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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

PRM With External Data (1)

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IN PROGRESS! Runs the PRM using data from an external on-line source.

Created: 2011-01-19 | Last updated: 2011-01-19

Credits: Nick Malleson

QSPR Model Discovery -- workflow structure... (2)

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replicates the structure of the QSPR model discovery workflow. Ref.: replicates the structure of the QSPR model discovery workflow. Ref.: http://www.openqsar.com/

Created: 2011-01-18 | Last updated: 2011-01-18

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan on provided sequencesThis workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2011-01-17 | Last updated: 2011-01-17

Credits: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes

Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan

Split Molecules Into Clusters (1)

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This workflow splits given molecules into their cluster memberships. The molecules are loaded from a SD file and the relationship data from a CSV file. The results are saved into N different SD files, where N is the number of clusters.

Created: 2011-01-17 | Last updated: 2011-07-21

2. Getting Started: Retrieve and Apply a M... (1)

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This getting started process demonstrates how to load (retrieve) a model from the repository and apply it to a data set. The result is a data set (at the lab output for "labeled data" ) with has a new "prediction" attribute which indicated the prediction for each example (ie. row/record). You will need to adjust the path of the retrieve data operator to the actual location where the model is stored by a previews execution of the "1. Getting Started: Learn and Store a...

Created: 2011-01-17 | Last updated: 2011-01-19

1. Getting Started: Learn and Store a Model (1)

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This getting started process shows the first step of learning and storing a model. After a model is learned, you can load (Retrieve operator) the model and apply it to a test data set (see 2. Getting Started: Retrieve and Apply Model). The process is NOT concerned with evaluation of the model. This process will not immediately run in RapidMiner because you have to adjust the repository path in the Retrieve operator. Tags: Rapidminer, model, learn, learning, training, train, store, first step

Created: 2011-01-17 | Last updated: 2011-01-17

Count co-occurences in matrix with Aggrega... (1)

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The process counts and shows all combinations of values of two attributes and shows them in a count matrix. The process uses the operators Aggregate and Pivot for this purpose.

Created: 2011-01-15

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Fluid Dynamics Error

Created: 2011-01-14 18:26:24 | Last updated: 2011-01-14 18:26:25

Credits: Mity

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Word document

Comments: 0 | Viewed: 25 times | Downloaded: 90 times

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Weka Clustering Considering Different Orig... (2)

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This workflow clusters the given CSV files with the chosen Weka algorithm. The results are visualized in a PDF file. The CSV files are loaded from hard disk and merged together. Afterwards they are converted into a Weka dataset which is the suitable data type for the Weka clustering activity. The results are visualized as a PDF file showing the cluster membership of each input CSV file.

Created: 2011-01-13 | Last updated: 2011-07-21

Population reconstruction and dynamic popu... (2)

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Runs the population reconstruction model (PRM) to create a synthetic individual-level population and then projects the population through a number of years. This is still in progress, results cannot be made public yet.

Created: 2011-01-12 | Last updated: 2011-01-19

Credits: Nick Malleson

Text stemming with Porter Stemmer (1)

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This workflow does text stemming. Stemming removes the inflicted endings of words. It is often used as text preprocessing for text mining, since stemmed words can be easily matched and counted. The input to the workflow is the text to be stemmed, the output is the stemmed text.  

Created: 2011-01-11 | Last updated: 2011-01-11

Credits: Petra Kralj Novak

JSI Subgroup Discovery operators (1)

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A simple example of how to use subgroup discovery operators for learning subgroup descriptions and how to test their classification accuracy using cross-validation.

Created: 2011-01-10 | Last updated: 2011-01-10

Text preprocessing (1)

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The input to this workflow is plain text. The text is preprocessed so that non- alfanumeric symbols are removed, the text is transformed to to lower case and stop words are removed. The workflow first removes the charachters from this set: `~!@#$%^&*()_+=-{}|\][":;'?><,./. Then it transforms the text to lower case. The user will be prompted to select a dictionary for stop words from a list. The workflow will, based on the selected list, remove the stop words. Stop words are...

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

Credits: Petra Kralj Novak

RBioconductor Tutorial Process (1)

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This Process illustrates how to create complex Data Analysis processes using R Scripts. In this case the Bioconductor Basic Tutorial is splitted into reusable components.

Created: 2011-01-03

Select from a list of possible web service... (1)

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The workflow for selecting from a list of possible web service parameter values has two input ports: the wsdl address of the web service and the variable name. It parses the web service wsdl description (the web service http://ropot.ijs.si/webservices/janez/getvalues.php?wsdl does that) and then it asks the user to select one value from a drop-down menu. This workflow is very useful when web services have inputs which expect as a parameter one value from a list of possible values.

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

Credits: Petra Kralj Novak Janez Kranjc

Lemmatization (3)

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The workflow lemmatizes the text in the input port. Takes text as input and returns (language dependent) lemmatized text as output. All the words in the resulting text are in the same order as in the original text, but they are transformed to their dictionary form. The workflow asks for the language of lemmatization. Currently, 12 languages are supported: en,sl,ge,bg,cs,et,fr,hu,ro,sr,it,sp.

Created: 2010-12-17 | Last updated: 2010-12-23

Credits: Petra Kralj Novak

Attributions: Select from a list of possible web service parameter values

Get Molecular Weight Distribution From QSA... (2)

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This workflow calculates a molecular weight distribution from given QSAR vector. The QSAR data containing the molecular weight values is read from a CSV file and converted into a QSAR vector. Finally, the Get_molecular_Weight_Distribution_From_QSAR_vector extracts the weight data and saves it as CSV files.

