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Wybór atrybutów na podstawie algorytmu g... (1)

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Workflow przedstawia wykorzystanie algorytmu genetycznego do znalezienia optymalnego zbioru atrybutów. Wybór atrybutów odbywa siÄ™ na podstawie sprawdzenia jakoÅ›ci klasyfikacji. Wykorzystanym klasyfikatorem jest algorytm k-najbliższych sÄ…siadów, zbiór danych jest dzielony na zbiór uczÄ…cy i zbiór testujÄ…cy w proporcji 70%-30%. WyjÅ›ciowy algorytm genetyczny wykorzystuje populacje o rozmiarze 10, ograniczajÄ…c liczbÄ™ pokoleÅ„ do 30.

Created: 2011-03-23 | Last updated: 2011-03-23

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Bilateral Perisylvian Polymicrogyria - Single Nucleo...

Created: 2011-03-17 11:21:06 | Last updated: 2011-03-17 11:21:12

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Pathways and Gene annotations forQTL region (2)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. 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 ...

Created: 2011-03-17 | Last updated: 2011-08-30

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

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Bilateral Perisylvian Polymicrogyria

Created: 2011-03-17 10:56:15 | Last updated: 2011-03-17 11:16:53

Credits: Paul Fisher

Attributions: Pathway and Gene to Pubmed Pathways and Gene annotations forQTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

Comments: 0 | Viewed: 86 times | Downloaded: 43 times

InterproScan without Looping (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text 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. This workflow will not work properly until we add looping.

Created: 2011-03-16 | Last updated: 2012-08-29

Credits: Katy Wolstencroft

Collaborative filtering recommender (1)

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This process executes a collaborative filtering recommender based on user to item score matrix. This recommender predicts one user’s score on some of his non scored items based on similarity with other users. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations and %{number_of_neighbors} defines the number of the most similar users taken into a...

Created: 2011-03-15 | Last updated: 2012-03-06

Content based recommender (1)

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This process is a special case of the item to item similarity matrix based recommender where the item to item similarity is calculated as cosine similarity over TF-IDF word vectors obtained from the textual analysis over all the available textual data. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations. The process internally uses an example set of...

Created: 2011-03-15 | Last updated: 2011-03-15

Item to item similarity matrix -based reco... (1)

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This process executes the recommendation based on item to item similarity matrix. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations. The process internally uses an item to item similarity matrix written in pairwise form (id1, id2, similarity). The process essentially filters out appearances of the required ID in both of the columns of the pairwis...

Created: 2011-03-15 | Last updated: 2011-03-15

Random recommender (1)

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This process does a random item recommendation; for a given item ID, from the example set of items, it randomly recommends a desired number of items. The purpose of this workflow is to produce a random recommendation baseline for comparison with different recommendation solutions, on different retrieval measures. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of ...

Created: 2011-03-15 | Last updated: 2011-03-15

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Output from workflow 1943 on 2011-03-13 in CSV format

Created: 2011-03-13 11:31:21

Credits: David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

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list of names of Taverna workflow contribu... (1)

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Created: 2011-03-13

Credits: David De Roure

Phylogenetic analysis workflow (1)

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Created: 2011-03-12 | Last updated: 2011-03-12

Credits: Yosr Bouhlal

DevinTheDevil (1)

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DevinTheDevil computes level populations for one or more ions of astrophysical interest using the XSTAR atomic database (uaDB).

Created: 2011-03-08

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This is Will's test pack

Created: 2011-03-08 04:31:38 | Last updated: 2011-03-08 04:31:39

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Automated Workflows for Accurate Mass-based Putative...

Created: 2011-03-03 15:27:04 | Last updated: 2011-03-03 15:27:07

Credits: Marie Brown

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

File type: application/x-zip-compressed

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WPS orchestration example, image metadata ... (1)

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1 image inputs (GeoTIFF, JPEG,PNG), metadata from gdalinfo and histogram analisys, histogram result is a PNG image in base64 coding (default WPS service encoding) that will be converted to binary.

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

Credits: Jorgejesus

Converting from coordinates in longitude l... (1)

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Based on lonlat2xy.pro Converts from Helioprojective-Cartesian Coordinate System to Stonyhurst Heliographic Coordinate SystemBased on lonlat2xy.pro http://hesperia.gsfc.nasa.gov/ssw/gen/idl/solar/lonlat2xy.pro Converts from Helioprojective-Cartesian Coordinate System to Stonyhurst Heliographic Coordinate System

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

Credits: Anja Le Blanc

Rocchio (1)

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This process calculates the average values for all attributes grouped by the class (label). The resulting prototypes or centroids are then used for a nearest neighbor model which is applied again on the full data set for demonstration purposes.

Created: 2011-02-28

[untitled] (1)

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gdalinfo test

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

Credits: Jorgejesus

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SVN commands for linux

Created: 2011-02-25 13:12:12 | Last updated: 2011-02-25 13:12:13

Credits: John Brookes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 1 | Viewed: 17 times | Downloaded: 44 times

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Taverna-eScience Central integration demo

Created: 2011-02-25 08:59:23 | Last updated: 2011-02-25 09:06:48

2 items in this pack

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Taverna-eScienceCentral integration demo (1)

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show how a eSC workflow can be embedded into a Taverna workflow

Created: 2011-02-25

Associate flares with active regions (1)

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This workflow is querying the HFC ActiveRegions list and HEC flare lists (names retrieved from the ontlogoy) It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: HFCout is a modified VOTable where a field per flare list is added with the number of associated flares. combined_output is a 2 dimensional list with an VOTable for each Active region and each one with an VOTable for all associated flares for that Active Region.

