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Licence: by-sa

Workflow Pathways and Gene annotations for QTL region (7)

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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: 2009-11-19 | Last updated: 2012-09-07

Credits: User Paul Fisher

Workflow BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

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This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Created: 2008-12-15 | Last updated: 2011-08-11

Credits: User Marco Roos Network-member AID

Workflow BiomartAndEMBOSSAnalysis (4)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2009-09-15 | Last updated: 2015-01-26

Workflow QR code (matrix code) generator (4)

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The latest (and greatest) version of the QR code generator workflow. This workflow uses the QR code service provided by the ChemTools project.

Created: 2007-10-07 | Last updated: 2012-08-15

Workflow Workflow for Protein Sequence Analysis (1)

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This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

Created: 2008-01-09 | Last updated: 2008-01-09

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simplify a BLAST text file Workflow conditional branch

Workflow Success-Abandonment-Classification (3)

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Retrieves data from FLOSSmole and from the Notre Dame SourceForge repository to compute project statistics based on releases, downloads and project lifespan. Project statistics are then used to classify projects according to the criteria set up in English & Schweik, but comparison criteria are parameterized so that a different set of criterion thresholds can be used to evaluate the project characteristics.

Created: 2008-02-06 | Last updated: 2008-07-02

Credits: User Andrea Wiggins User James Howison

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Workflow Mapping OligoNucleotides to an assembly (7)

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Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Created: 2009-02-13 | Last updated: 2009-02-13

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

Workflow KNIME workflow used to collate data for th... (1)

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KNIME workflow used to collate data from different sources (Open Data, in-house data) for certain protein targets of interest; further the data is filtered for certain activity endpoints, erraneous data is removed and data overlap between the different sources as well as the targets under study is determined and given as an output;Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community...

Created: 2015-11-02 | Last updated: 2016-03-29

Credits: User Barbara Zdrazil User Daniela Digles Network-member Open PHACTS

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

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This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Created: 2009-05-28

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Workflow blast_simplifier.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: User Paul Fisher

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