Workflows

111 (1)

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This process shows how several different classifiers could be graphically compared by means of multiple ROC curves.

Created: 2010-09-04 | Last updated: 2010-09-04

Sample for explaining the feature: - Type ... (1)

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The objective of this workflow is to explain the working of the Type Initializer in the Trident application.   For detailed information on type initializer and how it can be used please refer the following document:- http://tridentworkflow.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=138922  

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Trident

IfEls Activity sample for Trident v1.2 (v1) (1)

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The objective of this workflow is to explain the working of the If Else activity in the Trident application.  For more information on how to use the if else sample. Please refere the following document. IfElse-Sample Details

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Trident

Cow SNP annotation (1)

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SNP annotation

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Mkh

Replicator Activity sample for Trident v1.2 (1)

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The objective of this workflow is to explain the working of the Replicator activity in the Trident application. For detailed description of the worklfow please refer the following document. Sample Description

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Trident

Constructing user defined linear regressio... (1)

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This process shows how one can construct a user defined Linear Regression model using the execute script operator

Created: 2010-09-02 | Last updated: 2010-09-02

retrieve nucleotide sequence and do a BLAS... (1)

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retrieve nucleotide sequence and do a BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn 

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

Attributions: retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services

retrieve nucleotide sequence and do a high... (1)

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retrieve nucleotide sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

retrieve protein sequence and do a BLAST f... (1)

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retrieve protein sequence and do a BLAST from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

Attributions: retrieve protein sequence and do a BLAST and extract position from DDBJ Web services

retrieve protein sequence and do a high sp... (1)

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retrieve protein sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

Created: 2010-09-01 | Last updated: 2010-09-01

Credits: Lebreton

Attributions: retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services

Characterization Template - Proton NMR (1)

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Template for an NMR expriment and asasociated data files

Created: 2010-08-31 | Last updated: 2010-10-08

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

Cross tabulation via aggregation and pivoting (1)

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Creates a contingency table using the Aggregate and Pivot operators.

Created: 2010-08-25 | Last updated: 2010-08-25

Find and replace missing values with other... (1)

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Sometimes, it is helpful to replace a numerical attribute containing a missing value with a value from another attribute in the example row rather than using a constant such as an average or maximum value. This process generates some missing values, detects them and replaces with a calculation based on the value of another attribute. (Purists will be alarmed at the mathematical impossibility of taking the square root of a negative number). The process detects missing values by subtracti...

Created: 2010-08-25 | Last updated: 2010-08-25

Create custom-made GPCR alignments (1)

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This workflow allows you to create your own GPCR alignments. The alignments are built from the residues that are annotated with the general residue numbers. Alignments are therefore not built using standard alignment algorithms but are created by selecting residues that are likely to share the same position in the three-dimensional structure. Users can select the proteins and residue positions that should be aligned, allowing for the creation of e.g. an alignment of all binding pocket residue...

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

BLAST against the GPCRDB (1)

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With this workflow you can submit a BLAST query to the GPCRDB. Input requires a sequence with amino acids only.

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

Retrieve a protein from the GPCRDB (1)

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This small workflow illustrates how to use the web service access provided by the GPCRDB in Taverna. The proteinId input field is case sensitive and by default the identifiers in the GPCRDB are lowercase. You can try this mini-workflow with e.a. 'adrb2_human'.

Created: 2010-08-24 | Last updated: 2010-08-24

Credits: Bas Vroling

instruments in sxr and euv spectrum (1)

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ICS use case 5

Created: 2010-08-20 | Last updated: 2010-08-20

Credits: Anja Le Blanc

For loop sample for Trident v1.2 (1)

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  Please refere following link for more information http://tridentworkflow.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=138916

Created: 2010-08-19 | Last updated: 2010-08-24

Credits: Trident

Testing caBIG workflow (1)

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An example workflow to test the installation of caGrid Workflow Suite and the submission of a workflow to a caGrid workflow service.

Created: 2010-08-17 | Last updated: 2010-08-17

Credits: Wei Tan

caArray (1)

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preprocess data before it is sent to any GenePattern services.

Created: 2010-08-14 | Last updated: 2010-08-14

Credits: Wei Tan

KEIO Bioinformatics Web Service - a genera... (2)

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This workflow generates a sequence logo image for a set of amino acid sequences of FOXP2 gene, by downloading the amino acid sequences in Fasta format through Togo Web Service with UniProt identifiers (togoWS, provided by the G-language Genome Analysis Environment SOAP Service), running BLAST web service (runBLAST), retrieving a set of sequences from ID list (togoWS), aligning the sequence with MUSCLE (runMUSCLE), extracting a certain region from the alignment (extractalign, provided by Soapl...

Created: 2010-08-13 | Last updated: 2010-11-19

Credits: cory (Kazuki Oshita)

Visualize the boiling point data from the ... (1)

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 Downloads the RDF data from a HTML page, extracts the boiling point data, calculates atom counts from SMILES representations, and opens the data in a matrix editor, ready to be visualized in a scatter plot.

