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Items tagged with "VL-e" (15)

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Packs (3)

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Pack AIDA demo pack

Created: 14/12/08 @ 21:35:44 | Last updated: 01/05/09 @ 17:35:26

 Pack with AIDA demo material

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Pack Supporting material for Roos et al., BMC Bioinformatics, SWAT4LS supplement (2009)

Created: 15/05/09 @ 15:45:33 | Last updated: 15/05/09 @ 16:05:01

Supporting material for BMC Bioinformatics, supplement for Semantic Web Applications and Tools for Life Science (2009) Structuring and extracting knowledge for the support of hypothesis generation in molecular biology Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans Acknowledgements We thank the myGrid team and OMII-UK for their support in applying their e-Science tools, and M...

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Pack AIDA remote runners

Created: 15/05/09 @ 16:08:03 | Last updated: 15/05/09 @ 16:08:04

Runners for AIDA demonstrations and testing

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Network-member VL-e

Created: Wednesday 23 January 2008 @ 15:17:17 (GMT)

Group of researchers of the Virtual Laboratory e-Science (VL-e) project in the Netherlands. This is a large nation wide e-science research project funded by BSIK grants from the Dutch ministry of Economic Affairs. Its activities range from Grid infrastructure, to middleware, to (six) applications. The projects BioRange and BioAssist (also groups here) are tightly associated with VL-e.

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Workflows (11)
Taverna 1

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Workflow BioAID_ProteinToDiseases (v1)

Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44

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

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_proteintodiseases_16160
This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

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Taverna 1

Original Uploader

Workflow BioAID_protein_discovery (v1)

Created: 14/11/07 @ 12:46:33 | Last updated: 15/11/07 @ 09:01:13

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_protein_discovery_1051
This workflow finds proteins 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 Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) Discover proteins: extract proteins discovered in the set of relevant abstracts. Services by...

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Taverna 1

Original Uploader

Workflow BioAID_DiseaseDiscovery (v3)

Created: 12/11/07 @ 22:39:04 | Last updated: 15/12/08 @ 20:47:51

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_diseasediscoveryworkflow_070904_1__1_
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...

Rating: 4.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

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Taverna 1

Original Uploader

Workflow DiscoverProteinLink (v2)

Created: 03/10/07 @ 18:36:12 | Last updated: 15/11/07 @ 09:02:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Discoverproteinlink_6189
COMPETITION: For friends only: If you find any two topics that return true positives with this workflow I will buy you a bottle of wine (or equivalent). Terms: if we confirm that the protein was indeed never mentioned together with both input topics in one article, we will publish this together. ---- This workflow implements Swanson's prinicple with services from the AIDA toolbox. It tries to find proteins that link two topics, while they never mentioned together with both topics in ...

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

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Taverna 1

Original Uploader

Workflow Discover_proteins_from_text (v2)

Created: 15/11/07 @ 08:58:00 | Last updated: 15/11/07 @ 09:12:34

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Discover_proteins_from_text_18980_2
This workflow discovers proteins from plain text. It is built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

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

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Taverna 1

Original Uploader

Workflow TestIteratorStrategy_withNesting (v1)

Created: 29/11/07 @ 15:31:33

Credits: User Marco Roos User Tomoinn

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Testiteratorstrategy_withnesting_29185_1
Implementation of the iteration workaround by Tom Oin conform the Q&A below. The nested workflow 'NestedProcessor' is called that to conform to Tom's explanation. For an alternative solution using a java beanshell to clone list items see 'TestIteratorStrategy_withCloning. This workflow implements the following Q&A: Marco Roos wrote: > Dear Taverna user, > > Issue 1: Complex iteration > > I would like to perform an iteration including a dot product between > a list and a list of li...

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Taverna 1

Original Uploader

Workflow CloneItemsInList (v1)

Created: 29/11/07 @ 15:34:53

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cloneitemsinlist_10203_1
Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...

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

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Taverna 1

Original Uploader

Workflow TestIteratorStrategy_withCloning (v2)

Created: 29/11/07 @ 15:35:49 | Last updated: 29/11/07 @ 15:40:30

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Testiteratorstrategy_withcloning_21054_2
This workflow implements a strategy for this problem: > I would like to perform an iteration including a dot product between > a list and a list of lists; example: > Input: > > [1] (1) > [A,B,C] (2) > [[a,b],[c,d],[e,f]] (3) > > Desired output: > > [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...

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

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Taverna 1

Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v11)

Created: 29/02/08 @ 01:34:47 | Last updated: 28/05/09 @ 12:21:06

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

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_proteindiscovery_filteronhumanuniprot_perdoc_html
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

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Taverna 1

Original Uploader

Workflow pELM_getInstance_Return_Seq (v2)

Created: 03/10/07 @ 18:36:27 | Last updated: 02/05/08 @ 13:09:08

Credits: User Niall Haslam

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Pelm_getinstance_return_seq_4755
Simple workflow to retrieve the sequence of a phospho.ELM entry given the Instance identifier. Input requires xml as the namespace is not correctly handled by the xml splitter. Example input: I000299 Further outputs can easily be added, most are text with some xml. See list in InstanceXML.

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

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Taverna 1

Original Uploader

Workflow BioAID_EnirchBioModelWithProteinsFromText (v7)

Created: 22/08/08 @ 11:00:51 | Last updated: 16/05/09 @ 01:13:19

Credits: User Marco Roos User Sophia katrenko User Andrew Gibson User M. Scott Marshall User Willem van Hage User Edgar User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Roosetal_paper14_swat4ls_figure_06
This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0

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