Workflows

profilePublications_over_time (1)

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This workflow takes a list of arbitrary Europe PMC search queries and generates the corresponding profiles of the number of matching publications per publication year.

Created: 2017-04-19

Credits: Magnus Palmblad

Quality Recognition Model (QRM) (1)

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Quality Recognition Model (QRM) is a SVM-based Machine Learning supervised classification model that assigns label to the evidentiary documents on the basis of rigorousness of the contents. It assigns the label Rigor if the document is of quality otherwise assigns the Non-Rigor. It uses two type of features: data and metadata. Data features include title and abstract while the metadata features include MeSH terms and publication type.

Created: 2017-03-11

A Montage workflow in DATAVIEW. (1)

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A sample workflow that implements the Montage workflow in DATAVIEW.

Created: 2017-02-22 | Last updated: 2017-02-22

Credits: Shiyong Lu

recommenderSystem (1)

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Complementary workflow for the modelBuild. It can read the trained model parameters in order to classify samples in another dataset.

Created: 2017-01-20 | Last updated: 2017-01-20

modelBuild (1)

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Using this workflow one can train a softmax regression model (a machine learning algorithm) and the learnt parameters are exported to files.

Created: 2017-01-20 | Last updated: 2017-01-20

dataExploration (1)

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This workflow allows the user to explore and process a dataset file.

Created: 2017-01-20 | Last updated: 2017-01-20

repoRead (1)

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Workflow created to perform a search over the Harvard Dataverse. It can also download datasets linked files.

Created: 2017-01-20 | Last updated: 2017-01-20

SNPs@PSU (1)

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Example file test workflows.

Created: 2016-12-03 | Last updated: 2016-12-03

Credits: Sittisak Krotasuwan

phage display techniques (1)

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Created: 2016-11-22

Credits: Candy Swift

The automatic integrated workflow for Phyl... (2)

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update server address

Created: 2016-11-08 | Last updated: 2016-11-24

Credits: Kasikrit Damkliang

Interactive Service (4)

Interactive service is developed to provide an interface for human users to intervene the execution process of scientific workflow. This allows that certain steps in workflow can be operated by human users rather than an end-to-end automatic process. This is helpful for activities in the workflow that currently cannot be executed by automatic process, and for the inspection activities.The workflow here utilized a set of REST web services, HTML pages, authentication services, client ...

Created: 2016-10-26 | Last updated: 2016-10-26

Credits: Kewei Duan

Metavisitor: Spades test in Use Case 2-2 (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-10-10 | Last updated: 2016-10-10

Metavisitor: Trinity test in Use Case 2-2 (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-10-10 | Last updated: 2016-10-10

Metavisitor: Workflow for small RNA profil... (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server

Created: 2016-10-10 | Last updated: 2016-10-10

RapidMiner: Use a Macro at Detect Outliers... (1)

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a reply to @paavopdf 's question on twitter "Anyone having an idea how I can use a macro at "Detect Outliers" for the no. outliers in @RapidMiner? #rapidminer #DataScience"

Created: 2016-10-03

VCaP RNA-Seq Fusion gene detection with ST... (1)

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The end-to-end workflow starts by obtaining paired-end RNA-Seq data of the VCaP cell line via EGA. Galaxy determines the file type automatically with its built-in format detection system. The reads will be clipped before an alignment with STAR and STAR produces several output files that can be used for different analysis. The last tool is STAR-Fusion which was able to confirm the TMPRSS2-ERG fusion gene. 

Created: 2016-08-31 | Last updated: 2016-08-31

Credits: Y. Hoogstrate

vir-representative (1)

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Retrieve from NCBI and reduce redundancy in the viral database.

Created: 2016-08-09 | Last updated: 2016-08-09

Credits: Juliana Pegoraro

Test (1)

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Test

Created: 2016-08-02

Credits: Sue Tairaku

CARACTERÍSTICAS GEOQUÍMICAS DE LOS SEDIMEN... (1)

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Esta investigación tuvo como objetivo, evaluar algunos parámetros geoquímicos de los sedimentos superficiales de la laguna costera La Restinga, ubicada en la Isla de Margarita, estado Nueva Esparta, Venezuela. Utilizando metodología clásica para estudios geoquímicos, se analizó la composición granulométrica y textura del sedimento, porcentaje de carbono orgánico y materia orgánica total, así como, carbonato de...

Created: 2016-08-01

Credits: William Senior

ASPECTOS GEOQUÍMICOS Y AMBIENTALES DE LOS ... (1)

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Created: 2016-08-01 | Last updated: 2016-08-01

Credits: William Senior

TRPV1 Bioactivity from ChEMBLdb13 and ChEM... (1)

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This workflow allows to extract bioactivity data stored in ChEMBLdb for human TRPV1. Ensure you have installed Chembl and RDKit extensions to run the workflow.

Created: 2016-07-27 | Last updated: 2016-07-27

Credits: Daria Goldmann

KNIME workflow without hERG labels include... (1)

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KNIME workflow used to retrieve and process data from Open PHACTS for three targets of interest (hSERT, hDAT, hERG). Further, Murcko scaffolds are computed and selectivity trends towards hSERT and hDAT can be studied. Cutt off's for separating actives/inactives are tailored to the specific target and endpoint.Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community Contributions (2....

Created: 2016-07-20 | Last updated: 2016-07-20

Credits: Barbara Zdrazil Open PHACTS

KNIME workflow with hERG labels included f... (1)

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KNIME workflow used to retrieve and process data from Open PHACTS for three targets of interest (hSERT, hDAT, hERG). Further, Murcko scaffolds are computed and selectivity trends towards hSERT and hDAT can be studied. Compounds/scaffold series are flagged by their ability to also inhibit hERG.Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community Contributions (2.11)': EMBL-EBI No...

Created: 2016-07-20 | Last updated: 2016-07-20

Credits: Open PHACTS

An example BRAIN api call (1)

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An example brain API call.Note: This workflow require RServe library. Please refer to this link for the instructions to install RServer    

Created: 2016-07-11 | Last updated: 2016-07-11

Credits: Rajireturn

KEGG:Get PW for met (1)

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The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in.

Created: 2016-06-21

Credits: Kristina Hettne Harish Dharuri

Attributions: KEGG:Pathway Scheme