Created: 2011-02-22 | Last updated: 2011-08-24

Credits: Anja Le Blanc

Attributions: Associate goes X ray flares with active regions Associate hessi flares with active regions

Associate goes X ray flares with active r... (1)

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This workflow is querying the HFC ActiveRegions list and HEC goes_xray_flare list. It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: HFCout is a modified VOTable where a field is added with the number of associated hessi flares. combined_output is a 2 dimensional list with an VOTable for each Active region and one with an VOTable for all associated flares for that Active Region.

Created: 2011-02-18 | Last updated: 2011-02-18

Credits: Anja Le Blanc

Converting from heliocentric coordinate sy... (1)

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Converting from heliocentric coordinate system with coordinates in arcsec to coordinates in longitude latitude Based on the IDL script xy2lonlat.pro http://hesperia.gsfc.nasa.gov/ssw/gen/idl/solar/xy2lonlat.pro Stonyhurst Heliographic Coordinate System to Helioprojective-Cartesian Coordinate System

Created: 2011-02-18 | Last updated: 2011-02-18

Credits: Anja Le Blanc

Reaction Enumeration (1)

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This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. The SD files contain the educt lists for the enumeration. The products of the enumerated reaction are stored as RXN files and also a PDF will be created which visualizes the resulting reactions.

Created: 2011-02-18 | Last updated: 2011-07-21

QSAR Descriptor Calculation Workflow (2)

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This workflow calculates QSAR properties and saves them as a CSV file. The molecules are read iteratively from a SD file. Additionally it writes out the molecules with unknown atom types, salt counter ions, curated molecule library with UUIDs and the used calculation time of every QSAR descriptor as a CSV file.Furthermore explicit hydrogens are added and a Hueckel aromaticity detection is performed.

Created: 2011-02-18 | Last updated: 2011-07-21

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Trichuriasis Induced Colitis

Created: 2011-02-16 15:16:17 | Last updated: 2011-02-16 15:16:24

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for RefSeq ids KEGG pathways common to both QTL and microarray based investigations Pathways and Gene annotations for QTL region Pathway and Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

Comments: 0 | Viewed: 71 times | Downloaded: 35 times

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Trichuriasis induced Colitis

Created: 2011-02-16 12:49:21 | Last updated: 2011-02-16 15:26:36

5 items in this pack

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StRAnGER Web Service Workflow (1)

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 StRAnGER is a web-based application, which performs functional analysis of high-throughput genomic datasets, starting from a list of significant genes derived from statistical and empirical thresholds, by utilizing the GO database and the KEGG pathway database as well as established statistical methods in order to relate the identified significant genes with important nodes in the GO tree structure or map those genes to over-represented metabolic pathways.

Created: 2011-02-15 | Last updated: 2011-02-15

Credits: Elico stranger

Calculate Sun data from date (2)

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caluculates B0 (radians), position angle and sun radius (arcsec) B0 - heliographic latitude of the centre of disk position angle - of the north end of the axis of rotation, measured +ve if east of the north point of the disk radius - the apparent radus of the Sun in arcsec This is created using the calculations from the IDL routine get_sun.pro

Created: 2011-02-15 | Last updated: 2011-03-02

Credits: Anja Le Blanc

Associate hessi flares with active regions (3)

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This workflow is querying the HFC ActiveRegions list and HEC hessi_flare list. It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: HFCout is a modified VOTable where a field is added with the number of associated hessi flares. combined_output is a 2 dimensional list with an VOTable for each Active region and one with an VOTable for all associated flares for that Active Region.

Created: 2011-02-11 | Last updated: 2011-10-24

Credits: Anja Le Blanc

Pathway and Gene to Pubmed (2)

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This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The 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 PubMe...

Created: 2011-02-10 | Last updated: 2011-02-18

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed

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LOLUWT

Created: 2011-02-10 07:45:27

0 items in this pack

Comments: 0 | Viewed: 8 times | Downloaded: 4 times

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Testing Rapidminer interface (1)

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<table><tr><td><p>This process starts with loading the data. After finishing the input operator a typical learning step is performed. Here, an implementation of a decision tree learner is used which also can handle numerical values (similar to the well known C4.5 algorithm).</p></td><td><icon>groups/24/learner</icon></td></tr></table><p>Each operator may demand some input and delivers some output. These in- and outp...

Created: 2011-02-08

Gene to Pubmed (4)

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

Created: 2011-02-08 | Last updated: 2011-02-10

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms

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Presentation - myExperiment Architecture

Created: 2011-02-06 14:43:39 | Last updated: 2011-02-06 18:32:37

2 items in this pack

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gene and voice on the complete text (1)

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Created: 2011-02-05 | Last updated: 2011-02-05

Credits: Shivamuniraj0

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