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Items tagged with "demo" (22)

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Network-member RapidMiner Demo

Unique name: rapidminer_demo
Created: Saturday 01 May 2010 @ 09:49:28 (GMT)

This group is created for demo processes used in RapidMiner documentation, manual, or training. Feel free to add workflows if you consider them instructive examples.

5 shared items   |   1 announcements

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Latest announcement:: RCOMM 2011

Files (1)
Uploader

Blob From biologist to web service to Taverna to myExperi...

Created: 21/03/08 @ 19:00:12 | Last updated: 23/03/08 @ 10:39:27

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A movie to show the principle of the round trip from a biology question via pieces of code wrapped as web services and combined into a workflow (computational experiment) in Taverna, via uploading to myExperiment and back to the biologist through myExperiment's run facility. NB: at the time of uploading this movie the runner-option was in test-phase. It is important to note that the workflow combines the work of various scientists with different expertise and some at remote locations around ...

File type: AVI video

Rating: 1.0 / 5 (1 rating) | Comments: 1 | Viewed: 291 times | Downloaded: 251 times

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Workflows (18)
Original Uploader

Workflow Discover_entities (2)

Created: 10/12/07 @ 21:48:33 | Last updated: 10/12/07 @ 22:54:42

Credits: User Marco Roos User Sophia katrenko Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format. Known issues: The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations. The output is per document, which means entities will ...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 119 times | Downloaded: 53 times

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Original Uploader

Workflow Extract_proteins (2)

Created: 10/12/07 @ 22:10:51 | Last updated: 10/12/07 @ 22:30:53

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input). Internal information: This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive).

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 111 times | Downloaded: 55 times

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Original Uploader

Workflow Lucene_bioquery_optimizer_MR1 (1)

Created: 10/12/07 @ 22:14:26

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow does four things: it retrieves documents relevant for the query string it discovers entities in those documents, these are considered relevant entities it filters proteins from those entities (on the tag protein_molecule) it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the tag, ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 50 times | Downloaded: 32 times

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Original Uploader

Workflow Retrieve_bio_documents (2)

Created: 10/12/07 @ 22:15:54 | Last updated: 10/12/07 @ 22:45:49

Credits: User Marco Roos User Edgar Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 2 | Citations: 0

Viewed: 122 times | Downloaded: 44 times

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Original Uploader

Workflow Retrieve_documents_MR1 (1)

Created: 10/12/07 @ 22:17:00

Credits: User Marco Roos User Edgar Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 58 times | Downloaded: 38 times

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Original Uploader

Workflow Demo_DiseaseDiscovery_byHumanUniprot_scaffold (1)

Created: 10/12/07 @ 23:10:00

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds disease relevant to the query string via the following steps: 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. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 90 times | Downloaded: 65 times

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Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

Created: 28/05/09 @ 12:21:05

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

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 471 times | Downloaded: 173 times

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Original Uploader

Workflow Bio2rdf: Bind search, rdfise and load demo (1)

Created: 19/02/09 @ 05:07:30 | Last updated: 19/02/09 @ 05:39:51

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> {     CONSTRUCT { ?s, ?p, ?o . }     FROM <http://soap.bind.ca/wsdl/bind.wsdl>     WHERE {         SELECT ?s         FROM <http://soap.bind.ca/wsdl/bind.wsdl>         WHERE {              ?s, ?p, ?o .        ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 61 times | Downloaded: 32 times

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Original Uploader

Workflow Bio2RDF: CPath search, rdfise and load dem... (1)

Created: 19/02/09 @ 07:06:58 | Last updated: 19/02/09 @ 07:08:28

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH < http://localhost/sesame/mem_rdf_db> {     CONSTRUCT{ ?s, ?p, ?o . }     FROM < http://www.pathwaycommons.org/pc/webservice.do>     WHERE {         SELECT ?s         FROM <http://www.pathwaycommons.org/pc/webservice.do>  ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 52 times | Downloaded: 29 times

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Workflow Demo of ChemSpider InChi to SMILES webserv... (1)

Created: 28/03/09 @ 18:38:07 | Last updated: 28/03/09 @ 19:13:05

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This demo was created in Excel 2007, with the Office XP Webservices toolkit. Using the spreadsheet, the formula InChiToSMILES invokes the corresponding ChemSpider web service.  How I made this: 1. Installed Office XP Webservices toolkit from the Microsoft Download Center. 2. In Excel 2007 I turned on the Developer tab (hit Office button, then Excel options). 3. In the Developer ribbon I selected Visual Basic 4. In Tools->Web Services References I selected Web Service URL and ente...

Rating: 5.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 178 times | Downloaded: 164 times

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Workflow Demo of statistics webservice invoked from... (1)

Created: 29/03/09 @ 17:56:04

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This "spreadflow" was created by searching Seekda for a statistics webservice, adding it using "Web Services References" in Excel, and creating a simple VBA module to implement the corresponding Excel functions (sum, average, standard deviation etc) . The module simply gathers data from the cells to build an array of doubles that can be passed to the webservice. For more details about adding webservices to Excel see the inchidemo workflow http://www.myexperiment.org/workf...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 95 times | Downloaded: 36 times

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Original Uploader

Workflow ChEBI mashup from searched string (1)

Created: 29/04/10 @ 14:09:37

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint.A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint. First a full text search query is done, then we do a reverse link query to get all the related topic. Finally with a describe queries we obtain the complete graph of each topic. The ntriples result is a mashup of what is known about this searched topic form ChEBI. This graph can then be loaded in a triplestore for further exploration.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 25 times | Downloaded: 13 times

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Original Uploader

Workflow Explain concept scores (5)

Created: 07/02/12 @ 11:05:50 | Last updated: 14/09/12 @ 10:01:37

Credits: User Reinout van Schouwen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Rating: 0.0 / 5 (0 ratings) | Versions: 5 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 71 times | Downloaded: 15 times

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Packs (2)
Creator

Pack AIDA demo pack


Created: 14/12/08 @ 21:35:43 | Last updated: 01/05/09 @ 17:35:26

 Pack with AIDA demo material

2 items in this pack

Comments: 0 | Viewed: 123 times | Downloaded: 0 times

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Creator

Pack AIDA remote runners


Created: 15/05/09 @ 16:08:03 | Last updated: 15/05/09 @ 16:11:20

Runners for AIDA demonstrations and testing

2 items in this pack

Comments: 0 | Viewed: 19 times | Downloaded: 8 times

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