Workflows

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

• Download

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

GetCities2 (1)

• Download

 Get cities by entering a country name

Created: 2012-05-03 | Last updated: 2012-05-03

Credits: Xiaoxiaoshijie

SNP Position Information (1)

• Download

This workflow extracts information about the position of SNPs and the genes they are associated with, using BioMart (ENSEMBL Variation 66).

Created: 2012-04-17 | Last updated: 2012-04-17

Credits: Katy Wolstencroft

Match gene lists based on information in l... (7)

• Download

[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics

Attributions: Match concept profiles Explain concept scores

ICDAR 2011 End-to-End Applications contest... (1)

• Download

Full workflow for use with the DAE platform and as used for the ICDAR 2011 "Document Analysis Algorithm Contributions in End-to-End Applications" contest, including contributed algorithms.

Created: 2012-04-14 | Last updated: 2012-04-14

Credits: Bart Lamiroy

Create and execute a simulation on the RIS... (1)

• Download

Create and execute a simulation on the RISE server. This workflow take 3 inputs: the XML to configure the RISE framework, the URL of the ZIP file model (a zipped directory containing the model files), and the new framework name. This workflow produce on the output the simulation LOG file.

Created: 2012-04-09

Unix tool service using string replacement (1)

• Download

The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2012-04-05

Credits: Alan Williams

Spreadsheet Import Example (1)

• Download

Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2012-04-05

Credits: Alan Williams

Simple Python example (1)

• Download

This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2012-04-05

Credits: Alan Williams

Secure Web service call example (2)

• Download

This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu. You ...

Created: 2012-04-05 | Last updated: 2013-06-11

Credits: Alan Williams

Retrieve sequence in EMBL format (1)

• Download

This workflow retrieves a sequence associated with its features in embl format

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

Credits: Alan Williams

Render gene via BioGPS (3)

• Download

This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: Alan Williams

Pipelined list iteration (1)

• Download

Perform multiple iterations of services in order to show pipelining

Created: 2012-04-05

Credits: Alan Williams

Numerically adding two values. (1)

• Download

This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2012-04-05

Credits: Alan Williams

Multiple choice quiz (1)

• Download

A fun example workflow showing user-interaction and service looping

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

Credits: Alan Williams

Hello World (1)

• Download

One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

Hello Anyone (1)

• Download

An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

GBSeq test (1)

• Download

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

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

Credits: Alan Williams

Fetch Dragon images from BioMoby (1)

• Download

Fetch images and annotations of snapdragons

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

Credits: Alan Williams

Fetch today's xkcd comic (1)

• Download

Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2012-04-05

Credits: Alan Williams

Fetch PDB flatfile from RCSB server (1)

• Download

Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2012-04-05

Credits: Alan Williams

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

• Download

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 data from remote servers; XPath activity is then used to parse the XML data a...

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

Credits: Alan Williams

Example of explicit looping (1)

• Download

This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2012-04-05

Credits: Alan Williams

Example of conditional invocation (1)

• Download

This workflow demonstrates how nested workflows can be conditionally invoked

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

Credits: Alan Williams

Example for external tools with zip and unzip (1)

• Download

This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

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

Credits: Alan Williams