Workflows

Read files from Directory (1)

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This workflow reads files from a given directory, based on a known file extension (e.g. .txt), and then outputs the contents of each file in a single value/single list.

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Remove Non-ASCII (1)

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THis workflow removes any non-ascii characters from a segment of text. Any characters that are found are removed. Letters either side f the non-ASCII are concatenated - this may cause the loss of word meaning

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

PubMed Search (1)

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This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Using a Create_List script with a dot-prod... (1)

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Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

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

Credits: Stian Soiland-Reyes

Rank Phenotype Terms (1)

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

Credits: Paul Fisher

Attributions: Cosine vector space Rank Phenotype Terms

Select redundant accessions (1)

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Simple workflows to select accessions which appear more than once. Chose threshold to specify how many times an accession has to appear to be selected. This workflow uses a list of Comma-separated values as input. The accessions selected is the result which is presented in a String of Comma-separated values.

Created: 2011-01-31 | Last updated: 2011-01-31

Credits: Rafael C. Jimenez

Define one query and retrieve Molecular In... (3)

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Define one query and retrieve Molecular Interactions from PSICQUIC Services registered in the PSICQUIC registry.

Created: 2011-01-31 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

MythMiner - Recommendation system for Myth... (1)

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This process creates recommendations from the MythTV PVR database. Programs which have been recorded are assumed to be interesting, those not recorded to be not interesting. The model is then applied to future program data. Interesting programs are saved in an HTML file which can be mailed to the user. This process has a few dependencies, please note homepage: http://tud.at/programm/mythminer/

Created: 2011-01-30

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2011-01-27 | Last updated: 2011-01-27

Credits: Maninder

[deprecated] Probabilistic Model Checking ... (1)

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2267 . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/1790).

Created: 2011-01-26 | Last updated: 2011-07-20

Credits: trybik

[deprecated] Probabilistic Model Checking ... (1)

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2266.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations.

Created: 2011-01-26 | Last updated: 2011-07-20

Credits: trybik

[deprecated] Simulate SBML-derived ODEs (1)

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This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2264.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.

Created: 2011-01-26 | Last updated: 2011-07-20

Credits: trybik

mathPlot Web service (1)

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Plotting operation which uses Mathematica (http://www.wolfram.com/mathematica/) software.

Created: 2011-01-26 | Last updated: 2011-01-26

Credits: trybik

odeSolver Web service (1)

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SBML ODE Solver Library (http://www.tbi.univie.ac.at/~raim/odeSolver/) Web service.

Created: 2011-01-26 | Last updated: 2011-01-26

Credits: trybik

sbml2Prism Web service (1)

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For example of the SBML to PRISM translation and the description of its details see http://www.prismmodelchecker.org/manual/RunningPRISM/SupportForSBML .

Created: 2011-01-26 | Last updated: 2011-01-26

Credits: trybik

asynchronous prism Web service (1)

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Asynchronous version of the Prism Web service. Results XML list is sent via email.

Created: 2011-01-26 | Last updated: 2011-01-26

Credits: trybik

prism Web service (1)

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PRISM model checking (http://www.prismmodelchecker.org/manual/RunningPRISM/ModelChecking). The '-fixdl' switch is used, which means that all deadlock states in model are fixed by addition of self-loops.

Created: 2011-01-26 | Last updated: 2011-01-26

Credits: trybik

SELECT3 (2)

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Select3 decides if a particular transition matches the selection criteria based on the line strength and line opacity in a given medium. To do that select3 requires a model of the medium (temperature, pressure, node spacing), chemical composition and boundary conditions. Only 1D models are supported at the moment. Select3 processes one transition at a time working in two modes: opacity and synthesis. In the first mode it computes line opacity, compares it to the reference (e.g. bf and ff opa...

Created: 2011-01-22 | Last updated: 2011-02-27

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. 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 Entrez and 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 data...

Created: 2011-01-21 | Last updated: 2011-01-21

Credits: Paul Fisher

Change Class Distribution of Your Training... (1)

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This example process shows how to change the class distribution of your training data set (in this case the training data is what ever comes out of the "myData reader"). The given training set has a distribution of 10 "Iris-setosa" examples, 40 "Iris-versicolor" examples and 50 "Iris-virginica" examples. The aim is to get a data set which has the class distribution for the label, lets say 10 "Iris-setosa", 20 "Iris-versicolor" and 20 "Iris-virginica. Beware that this may change some propert...

Created: 2011-01-21 | Last updated: 2011-01-21