gml:coordinate element structure. This GMl is easely generated with GDAL. The coodinate structure will be converted to WKT and used to create a polygon using shapely, the output will be a buffer polygon with a defined width. Output polygon will replace the orginal polygon and the existing XML will be return...

Created: 2010-10-26 | Last updated: 2010-10-26

Credits: Jorgejesus

Decode base64 to byte[] (1)

• Download

The decode base64 to byte[] service decodes the base64 string. The byte array is then converted into the string 'Hello world'.

Created: 2010-10-28

Encode byte[] to base64 (1)

• Download

The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

Created: 2010-10-28

Read GenBank file (1)

• Download

The Read_GenBank_file service reads the file at the genbank_file_url and converts the GenBank data into Agave format. The result is then sent to the workflow's gen_bank_data port.

Created: 2010-10-28 | Last updated: 2010-10-28

Read SwissProt file (1)

• Download

The Read_SwissProt_file service reads the file at the swiss_prot_file_url and converts the SwissProt data into Agave format. The result is then sent to the workflow's swiss_prot_data port.

Created: 2010-10-28 | Last updated: 2010-10-28

Reverse complement DNA (1)

• Download

The Reverse Complement DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding reverse complement sequence, in this example, 'atggaggatc'.

Created: 2010-10-28

Transcribe DNA (1)

• Download

The Transcribe DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding transcribed RNA sequence, in this example, 'gauccuccau'.

Created: 2010-10-28

Concatenate files - echo results and multi... (1)

• Download

The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has been given a default value of...

Created: 2010-10-28

Concatenate files - echo results but no files (1)

• Download

The split_string_into_string_list_by_regular_expresson outputs an empty list since the string to be split is defaulted to ''. As there are no input values, the create_and_populate_temporary_file generates an empty list. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service does not write anything to the temporary output file. Because the displayresults port has been given a default value of 'true', the empty string is ...

Created: 2010-10-28

Concatenate files - multiple files (1)

• Download

The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has no value, the results are not...

Created: 2010-10-28

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

• Download

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: 2010-10-28 | Last updated: 2010-10-28

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

• Download

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 output port of the workflow.

Created: 2010-10-28 | Last updated: 2010-10-28

Get Environment Variables as XML (1)

• Download

The Get_Environment_Variables_as_XML service returns an XML file containing a set of property elements each of which contains the name and value of an environment variable.The Get_Environment_Variables_as_XML service returns an XML file containing

Created: 2010-10-28

List files by extension - empty directory (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_extension service. Since no files end in ".png", an empty list is output.

Created: 2010-10-28

List files by extension - no matches (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service. Since no files end in ".fred", an empty list is output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by extension - several matches (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file paths to the three files ending in ".png" are output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by extension - single match (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file path to the one file ending in ".bin" is output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by regex - empty directory (1)

• Download

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_regex service. Since there are no files, an empty list is output.

Created: 2010-10-28 | Last updated: 2010-10-28