Workflows in this Topic

Genome annotation pipeline demonstrator wo... (2)

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Part of a workflow by Hannah Tipney, adapted by Duncan Hull using GenScan, RepeatMasker and BLAST. http://dx.doi.org/10.1093/nar/gkl320

Created: 2007-10-03

fetchEnsemblSeqsAndBlast (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2008-04-18 | Last updated: 2008-04-18

Credits: Bela

blast_simplifier.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

add_ncbi_to_string.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

parse_uniprot_2.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

swiss_and_name_seq.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

get_best_best_neighbors_by_gene (1)

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Search the best-best neighbor of a gene in all organisms. Example of input: gene_id: eco:b0002 offset: 1 limit: 10

Created: 2008-10-02

Credits: Franck Tanoh

firstwf (1)

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No description

Created: 2008-11-13

Credits: Rory

t ... (2)

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Created: 2009-08-21 | Last updated: 2009-10-09

Credits: Ctindal

example of a 2-deep nested workflow (1)

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used for testing provenance as well as experimenting with Scufl2 specfications

Created: 2009-09-11

Credits: Paolo

Provenance Challenge 1 workflow -- mockup ... (1)

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simulates the image processing for the PC1 workflow using beanshell that simply track test strings an image is a pair (header, image) specified as a list of depth 1: [header,image] so each processor with image input takes an input list. Note that the processors are designed to operate on single images (except softmean that operates on a list of images), but because the initial input is a list of images, all are processed by implicit iteration.

Created: 2010-05-28

Credits: Paolo

Quality control processing of GEO datasets (2)

The workflow performs a quality control process on gene expression data sets stored in the Gene Expression Omnibus database. The QC process is performed using Bioconductor R packages. A variety of statistics are produced by the workflow including a diagnostic plot from snm normalisation and nucleotide composition bias.

Created: 2011-04-06 | Last updated: 2011-04-11

Credits: Peter Li Bhmecham

External Tool: Numerically adding two valu... (1)

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The workflow is an examples for the External Tools / UseCase plugin to integrate external tools. It wraps the "bc" command line calculator. Internally, it executes the following script: if [ ! -r "$1" ]; then echo "Cannot read file indicated by first argument '$1'." ; exit -1 ; fi ; if [ ! -r "$2" ];then echo "Cannot read file indicated by second argument '$1'." ; exit -1 ; fi if [ -x /usr/bin/bc ]; then ...

Created: 2011-05-06 | Last updated: 2011-05-06

Credits: Steffen Möller

DAS features retrieval and parsing with JDAS (2)

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Retrieve Protein or Genome features using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.

Created: 2011-06-01 | Last updated: 2011-06-02

Credits: Rafael C. Jimenez

Extract histogram features from image file (1)

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As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This project enables creation of WSDL web service that wraps command line tool like ‘extractFeatures’ or ‘create’. The workflow for ‘extractFeatures’ tool has two input parameters. The URL to the input image file and the number of histogram bins as integer. This workflow extracts histogram feature...

Created: 2011-06-16 | Last updated: 2012-04-04

Credits: Roman

Compare histogram features of image files (1)

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As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This project enables creation of WSDL web service that wraps command line tool like ‘extractFeatures’ or ‘create’. The workflow for ‘compare’ tool has three input parameters. These are two URLs to the XML histogram files that comprise information about image features. These files are acquired us...

Created: 2011-06-16 | Last updated: 2012-04-04

Credits: Roman

[untitled] (1)

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This is simly a test fortest

Created: 2011-06-19 | Last updated: 2011-06-19

Credits: Merdmann

Extract histogram features from image file... (1)

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The main element of this workflow is a RESTful service designed in the SCAPE QA command line tools RESTful package https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper-rest. The Github project https://github.com/openplanets/scape/tree/master/xa-rester from Andy Jackson is a basis implementation for pc-qa-toolwrapper-rest package. The QA REST package enables creation of RESTful web service that wraps QA command line tool like ‘extractfeatures’ or ‘create’...

Created: 2011-07-01 | Last updated: 2012-04-04

Credits: Roman

Common SCAPE QA command line tool RESTful ... (1)

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The QA REST package enables creation of RESTful web service that wraps any QA command line tools. The main element of this workflow is a RESTful service designed in the SCAPE QA command line tools RESTful package https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper-rest. The Github project https://github.com/openplanets/scape/tree/master/xa-rester from Andy Jackson is a basis implementation for pc-qa-toolwrapper-rest package. The workflow comprises path to the RESTful servi...

Created: 2011-07-01 | Last updated: 2012-04-04

Credits: Roman

OpenTox Upload and merge data sets (1)

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Uploads 2 data sets to OpenTox, merges them and returns the merged data set.

