Workflows

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

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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

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 output port of the workflow.

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

Get Environment Variables as XML (1)

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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)

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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)

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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)

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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)

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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)

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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