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Items tagged with "e-science" (18)

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30?size=60x60 Nl Marco Roos
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Blob From biologist to web service to Taverna to myExperi...

Created: 2008-03-21 19:00:12 | Last updated: 2008-03-23 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

Comments: 1 | Viewed: 469 times | Downloaded: 373 times

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Groups (10)
Owner
1217?size=80x80 Gb Alan Williams
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Network-member myGrid

Unique name: myGrid
Created: Friday 30 November 2007 12:19:26 (UTC)

People working or contributing to the myGrid project, including the Taverna developers. You do not need to join this group to see the shared items. If you are interested in contributing to myGrid or Taverna development or have questions about Taverna, then please email support@mygrid.org.uk

376 shared items   |   0 announcements

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Owner
30?size=80x80 Nl Marco Roos
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Network-member e-science support team for NBIC

Unique name: eScienceSupportTeam4NBIC
Created: Sunday 16 March 2008 22:23:11 (UTC)

This group brings together scientists with expertise in both (medical) bioinformatics and e-science. The members can give advice to bioinformaticians who want to adopt an 'e-science approach'. They want to share their expertise and experience for the application of technologies such as workflow, web/biomoby services, grid, semantic web, etcetera. The group was founded in particular for the Du...

3 shared items   |   0 announcements

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Owner
30?size=80x80 Nl Marco Roos
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Network-member e-(bio)science tool group


Created: Tuesday 03 June 2008 09:46:58 (UTC)

Group for sharing bioinformatics tools that can enhance life science research.

3 shared items   |   0 announcements

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Owner
30?size=80x80 Nl Marco Roos
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Network-member Semantic_BioAID_collaboration


Created: Friday 22 August 2008 10:49:27 (UTC)

Group for collaboration of Andy, Scott, and Marco.

5 shared items   |   1 announcements

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Owner
3947?size=80x80 Gb Don Cruickshank
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Network-member myExperiment

Unique name: myexperiment
Created: Monday 23 July 2007 17:02:58 (UTC)

This is the official group for the myExperiment team.

6 shared items   |   0 announcements

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Owner
30?size=80x80 Nl Marco Roos
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Network-member CWA working group 2.1 - Content Capture

Unique name: CWA_ContentCapture
Created: Tuesday 01 September 2009 13:06:04 (UTC)

Concept Web Alliance working group on content capture CWA wants to help disclose experiment-derived knowledge from within the scientific community via concepts and relations between concepts, stored as concept-relation-concept triples that together form a 'nano-publication'. A nano-publication contains a single 'unit of though', and minimal provenance about who made it, where it was stated, ho...

1 shared item   |   1 announcements

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Owner
30?size=80x80 Nl Marco Roos
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Network-member BioSemantics Privileged Users @ Human Gene...

Unique name: LeidenBioSemanticsUsers
Created: Wednesday 23 September 2009 01:10:24 (UTC)

Group of colleagues at the Human Genetics Department of the Leiden University Medical Centre and closely collaborating groups who are interested to be prime users of new developments in BioSemantics and e-Science, and in return are willing to provide feedback and suggestions. See http://biosemantics.org for more information about the BioSemantics collaboration in the Netherlands.

15 shared items   |   1 announcements

Members (12):

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Owner
Avatar Gb Andrew David King
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Network-member Baywatch Solutions

Unique name: teambncl
Created: Wednesday 10 March 2010 18:39:50 (UTC)

MyExperiment Group for the Team Baywatch (Solutions). Newcastle University, 2010 MSc Bioinformatics e-Science Group B. 2010 Prize Winners!!!  

10 shared items   |   1 announcements

Members (6):

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Owner
71?size=80x80 Nl Katy Wolstencroft
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Network-member Bonn eScience Workshop


Created: Wednesday 16 March 2011 10:43:40 (UTC)

This group contains workflows and other resources for the Bonn e-Science workshop. Use this space for sharing with other members of the group. Finished workflow 'solutions' will also be posted here as the course progresses

32 shared items   |   0 announcements

Members (16):

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Owner
30?size=80x80 Nl Marco Roos
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Network-member BioSemantics

Unique name: biosemantics
Created: Thursday 30 June 2011 13:06:48 (UTC)

Group for members of the BioSemantics group and their close collaborators.BiosemanticsWith the explosion of information in the biomolecular field, there is a dire need for information technology that assists in retrieving, extracting, and relating information and knowledge in the biomedical literature and databases. Biosemantics researchers and developers develop, evaluate, and apply such techn...

70 shared items   |   0 announcements

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Packs (5)
Creator
30?size=60x60 Nl Marco Roos
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Pack e-science tool pack


Created: 2008-08-01 10:52:42 | Last updated: 2008-08-01 12:06:07

Pack of tools and software components that can be used to enhance your research. 'e-science' characteristics: interoperabie with other tools free to use by academics components can be shared and reused, potentially for other means stimulating sharing and reusing components  

1 item in this pack

Comments: 0 | Viewed: 126 times | Downloaded: 37 times

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Creator
30?size=60x60 Nl Marco Roos
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Pack AIDA toolbox


Created: 2008-08-01 11:33:03 | Last updated: 2010-02-14 16:04:25

Adaptive Information Disclosure Application toolbox: AIDA web services for automated knowledge extraction and knowledge management Documentation    

9 items in this pack

Comments: 0 | Viewed: 238 times | Downloaded: 43 times

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Creator
30?size=60x60 Nl Marco Roos
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Pack AIDA demo pack


Created: 2008-12-14 21:35:43 | Last updated: 2009-05-01 17:35:26

 Pack with AIDA demo material

5 items in this pack

Comments: 0 | Viewed: 178 times | Downloaded: 0 times

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Creator
30?size=60x60 Nl Marco Roos
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Pack Supporting material for Roos et al., BMC Bioinformat...


Created: 2009-05-15 15:45:32 | Last updated: 2011-08-11 10:01:23

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...

5 items in this pack

Comments: 0 | Viewed: 133 times | Downloaded: 46 times

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Creator
30?size=60x60 Nl Marco Roos
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Pack AIDA remote runners


Created: 2009-05-15 16:08:03 | Last updated: 2009-05-15 16:11:20

Runners for AIDA demonstrations and testing

2 items in this pack

Comments: 0 | Viewed: 52 times | Downloaded: 27 times

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Workflows (2)
Taverna 1
Uploader
30?size=60x60 Nl Marco Roos

Workflow BioAID_EnirchBioModelWithProteinsFromText (7)

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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...

Created: 2009-05-16 | Last updated: 2009-05-16

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

Taverna 2
Uploader
30?size=60x60 Nl Marco Roos

Workflow Gene expression interpretation by the Glob... (1)

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This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: User Marco Roos

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Non-Information Resource URI: http://www.myexperiment.org/tags/701


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Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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