Created: 2011-08-08 | Last updated: 2011-08-08

Get My Weather (1)

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Gets a variety weather info for "Cleveland" and "Indianapolis" Based on "Get weather information" by Franck Tanoh

Created: 2011-09-13 | Last updated: 2011-09-13

Credits: Mutanthumb

Population histogram in R (1)

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This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: Wdsnellg

New York vs. New Jersey Broccoli Production (1)

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Uses the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports two files and generates a single graph comparing the information from the two spreadsheets.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: tpacurtis Alan Williams

Attributions: Spreadsheet Import Example NY Broccoli Production NJ Broccoli Production

DNA Shuffling Template - part 3: PCR (1)

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No description

Created: 2011-10-12 | Last updated: 2011-10-12

Credits: http://thebluerhino.myopenid.com/

Sample IMPACT hackathon workflow (1)

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Workflow that implements the Use Case for Group 2 at the IMPACT/Taverna hackathon. What it does is to take the URL of a TIFF image and compute the Levenshtein difference between the OCR output of the uncompressed version with various ones compressed at various bit rates.

Created: 2011-11-14 | Last updated: 2012-06-19

Credits: Donal Fellows

Image files comparison using histograms an... (2)

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This workflow extracts histogram and profile features from image file applying image processing command line tool. Necessary configuration files are stored on Github (https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper). As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This workflow provides WSDL web service that wraps command line tool with tho options ‘extra...

Created: 2011-11-22 | Last updated: 2011-11-23

Credits: Roman

Literacy Rate and GDP/Capita Increase (Per... (1)

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This is a workflow for a Cyberinfrastructure class (Fall 2011) at Syracuse University. It takes information from GapMinder and runs it through a workflow to produce a graph. The original data sets can be found here: https://spreadsheets.google.com/pub?key=pyj6tScZqmEdrsBnj2ROXAg&gid=0 (Literacy rate, adult total) https://spreadsheets.google.com/pub?key=phAwcNAVuyj1jiMAkmq1iMg&gid=0 (Income per person)

Created: 2011-11-28 | Last updated: 2011-11-28

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example

A heuristic measure for detecting undesire... (2)

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The workflow takes TIFF image instances as input, applies a list of JP2 compression parameter values, executes OCR using an open source OCR engine, evaluates the results, and creates a diagram visualising the results. Dependencies on external tools for the tool service components: Tesseract ImageMagick Kakadu Gnuplot Dependencies on external Java libraries of beanshells: Apache commons lang

Created: 2012-02-06 | Last updated: 2012-03-09

Credits: Sven

Get a list of Protein Identification exper... (3)

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Get a list of Protein Identification experiments from PRIDE by a Gene Ontology query

Created: 2012-02-21 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Image Characterisation - Fits (Simple) (1)

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Extracts metadata from images.

Created: 2012-02-27 | Last updated: 2012-02-27

Credits: Markus Plangg

Planning Overview (Scp, Migration, Charact... (1)

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Copies an image from a remote path using scp. Then starts a migration action on the image and extracts properties from the original and migrated image. The properties are compared and on the image data itself, QA algorithms are started.

Created: 2012-02-28

Credits: Markus Plangg

Jpylyzer Review Demonstration (1)

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 Review demonstration workflow that compares the jpylyzer tool with the struct checker and jhove.  Runs on British Library JISC 1 content, looking for invalid images.

Created: 2012-03-15 | Last updated: 2012-03-15

Credits: Carl

Get FlyTED Gene Expression Images for a Ge... (1)

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This is a simple workflow testing running a restful service in Taverna. This restful service http://www.open-biomed.org.uk/service/flyted/records/probe/{probe} is part of the flykit/flyted services http://code.google.com/p/open-biomed/wiki/Flyted, which is built using the Talis Puelia Linked Data API (http://code.google.com/p/puelia-php/). We want to use this simple workflow to test the idea of bridging linked data and scientific workflows using Restful services. A test input gene name can ...

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Junzhao

Get Alternative Gene Names for a Drosophil... (1)

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This is a simple workflow testing running a restful service in Taverna. This restful service http://www.open-biomed.org.uk/service/flybase/features/name/{name} is part of the flykit/flybase services http://code.google.com/p/open-biomed/wiki/Flybase, which is built using the Talis Puelia Linked Data API (http://code.google.com/p/puelia-php/). We want to use this simple workflow to test the idea of bridging linked data and scientific workflows using Restful services. A test input gene name...

Created: 2012-05-04 | Last updated: 2012-05-04

Credits: Junzhao

Search for Gene Expression Images using an... (1)

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This is a simple workflow demonstrating how to integrate multiple linked data sources using restful services in Taverna. In this workflow it first searches for all possible gene names for a query gene from FlyBase repository, an authorative genetic database for Drosophila research, and then it uses returned gene names to search for gene expression images from Oxford FlyTED image repository. Two Restful services were used: One for retrieving all flybase features matching a querying ge...

Created: 2012-05-04 | Last updated: 2012-05-08

Credits: Junzhao

Simple image migration (1)

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Then starts a migration action on an image and extracts properties from the original and migrated image. The properties are compared and a QA algorithms is started on the image data itself .