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Egon Willighagen

Generate CombiUgi library (1)

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Generates a CombiUgi library using data from a Goolgle spreadsheet containing smiles strings of compounds to undergo virtual Ugi reactions

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Peter Li Romney

Predict Abraham descriptors (1)

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Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values. The workflow returns all the Abraham descriptors E, S, A, B and V in a HTML file.Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values

Created: 2010-08-05 | Last updated: 2010-08-05

Credits: Peter Li

AUTOSTRUCTURE (4)

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This is a simple workflow designed to run AUTOSTRUCTURE with an user selected input. The code is a full implementation of the program AUTOSTRUCTURE developed by N. R. Badnell. The entire capability of the original program for arbitrary structure, Auger rate and Radiative rate calculation has been retained. However input driver file selection, driver templates, output selection and output routing have been enabled within the ADAS framework to simplify the production of two types of data, name...

Created: 2010-08-04 | Last updated: 2011-02-27

Count the number of MetaPrint2D predicted ... (1)

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 MetaPrint2D (doi: 10.1186/1471-2105-11-362) is used to calculate the number of red, orange, and green markers that indicate how likely an atom in the drug is metabolized (read the paper for the fine prints). It counts them for each molecule and reports them, as a set of three molecular descriptors that could potentially correlate with how well the molecule is metabolized (hypothesis).

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Egon Willighagen

Create an OpenTox API dataset and add mole... (2)

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 Bioclipse script that creates a data set  at an OpenTox API capable server, and adds molecules to it.

Created: 2010-08-04 | Last updated: 2010-11-13

Credits: Egon Willighagen

Predict chemical solubility in solvents (2)

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Predicts solubility in molar units for a given chemical compound represented as a SMILES string in a given solvent. Uses a beanshell script to enable the user to select the solvent from a list.

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Peter Li

Call VSO web service with HELIO input data (1)

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  date transformation from 2000-10-02T23:00:00 to 20001002230000 HELIO instrument names as in http://helio-dev.i4ds.ch/xsd/instruments.xsd spitt into source and instrument names; if these pair don't exist only first part (source) is tried.

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Anja Le Blanc

Connect to twitter and analyze the key words (1)

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Hi All, This workflow connects RapidMiner to Twitter and downloads the timeline. It then creates a wordlist from the tweets and breaks them into key words that are mentioned in the tweets. You can then visualize the key words mentioned in the tweets. This workflow can be further modified to review various key events that have been talked about in the twitterland. Do let me know your feedback and feel free to ask me any questions that you may have. Shaily web: http://advanced-analyti...

Created: 2010-07-26 | Last updated: 2010-07-26

Protein Mutation Analysis Using the BioExt... (1)

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This workflow, created using the BioExtract Server, contains a protein query (using the NCBI Protein Database), Blastp, ClustalW, Transeq, Garnier, PepWindowWall, PepInfo, and Octanol. For this workflow, a mutated protein sequence needs to be selected. Once the corresponding non-mutated sequence has been queried, the Blastp tool can be used to find sequences similar to the one queried, and the ClustalW tool can be used to analyze whether the mutation is conserved within species.  The Tra...

Created: 2010-07-22 | Last updated: 2010-07-22

Credits: Kendra Giesey Yosr Bouhlal BioExtract Server for Genomics

retrieve nucleotide sequence and do a VecS... (1)

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retrieve nucleotide sequence and do a VecScreen from DDBJ Web services : A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin   informations on Web services available at http://xml.nig.ac.jp/index.html accession : AB000100

Created: 2010-07-21 | Last updated: 2010-09-01

Credits: Lebreton

retrieve nucleotide sequence and do a BLAS... (1)

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retrieve nucleotide sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

retrieve nucleotide sequence and do a high... (4)

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retrieve nucleotide sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : AB000100 database : DDBJ program : blastn param : -b 5 -m 7

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

Credits: Lebreton

retrieve nucleotide sequence and do a BLAS... (1)

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retrieve nucleotide sequence and do a BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example : accession : AB000100 database : DDBJ program : blastn    

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

Attributions: BLAST using DDBJ service

retrieve protein sequence and do a BLAST w... (1)

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retrieve protein sequence and do a BLAST with options from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html exxample accession : Q9NRA8 database : UNIPROT program : blastp param : -b 5 -m 7    

Created: 2010-07-21 | Last updated: 2010-09-01

Credits: Lebreton

retrieve protein sequence and do a high sp... (1)

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retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

retrieve protein sequence and do a BLAST a... (1)

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retrieve protein sequence and do a BLAST and extract position from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

Attributions: BLAST using DDBJ service

download (2)

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Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

PubChem substructure search (2)

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Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

smiles-identity-idlist (2)

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Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

smiles-identity-idlist (1)

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Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

file-similarity-entrez-url (2)

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Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

CTF - MEG SAM Analysis (1)

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Uses a user-defined text protocol file containing SAM analysis parameters and applies them to a set of MEG datasets. The dataset must be in CTF MEG system format.

Created: 2010-07-15 | Last updated: 2010-07-15

Credits: Lakelander

Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2010-07-14 | Last updated: 2010-07-14

Credits: EdwardKawas Tomoinn

Attributions: Fetch Dragon images from BioMoby

Simple search (1)

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Performs a lite search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Search structures in ChEBI database (1)

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 Does a substructure, similarity or identity search using a structure in the Chebi database

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get ontology children (1)

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Retrieves the ontology children of an entity including the relationship type, using the ChEBI identifier.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get ontology parents (1)

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get complete entity by list (1)

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Returns information from the chebi database for a list of chebi identifiers

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li