Workflows

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

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

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

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

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

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

searchPublications_and_MapAffil (1)

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This is a workflow for spatiotemporal analysis of literature indexed in PubMed. The workflow takes an arbitrary Europe PMC search query, calls the Europe PMC Web service searchPublications and extracts the publication year and PubMed ID from the results. The first author affiliation is then geoparsed by the MapAffil Web server to get latitude and longitudes. The coordinates are then concatenated together with the publication year, to produce a single list of publication years, latitudes and ...

Created: 2017-04-19

Credits: Magnus Palmblad

Color auto balancing (1)

Color auto balancing of RGB image

Created: 2017-05-02

Credits: Christian S.

H1-2-H4-SLEEPDEMO (1)

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H1-2-H4-SLEEPDEMO

Created: 2017-09-11

Credits: Kasikrit Damkliang

8_nested_workflows (1)

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8_nested_workflows

Created: 2017-09-11

Credits: Kasikrit Damkliang

WSDL Calculator (1)

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Utiliza uma calculadora com métodos disponíveis via WSDL para somar dois números.

Created: 2017-10-10

Credits: Johnathan Melo Neto

Variant Annotation with VEP (Variant Effec... (1)

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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2017-10-19

Credits: alabarga

Tratamento de erro para WSDL (1)

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Verifica se web service está ativo antes de propriamente executá-lo, como forma de tratamento de erro, enviando mensagem de alerta caso erro ocorra.

Created: 2017-10-30

Credits: Johnathan Melo Neto

Predador Presa v1 (1)

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Envia dois textos e três parâmetros numéricos para um web service, e recebe um texto como saída. O web service implementa um modelo de predador-presa.

Created: 2017-10-30 | Last updated: 2017-10-30

Credits: Johnathan Melo Neto

Text search within sparql point (1)

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This workflow make possible full text search within different sparql point made available by the Bio2RDF project.

Created: 2009-01-19

Credits: Francois Belleau

Run XMPP cloud services. (2)

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Basic workflow indicating how a XMPP service can be called with XML input and output. Source code for the activity is available from: github.com/egonw/xws-taverna/tree/master That page explains you how to install the plugin you must install on top of Taverna 2.0. The workflow will not work otherwise.

Created: 2009-04-25 | Last updated: 2010-03-22

Credits: Egon Willighagen

Author's collaborators according to pubmed (1)

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SELECT distinct ?s2 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "author" .   ?s2 ?p2 ?s1 .   FILTER( regex(?s1, "pubmed") ) } followed by SELECT ?creator, count() FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 .   ?s1 ?p2 ?o2 .   FILTER( regex(?o2, "author"))   ?s1 ?creator . } ORDER BY DESC(count())

Created: 2009-01-20 | Last updated: 2009-01-20

Credits: Francois Belleau

What is Paget's disease sparql query example (3)

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SELECT distinct ?s1 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   FILTER( regex(?s1, "omim")   OR regex(?s1, "geneid") OR regex(?s1, "uniprot")) }   followed by SELECT ?type1, count(*) FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   ?s1  

Created: 2009-01-20

Credits: Francois Belleau

Download pathways for external references ... (2)

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Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2009-02-03

Credits: Thomaskelder

What is known about HIV using Bio2RDF's SP... (2)

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: Francois Belleau

Pubmed mashup demo in a Virtuoso triplestore (1)

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This workflow build a mashup in your local virtuoso server (available at http://localhost:8890/sparql) by downloading the needed pubmed documents from NCBI and by converting them into N3 format.  Once all documents loaded into the triplestore you can query them with SPARQL. For example try those queries : SELECT count(*) WHERE {?s ?p ?o} SELECT ?o, count(*) WHERE {?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?o} Dr Labrie's MeSH subject of interest : SELECT ?o, count...

Created: 2009-02-11

Credits: Francois Belleau

Initialize triplestore with Murin's protoc... (1)

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This workflow initialize the Sesame triplestore with initial data.  The 5 rdfiser in JSP are needed, they are executed on localhost.

Created: 2009-02-17 | Last updated: 2009-02-17

Credits: Francois Belleau