Created: 2012-05-08 | Last updated: 2012-05-08

Credits: Markus Plangg

Mp3ToWav Mig+QA (2)

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Migrates Mp3 files from input List to Wav files and performs QA. The QA steps include File Format Validation, Significant Property Comparison and migrationQA file content comparison (all CLI). This workflow matches solution SO4 on the SCAPE opf wiki, see http://wiki.opf-labs.org/display/SP/SO4+Audio+mp3+to+wav+Migration+and+QA+Workflow

Created: 2012-05-21 | Last updated: 2013-04-24

Credits: Bolette Jurik

Image Characterisation - Fits (Extended) (1)

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Extracts metadata from images.

Created: 2012-06-06 | Last updated: 2012-06-06

Credits: Markus Plangg

Simple executable plan example (1)

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A simple executable plan containing a migration action component and a QA component. The migration action uses imagemagick convert. The QA component consists of two characterisation components (fits) and another QA components (imagemagick compare).

Created: 2012-06-29

Credits: Markus Plangg

Find Duplicates using Matchbox command lin... (1)

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The workflow takes a list of digital documents as input, extracts SIFT features using image processing algorithms, creates dictionary of visual words, generates BoW (Bag of Words) histogramms and finds duplicates. The count of parallel threads can be passed as a parameter. Finally search results are stored in a text file that contains a list of possible duplicates with associated similarity score. This score values are spread between 0 (low similarity) and 1 (high similarity). Image compariso...

Created: 2012-07-31 | Last updated: 2012-07-31

Credits: Roman

Hadoop Large Document Collection Data Prep... (1)

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Workflow for preparing large document collections for data analysis. Different types of hadoop jobs (Hadoop-Streaming-API, Hadoop Map/Reduce, and Hive) are used for specific purposes. The *PathCreator components create text files with absolute file paths using the unix command 'find'. The workflow then uses 1) a Hadoop Streaming API component (HadoopStreamingExiftoolRead) based on a bash script for reading image metadata using Exiftool, 2) the Map/Reduce component (HadoopHocrAvBlockWidthMapR...

Created: 2012-08-17 | Last updated: 2012-08-18

Credits: Sven

Matchbox Evaluation (1)

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Matchbox evaluation against ground truth. The evaluation process first creates the matchbox output and ground truth lists. It then counts each page tuple from the matchbox output that is in the ground truth as correctly identified tuple (true positive). Those that are not in the ground truth are counted as incorrectly identified tuples (false positives), and finally, those that are in the ground truth but not in the matchbox output are counted as missed tuples (false negatives). The precision...

Created: 2012-10-02 | Last updated: 2012-10-02

Credits: Sven

Tesseract 2.04 Basic Workflow (1)

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 Elementary workflow for execution on the on-line DAE platform. (requires an uncompressed tiff image URL as input or will fail otherwise)

Created: 2012-10-16

Credits: Bart Lamiroy

Ocrad 0.19 Basic Workflow (1)

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Elementary OCR workflow for execution on the on-line DAE platform. Implement v0.19 of the ocrad OCR engine. (requires an PGM or PMB input image URL) 

Created: 2012-10-16 | Last updated: 2012-10-16

Credits: Bart Lamiroy

Convert (1)

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Elementary workflow for execution on the on-line DAE platform. Converts an input image into another format by using the ImageMagick "convert" program.

Created: 2012-10-16 | Last updated: 2012-10-16

Credits: Bart Lamiroy

Mp3 To Wav Migrate QA CLI List Test (4)

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Migrates Mp3 files from input List to Wav files and performs QA. The QA steps include File Format Validation, Significant Property Comparison and migrationQA file content comparison (all CLI). As this is a Test workflow, the (very large) Wav files are deleted, and only the QA results and log files are saved for analysis. This workflow matches solution SO4 on the SCAPE opf wiki, see http://wiki.opf-labs.org/display/SP/SO4+Audio+mp3+to+wav+Migration+and+QA+Workflow

Created: 2012-11-05 | Last updated: 2012-11-13

Credits: Bolette Jurik

AIT Matchbox Scenario All (1)

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In this scenario matchbox will find duplicates in passed digital collection. All matchbox workflow steps are executed automatically in one turn. User will get a list of duplicates in result. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24 | Last updated: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Professional (3)

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In this scenario matchbox will find duplicates in passed digital collection. Each matchbox workflow step can be executed separately. User will get a list of duplicates in result. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine. This workflow starts duplicate finding process using the FindDuplicates python script of the matchbox tool. Matchbox tool support python in version 2.7. Execution starts from the directory where python scripts ...

Created: 2012-11-24 | Last updated: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Find Duplicates usin... (1)

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In this scenario matchbox will find duplicates in passed digital collection. All matchbox workflow steps are defined separately using input parameter sequence: clean, extract, train, bowhist and compare. User will get a list of duplicates in result. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Check Duplicate Pair... (1)

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In this scenario matchbox will check duplicate pair of previously found duplicates in passed digital collection if output information was lost. The pair check does not require the time consumpting whole analysis and is very fast. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Compare Image Pair b... (1)

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In this scenario matchbox will compare given image pair based on extracted profile information. User will get a histogram intersection distance value in result. Small value means high similarity, high value means different images. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24

Credits: Roman