Created: 2010-12-15 | Last updated: 2011-07-21

Compound Library Screen For Reaction Enume... (2)

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This workflow performs a compound library screen for molecules which match the given template reaction. The reaction is loaded from a RXN file and the Reaction_Reactant_Splitter splits the reaction into its reactants. The compound library is loaded iteratively from a SD file. Afterwards a substructure search is performed for each reactant and the results are saved as SD files.

Created: 2010-12-14 | Last updated: 2011-07-21

Biomart and 2x BLAST (1)

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Perform Roden and Invertebrates BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). blast_ddbj_invertebrates and blast_ddbj_rodents should execute in parallel as they don't depend on each other.

Created: 2010-12-13 | Last updated: 2010-12-13

Biomart and Blast with concatinated gene id (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service Biomart and Blast

Biomart and Blast (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service

ART-2a Classification Considering Differen... (2)

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This workflow classifies the given CSV files with the ART-2a algorithm. The results are visualized in a PDF file. The QSAR dara is loaded from CSV files and merged together by the Merge_QSAR_Vectors worker. Afterwards they are converted into a fingerprint items list which is the suitable data type for the ART-2a algorithm.

Created: 2010-12-13 | Last updated: 2011-07-21

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Example R workflows

Created: 2010-12-13 10:44:04 | Last updated: 2010-12-13 16:28:58

10 items in this pack

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Loop Repository and Append Data (1)

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This process flow loops through all exampleset '.ioo' files in a repository directory and appends their values. It can also be used as a template for batch processing on different repository entries, or for general data appending.

Created: 2010-12-10 | Last updated: 2010-12-10

Using R to add two columns (1)

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This process shows a simple R script which adds two columns of a data set with R. Of course this is much simpler by using the operator "Generate Attributes" which is done in parallel, but maybe some of you find this short process helpful in order to get started with R.

Created: 2010-12-10 | Last updated: 2010-12-10

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Presentation - Why Linked Data is Not Enough for Sci...

Created: 2010-12-09 22:18:43 | Last updated: 2010-12-10 01:58:30

2 items in this pack

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ART-2a Classification Result As PDF (2)

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This workflow classifies a given CSV file with the ART-2a algorithm. The results are visualized in a PDF file. The QSAR data is loaded from a CSV file and converted into a fingerprint items list which is the suitable data type for the ART-2a algorithm.

Created: 2010-12-09 | Last updated: 2011-07-21

Curate QSAR descriptor CSV file (2)

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This workflow erases descriptor entries which were not calculated. The QSAR data is loaded from a CSV file and afterwards processed by the Curate_QSAR_Vector worker. At the end the curated CSV file is written to hard disk.

Created: 2010-12-09 | Last updated: 2011-07-21

Merge QSAR descriptor CSV files (3)

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This workflow merges QSAR descriptor CSV files into a single CSV file. The workflow loads the CSV files from hard disk and builds a single QSAR descriptor vector. Afterwards the vector is converted in one single CSV file and saved to hard disk.

Created: 2010-12-09 | Last updated: 2011-07-21

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Presentation - The Evolution of myExperiment

Created: 2010-12-09 05:11:17 | Last updated: 2010-12-09 05:49:11

2 items in this pack

Comments: 0 | Viewed: 20 times | Downloaded: 6 times

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Text Mining Workflows

Created: 2010-12-08 11:55:03 | Last updated: 2011-02-01 11:33:11

5 items in this pack

Comments: 0 | Viewed: 210 times | Downloaded: 67 times

Extract Scientific Terms (2)

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This workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Pathway to Pubmed (2)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Rank Phenotype Terms (2)

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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: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Rank Phenotype Terms

Cosine vector space (2)

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This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Cosine vector space

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Bilateral Perisylvian Polymicrogyria (Epilepsy)

Created: 2010-12-07 16:34:31 | Last updated: 2010-12-07 16:34:37

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

Comments: 0 | Viewed: 85 times | Downloaded: 0 times

WS-Security + HTTPS example workflow (1)

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This workflow shows an example access to various secure Web services protected by WS-Security authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

Created: 2010-12-03 | Last updated: 2010-12-03

Credits: Alex Nenadic

WS-Security example workflow (1)

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This workflow shows an example access to various secure Web services protected by WS-Security authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

Created: 2010-12-03 | Last updated: 2010-12-03

Credits: Alex Nenadic

HTTP Digest authentication + HTTPS example... (1)

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This workflow shows an example access to a resource protected by HTTP Digest  authentication and HTTPS. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

Created: 2010-12-03 | Last updated: 2010-12-03

Credits: Alex Nenadic

HTTP Digest authentication example workflow (1)

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This workflow shows an example access to a resource protected by HTTP Digest  authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.  

Created: 2010-12-03 | Last updated: 2010-12-03

Credits: Alex Nenadic

HTTP Basic authentication + HTTPS example ... (1)

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This workflow shows an example access to a resource protected by HTTP Basic authentication and HTTPS. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

Created: 2010-12-03 | Last updated: 2010-12-03

Credits: Alex Nenadic

HTTP Basic authentication example workflow (1)

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This workflow shows an example access to a resource protected by HTTP Basic authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

Created: 2010-12-03 | Last updated: 2010-12-03

Credits: Alex Nenadic