Workflows

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: EdwardKawas

BiomartAndEMBOSSAnalysis (1)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams

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: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

Extracting data from VOTable format by usi... (1)

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Input VOTable and 'name' of a Output corrosponding data of that field in an arrayInput VOTable and 'name' of a Field

Created: 2010-07-01 | Last updated: 2010-07-01

Credits: Anja Le Blanc Donal Fellows

Holograph Reduced Representation (1)

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After Kanerwa

Created: 2010-06-29

Workflow for Automated Comparative Protein... (2)

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This workflow performs "parallel" generic protein sequence analysis. In order to do that a list of known protein identifiers chosen by the biologist enters into the software to perform different multiple sequence alignments and finally phylogenetic analysis.

Created: 2010-06-29 | Last updated: 2010-08-31

Credits: Achille Zappa

Attributions: EBI_ClustalW_alignment_tree

Macro Propagation into Subprocesses and Ex... (1)

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<p> This small process demonstrates how to propagate macros into a subprocess or Execute Process operator </p> <p> When macros are set once, they are available in subprocesses imediatly (see Generate Attributes in the seconde Subprocess operator) </p> <p> If someone wants to propagate a macro into a Excecute Process operator one need to edit the "macros" parameter in the Parameters list of the Execute Process operator. </p> Tags: Subprocess, Execute Proc...

Created: 2010-06-25

Resolve an InChIKey on ChemSpider (1)

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 Resolves an InChIKey on ChemSpider and opens the search results in a molecules table.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Downloads all Bioclipse Scripting Language... (1)

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 Downloads all Bioclipse Scripting Language scripts uploaded to MyExperiment into the Bioclipse workspace, and opens them in JavaScript editors.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Syntetic population mapper (3)

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This workflow creates individual-level population from census data and then joins with the BHPS (British Household Panel Survey) and reaggregates. In the last stage it maps the chosen BHPS field.

Created: 2010-06-23 | Last updated: 2010-12-09

Credits: Alex Nenadic

Pre process data per group using recall re... (1)

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This process takes as input a dataset with different groups. For each group it discretises attributes into High, Medium, Low. This creates a group invariant representation.

Created: 2010-06-23 | Last updated: 2010-06-23

Discretization into Deviation Interval aro... (1)

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This process shows how numerical attributes can be discretized into intervals based on the standard deviation for each attribute around their mean values.

Created: 2010-06-22 | Last updated: 2010-06-22

Finding all Examples that have duplicate v... (1)

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This process will retrieve all examples, who have identical values in a specific attribute. For testing, the following data can be writen into the file, that will be read by the Read CSV operator: CID,Value 3596,X 4054,X 4054,X 3000,S 3000,T 3000,U 32135,S The target of this process is to return the two examples having the same value in the CID column. To achieve this, first a real id is generated by the generate id. After this, we have to find all duplicates: For this we first remove dupl...

Created: 2010-06-18

Optimizing Discretization (1)

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This process generates a decision tree on the Iris data set. Before the decision tree is generated, the input attributes are discretised so we only work on nominal attributes. We use a combination of "Select Subprocess" and "Optimize Parameters" to select the best out of five different discretizazion methods independently for each of the attributes. The process shows, that the resulting accuracy heavily depends on the choice of the method. It varies between 64% and 94%.

Created: 2010-06-18 | Last updated: 2010-06-18

Phylogenetic Study Using the Bio Extract S... (2)

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This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced the...

Created: 2010-06-17 | Last updated: 2010-07-19

Credits: Kendra Giesey BioExtract Server for Genomics

SDS-Page Gel (1)

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Created: 2010-06-17 | Last updated: 2010-06-17

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

Unbiasing procedure (1)

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It is a workflow for description of our unbiasing procedure that is used in LiquidPub project,  "Peer Review and Reviewer Behavior" branch. The procedure is used  for conducting experiments on conference data.

Created: 2010-06-16 | Last updated: 2010-06-16

Credits: Katsiaryna Mirylenka

Preprocessing nominal data for frequent it... (1)

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This process will first create artificial data that can be compared to usual data loaded for frequent item set mining: Nominal Data with a true and false value, but differently mapped to internal indices. For ItemSet Mining these must be preprocessed to avoid problems: First they have to be transformed to Binominal Attributes, then it has to be defined, which is the positive and the negative value.

Created: 2010-06-16 | Last updated: 2010-06-16

PI_Calculation (1)

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Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou