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Get a list of proteins from a Gene Ontolog... (1)

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Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow uses the the QuickGO service

Created: 2012-02-20 | Last updated: 2012-02-22

Credits: Rafael C. Jimenez

Run a Workflow on Taverna Server (local t2... (1)

Uses a local t2flow file to submit and run this workflow on the taverna server. You need a user name and password to execute this workflow. Input to the workflow which runs remotely will be requested interactively.

Created: 2012-02-20

Credits: Anja Le Blanc

Attributions: Run a Workflow on Taverna Server

Run a Workflow on Taverna Server (1)

Uses the URL to a t2flow file to submit and run this workflow on the taverna server. You need a user name and password to execute this workflow. Input to the workflow which runs remotely will be requested interactively.

Created: 2012-02-17 | Last updated: 2012-02-17

Credits: Anja Le Blanc

Simulation workflow for flooding emergency... (1)

Simulation workflow for flooding emergency simulation. This workflow cannot be executed as is due to authentification restriction, and local tools dependancies.

Created: 2012-02-15

document clustering (1)

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Tesla Experiment Clustering wikipedia articles of different topics Evaluation of the results with the purity measure and rand index

Created: 2012-02-15 | Last updated: 2012-02-17

Credits: AGeduldig

Radio lists search over time period (2)

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This workflow searches the wind stereo II IV radioburst list, wind tyhpe II soho cme list, hfc radioburst type III list, tsrs solar radio event list and combines the return of these lists chronologically. Only time_start, time_end, and comment sections are preserved in the result list.

Created: 2012-02-13 | Last updated: 2012-02-14

Credits: Anja Le Blanc

Render gene via BioGPS (2)

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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: 2012-02-10 | Last updated: 2012-02-15

Credits: Alan Williams

Parameter optimization (1)

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This is a parameter optimization workflow for rating prediction recommendation operators.

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

Credits: Matej Mihelčić

Associated Region to Gene List (1)

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Produces a gene list from the Associated Region XML file

Created: 2012-02-08 | Last updated: 2012-02-08

Credits: Paul martin

Make XML Parameters (1)

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Reformats a SNP list with optional p-value into the required XML input for the 'Define Associated Regions and Genes' workflow. Additional parameters can be supplied to add to the XML document.

Created: 2012-02-08 | Last updated: 2012-02-08

Credits: Paul martin

Define Associated Regions and Genes (2)

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Created: 2012-02-08 | Last updated: 2012-05-09

Credits: Paul martin

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

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HELIO Service Provider Set

Created: 2012-02-01 08:23:53 | Last updated: 2012-02-01 15:24:42

Credits: Anja Le Blanc

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 49 times | Downloaded: 38 times

Experimentation through repository access (1)

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This workflow reads train/test dataset from a specified RapidMiner repository and tests selected operator on that datasets. Only datasets specified with a proper regular expression are considered. Train and test data filenames must correspond e.g (train1, test1). Informations about training and testing data, performanse measures of a selected operator are stored as an Excel file. Note: Train/test file names should not be contained in the repository path. E.g training/train is not a god path,...

Created: 2012-01-31 | Last updated: 2012-02-01

Credits: Matej Mihelčić Matko Bošnjak tomS

Latex Text Cloud Visualization (1)

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An experiment to visualise my dissertation text within a word cloud. This experiment is configured for Windows. To run it under Linux or Mac, change the configuration file of the tree tagger wrapper.

Created: 2012-01-30 | Last updated: 2012-05-22

Credits: jhermes

Transforming user/item description dataset... (1)

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This workflow provides transformation of an user/item description attribute set, into a format required by attribute based k-NN operators of the Recommender extension. See: http://zel.irb.hr/wiki/lib/exe/fetch.php?media=del:projects:elico:recsys_manual_v1.1.pdf to learn about formats of datasets required by Recommender extension.

Created: 2012-01-30

Data iteration workflow (RP) (1)

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This is a data iteration workflow used to iterate throug query update sets.

Created: 2012-01-29

Credits: Matej Mihelčić Matko Bošnjak

Model update workflow (RP) (1)

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This is a Model update workflow called from data iteration workflow on every given query set. In the Loop operator model and current training set are retrieved from the repository. Model update is performed on a given query set creating new model. Model and updated train set are saved in the repository.

Created: 2012-01-29 | Last updated: 2012-01-30

Credits: Matej Mihelčić

recommender workflow (RP) (1)

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This is a main online update experimentation workflow. It consists of three Execute Process operators. First operator executes model training workflow. Second operator executes online updates workflow for multiple query update sets. The last operator executes performance testing and comparison workflow. Final performance results are saved in an Excel file.

Created: 2012-01-29

Credits: Matej Mihelčić

Model testing workflow (RP) (1)

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This workflow measures performance of three models. Model learned on train data and upgraded using online model updates. Model learned on train data + all query update sets. Model learned on train data only.

Created: 2012-01-29 | Last updated: 2012-01-30

Credits: Matej Mihelčić

Model saving workflow (RP) (1)

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This workflow trains and saves model for a selected rating prediction operator.

Created: 2012-01-29 | Last updated: 2012-01-30

Credits: Matej Mihelčić

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Rating prediction query datasets

Created: 2012-01-29 17:05:46 | Last updated: 2012-01-29 17:07:49

Credits: tomS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

Comments: 0 | Viewed: 66 times | Downloaded: 48 times

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Item recommendation query datasets

Created: 2012-01-29 17:02:50 | Last updated: 2012-01-30 13:20:16

Credits: tomS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

Comments: 0 | Viewed: 81 times | Downloaded: 70 times

Model update workflow (1)

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This is a Model update workflow called from data iteration workflow on every given query set. In the Loop operator model and current training set are retrieved from the repository. Model update is performed on a given query set creating new model. Model and updated train set are saved in the repository.

Created: 2012-01-29 | Last updated: 2012-01-29

Credits: Matej Mihelčić Matko Bošnjak

Data iteration workflow (1)

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This is a data iteration workflow used to iterate throug query update sets.

Created: 2012-01-29

Credits: Matej Mihelčić Matko Bošnjak

Model testing workflow (1)

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This workflow measures performance of three models. Model learned on train data and upgraded using online model updates. Model learned on train data + all query update sets. Model learned on train data only.

Created: 2012-01-29

Credits: Matej Mihelčić

Model saving workflow (1)

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This workflow trains and saves a model for a selected item recommendation operator.

Created: 2012-01-29 | Last updated: 2012-01-30

Credits: Matej Mihelčić

Recommender workflow (1)

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This is a main online update experimentation workflow. It consists of three Execute Process operators. First operator executes model training workflow. Second operator executes online updates workflow for multiple query update sets. The last operator executes performance testing and comparison workflow. Final performance results are saved in an Excel file.

Created: 2012-01-29

Credits: Matej Mihelčić

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Digital Multimedia Repositories Ontology (DMRO) and ...

Created: 2012-01-29 16:35:26 | Last updated: 2012-01-29 16:38:25

Credits: Lawrynka

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

Comments: 0 | Viewed: 226 times | Downloaded: 44 times

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Online update experiment pack

Created: 2012-01-29 16:29:09 | Last updated: 2012-01-29 22:06:46

12 items in this pack

Comments: 0 | Viewed: 100 times | Downloaded: 69 times

Loading OWL files (RDF version of videolec... (1)

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The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/). Operator "Build knowledge base" is responsible for collecting data either from OWL files or SPARQL endpoints or RDF repositories and provide it to the subsequent operators in a workflow. In this workflow it is parametrized in this way, that is builds a Sesame/OWLIM repository from the files specified in "Load file" operators. Paths to OWL files are specified as parameter va...

Created: 2012-01-29 | Last updated: 2012-01-29

Semantic clustering (with alpha-clustering... (1)

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The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/) to perform clustering of SPARQL query results based on chosen semantic similarity measure. The measure used in this particualr workflow is a kernel that exploits membership of clustered individuals to OWL classes from a background ontology ("Epistemic" kernel from [1]). Since the semantics of the backgound ontology is used in this way, we use the name "semantic clustering". This ...

Created: 2012-01-29 | Last updated: 2012-01-30

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Help for using experimentation workflows with recomm...

Created: 2012-01-29 11:59:49 | Last updated: 2012-01-29 17:28:20

Credits: Matej Mihelčić

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/publicationlist

Comments: 0 | Viewed: 72 times | Downloaded: 60 times

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Data example for experimentation with recommender ex...

Created: 2012-01-29 11:53:41 | Last updated: 2012-01-30 13:19:23

Credits: tomS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

Comments: 0 | Viewed: 108 times | Downloaded: 84 times

Operator testing workflow (1)

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This workflow is used for operator testing. It joins dataset metafeatures with execution times and performanse measures of the selected recommendation operator. In the Extract train and Extract test Execute Process operator user should open Metafeature extraction workflow. In the Loop Operator train/test data are used to evaluate performanse of the selected operator. Result is remebered and joined with the time and metafeature informations. This workflow can be used both for Item Recommend...

Created: 2012-01-29

Credits: Matej Mihelčić Matko Bošnjak

Metafeature extraction (1)

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This is a metafeature extraction workflow used in Experimentation workflow for recommender extension operators. This workflow extracts metadata from the train/test datasets (user/item counts, rating count, sparsity etc). This workflow is called from the operator testing workflow using Execute Process operator.

Created: 2012-01-29 | Last updated: 2012-01-30

Credits: Matko Bošnjak

Iterate through datasets (1)

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This is a dataset iteration workflow. It is a part of Experimentation workflow for recommender extension. Loop FIles operator iterates through datasets from a specified directory using read aml operator. Only datasets specified with a proper regular expression are considered. Train and test data filenames must correspond e.g (train1.aml, test1.aml). In each iteration Loop Files calles specified operator testing workflow with Execute subprocess operator. Informations about training and t...

Created: 2012-01-29

Credits: Matej Mihelčić Matko Bošnjak

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RMonto pack

Created: 2012-01-29 09:47:09 | Last updated: 2012-03-05 22:24:02

9 items in this pack

Comments: 0 | Viewed: 142 times | Downloaded: 31 times

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Semantic clustering (with AHC) of SPARQL q... (1)

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The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/) to perform clustering of SPARQL query results based on chosen semantic similarity measure. The measure used in this particualr workflow is a kernel that exploits membership of clustered individuals to OWL classes from a background ontology ("Common classes" kernel from [1]). Since the semantics of the backgound ontology is used in this way, we use the name "semantic clustering". ...

Created: 2012-01-29 | Last updated: 2012-01-29

Semantic clustering (with k-medoids) of SP... (1)

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The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/) to perform clustering of SPARQL query results based on chosen semantic similarity measure. Since the semantics of the backgound ontology is used in this way, we use the name "semantic clustering". The SPARQL query is entered in a parameter of "SPARQL selector" operator. The clustering operator (k-medoids) allows to specify which of the query variables are to be used as clustering criteria. If more ...

Created: 2012-01-29

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Experimentation for recommender extension templates

Created: 2012-01-28 21:54:16 | Last updated: 2012-01-31 16:01:43

6 items in this pack

Comments: 0 | Viewed: 102 times | Downloaded: 52 times

BLAST (1)

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This is a simple workflow demonstrating a sequence Basic Local Alignment Search Tool (BLAST).                                                                                           

Created: 2012-01-26 | Last updated: 2012-01-26

Credits: Pipeline

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 the mouse, Mus musculus. 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 path...

Created: 2012-01-20 | Last updated: 2012-01-20

Credits: Bonilla

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Dataset for item rating predictions

Created: 2012-01-19 14:56:28 | Last updated: 2012-01-19 14:57:13

Credits: Ninoaf

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

Comments: 0 | Viewed: 113 times | Downloaded: 60 times

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Item rating predictions collaborative-based (1)

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This workflow takes input 2 as as train set for several item recommendation predictions. We build four different recommendation model which are combined into one model with operator Model Combiner. Then we take input 1 as a test set and apply merged model. Train and test set must contain user_id, item_id and rating attributes which need to have special roles user identification, item identification and label. This workflow uses recommender system extension.

Created: 2012-01-19

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Dataset for item recommendation hybrid-based

Created: 2012-01-19 14:26:56 | Last updated: 2012-06-03 19:49:28

Credits: Ninoaf

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

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Item recommendation hybrid-based workflow (1)

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This workflow takes input 2 as a train set for recommender systems. We build two item recommendation models: item k-NN (collaborative based) and item attribute k-NN (content based). Item attribute k-NN operator takes additional item attributes from input 3. We combine two models with operator model combiner and test performance on test set (input 1). Train and test set must contain user_id and item_id attributes which need to have special roles user identification and item identification. Th...

Created: 2012-01-19

RDKit-bioisosteres (1)

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Implementation of a simple bioisostere replacement workflow using the RDKit (2.0.0) nodes in KNIME (2.5.1). Includes short list of classical bioisostere replacements (not exhaustive), selectable by the functional group to be transformed. We added this control to the workflow as our own internal list of bioisostere replacements generated huge libraries for each structure fed into the workflow. The bioisostere replacement list is stored in a tab separated text file, so can be replaced...

Created: 2012-01-18 | Last updated: 2012-01-18

Credits: sauberns

Attributions: RDKit-pains

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Taverna Tutorial Chip-Seq Downstream analysis

Created: 2012-01-17 13:26:09

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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document clustering

Created: 2012-01-17 11:16:46 | Last updated: 2012-02-15 16:05:57

2 items in this pack

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