Workflows

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

Frequent Itemset and association rules ana... (1)

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Generates frequent itemsets and association rules from the gene data. Frequent itemsets correspond to different gene characteristics (locations and functions) that frequently occur together across different genes. The quality of a frequent itemset is given by its support which is the fraction of genes for which a given combination of gene characteristics hold; the longer the itemset the lower its support. Based on the frequent itemset this WF also generates association rules which have some...

Created: 2011-05-23 | Last updated: 2011-05-24

Prepares data for gene correlation analysis (1)

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Prepares data for gene correlation analysis.

Created: 2011-05-23 | Last updated: 2011-05-23

Prepares data for the analysis of fibrosis... (1)

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Prepares gene data for fibrosis by joining datasets from different studies on fibrosis across various organs including the kidney.

Created: 2011-05-23 | Last updated: 2011-05-25

Get names of proteins similar to RNA bindi... (1)

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A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: hindlem

EBI PICR, find cross-references for protei... (2)

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Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

Created: 2011-05-18 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Example for external tools with gzip and g... (1)

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This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: Steffen Möller Alan Williams

Molecular Interactions from IntAct PSICQUI... (2)

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Get molecular interaction data in psi-mitab25 from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file.

Created: 2011-05-17 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

Plotting distribution of natural product l... (1)

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

Extract chemical structures from a Beilste... (1)

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 Uses the Oscar4 text mining tool to extract chemical structures from a Beilstein Journal of Organic Chemistry paper and visualizes them in the molecules table. Jericho is used to extract text from the paper's HTML page.

Created: 2011-05-12 | Last updated: 2011-05-12

Credits: Egon Willighagen

SVD user-based collaborative filtering rec... (1)

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This workflow takes user-item matrix A as a input. Then it calculates reduced SVD decomposition A_k by taking only k greatest singular values and corresponding singular vectors. This worfkflow calculates recommendations and predictions for particular user %{id} from matrix A. Particular row %{id} is taken from original matrix A and replaced with %{id} row in A_k matrix. Predictions are made for %{id} user based on another users A_k. Note: This workflow uses R-script operator with R library ...

Created: 2011-05-09 | Last updated: 2011-05-09

Credits: Ninoaf Matko Bošnjak

Attributions: User-based collaborative filtering recommender system template Datasets for the pack: RCOMM2011 recommender systems workflow templates

LSI content based recommender system template (1)

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This workflow performs LSI text-mining content based recommendation. We use SVD to capture latent semantics between items and words and to obtain low-dimensional representation of items. Latent Semantic Indexing (LSI) takes k greatest singular values and left and right singular vectors to obtain matrix  A_k=U_k * S_k * V_k^T. Items are represented as word-vectors in the original space, where each row in matrix A represents word-vector of particular item. Matrix U_k, on the other hand ...

Created: 2011-05-06 | Last updated: 2011-05-09

Credits: Ninoaf Matko Bošnjak

Attributions: Content based recommender system template Datasets for the pack: RCOMM2011 recommender systems workflow templates

External Tool: Numerically adding two valu... (1)

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The workflow is an examples for the External Tools / UseCase plugin to integrate external tools. It wraps the "bc" command line calculator. Internally, it executes the following script: if [ ! -r "$1" ]; then echo "Cannot read file indicated by first argument '$1'." ; exit -1 ; fi ; if [ ! -r "$2" ];then echo "Cannot read file indicated by second argument '$1'." ; exit -1 ; fi if [ -x /usr/bin/bc ]; then ...

Created: 2011-05-06 | Last updated: 2011-05-06

Credits: Steffen Möller

Item-based collaborative filtering recomme... (1)

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The workflow for item-based collaborative filtering receives a user-item matrix for its input, and the same context defined macros as the user-based recommender template, namely %{id}, %{recommendation_no}, and %{number_of_neighbors}. Although this process is in theory very similar to user-based technique, it differs in several processing steps since we are dealing with an item-user matrix, the transposed user-item example set. The first step of the workflow, after declaring zero values miss...

Created: 2011-05-05 | Last updated: 2011-05-09

Credits: Matko Bošnjak Ninoaf

Attributions: Datasets for the pack: RCOMM2011 recommender systems workflow templates

User-based collaborative filtering recomme... (1)

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The workflow for user-based collaborative filtering, takes only one example set as an input: a user-item matrix, where the attributes denote item IDs, and rows denote users. If a user i has rated an item j with a score s, the matrix will have the value s written in i-th row and j-th column. In the context of the process we define the ID of the user %{id}, desired number of recommendations %{recommendation_no}, and the number of neighbors used in ca...

Created: 2011-05-05 | Last updated: 2011-05-09

Credits: Matko Bošnjak Ninoaf

Attributions: Datasets for the pack: RCOMM2011 recommender systems workflow templates

Content based recommender system template (1)

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As an input, this workflow takes two distinct example sets: a complete set of items with IDs and appropriate textual attributes (item example set) and a set of IDs of items our user had interaction with (user example set). Also, a macro %{recommendation_no} is defined in the process context, as a required number of outputted recommendations. The first steps of the workflow are to preprocess those example sets; select only textual attributes of item example set, and set ID roles on both of th...

Created: 2011-05-05 | Last updated: 2011-05-09

Credits: Matko Bošnjak Ninoaf

Attributions: Datasets for the pack: RCOMM2011 recommender systems workflow templates

CGR from multiple fasta files (1)

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 The workflow generates Chaos Game Represenations (CGR) image from multiple fasta files. See http://www.g-language.org/wiki/cgr for more information about the Chaos Game Representations.

Created: 2011-04-29 | Last updated: 2011-04-29

Credits: cory (Kazuki Oshita)

Voronoi polygon generation using GRASS-GIS... (1)

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Generic example on how to deal with vectorial data. Major pitfall is the need to process ProcessOutputs using Xpath plugin. A random point file in GML 2.1.2 is sent to the v.voronoi service and after it is sent to a service that runs v.out.svg generating a SVG image that can be rendered in Taverna (need to set output to SVG image)

Created: 2011-04-27 | Last updated: 2011-04-27

Credits: Jorgejesus