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Posted to commits@taverna.apache.org by br...@apache.org on 2015/02/04 14:45:10 UTC
svn commit: r1657225 -
/incubator/taverna/site/trunk/content/introduction/taverna-in-use/databases.md
Author: brenninc
Date: Wed Feb 4 13:45:10 2015
New Revision: 1657225
URL: http://svn.apache.org/r1657225
Log:
Added database examples
Modified:
incubator/taverna/site/trunk/content/introduction/taverna-in-use/databases.md
Modified: incubator/taverna/site/trunk/content/introduction/taverna-in-use/databases.md
URL: http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/taverna-in-use/databases.md?rev=1657225&r1=1657224&r2=1657225&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/introduction/taverna-in-use/databases.md (original)
+++ incubator/taverna/site/trunk/content/introduction/taverna-in-use/databases.md Wed Feb 4 13:45:10 2015
@@ -26,12 +26,74 @@ Various projects and researchers use Tav
- [ProDom][6] - running of Taverna workflows behind a portal to search a protein database
<a name="efamily"></a>
+##eFamily##
+
+The [eFamily project][7] was designed to integrate the information contained in five major protein databases.
+ The project developed webservices to allow the calculation of results based upon the content of
+ several databases, and upon annotation of the data.
+
+The project made use of Taverna workflows to integrate the webservices,
+ both those provided by the eFamily project and those developed externally.
+
+###Publications###
+Some details of this work are given in the http://www.allhands.org.uk/2004/proceedings/papers/211.pdf
+ *eFamily: Bridging Sequence and Structure* by Finn et al.
+
<a name="embrace"></a>
+##EMBRACE##
+[EMBRACE][8] is the European Model for Bioinformatics Research And Community Education (EMBRACE).
+It consists of a large number of partners throughout Europe
+
+> The objective of EMBRACE is to draw together a wide group of experts
+> throughout Europe who are involved in the use of information
+> technology in the biomolecular sciences.
+> The EMBRACE Network of Excellence will optimise informatics and information exploitation by
+> pure and applied biological scientists in both the academic and commercial sectors.
+
+The [University of Manchester][9] is a member of the EMBRACE project,
+ and the Taverna Workbench has been adopted by EMBRACE as its workflow system of choice.
+
+The suitability of Taverna Workbench has been confirmed by its use in several test cases:
+
+ - The use of Taverna to access Grid Protein Sequence Analysis (GPSA) Web services as described by
+ Blanchet et al. in the [paper][10]
+ *Web Services Interface to Run Protein Sequence Tools on Grid, Testcase of Protein Sequence Alignment*.
+ This includes the running of the Web services on [EGEE][11] grid.
+ - Taverna has been used to automate the cleaning up and extraction of data by the EMBRACE project from the
+ tGRAP database of mutated G-protein coupled receptors.
+ - The ProDom-based protein family analyses test case includes the use of Taverna within [ProDom][12].
+
+The tGRAP work is described in the [document][13] *The reincarnation of the tGRAP database* by Vroling.
+
+Use of Taverna allows the members of EMBRACE to have ready access to the existing bioinformatics services and
+ also to the myGrid teamâs expertise in this area. Correspondingly, the members of EMBRACE represent
+ a diverse group of users with different backgrounds and infrastructure.
+
<a name="omixed"></a>
+##omixed##
+
+[omixed][14]</a> is a âcustomisable storage system for scientific data, completely managed via web servicesâ.
+Its developers have written a Taverna 1.7.x [plugin][15] to allow users to access data.
+
+The plugin âprovides two endpoints giving full control of omixed resources.
+The first endpoint, known as the server endpoint, is designed for most users who want to browse, download,
+ or add to or modify existing resources.
+The second point, known as the admin endpoint, is designed for administrators to create and delete resources,
+ assign schema to them, and modify user privileges.â
+
[1]: /introduction/taverna-in-use/multimedia.html#echase
[2]: #efamily
[3]: #embrace
[4]: /introduction/related-projects.html#ispider
[5]: #omixed
- [6]: /introduction/taverna-in-use/protein-and-proteomics.html#prodom
\ No newline at end of file
+ [6]: /introduction/taverna-in-use/protein-and-proteomics.html#prodom
+ [7]: http://www.ebi.ac.uk/pdbe/docs/sifts/efamily.html
+ [8]: http://www.embracegrid.info/
+ [9]: http://www.manchester.ac.uk/
+ [10]: http://dx.doi.org/10.1007/11946465_22
+ [11]: https://eu-egee-org.web.cern.ch/eu-egee-org/index.html
+ [12]: /introduction/taverna-in-use/protein-and-proteomics.html#prodom
+ [13]: http://www.myexperiment.org/files/29
+ [14]: http://nebc.nerc.ac.uk/tools/omixed/overview
+ [15]: http://www.omixed.org/documentation/omixed%20taverna%20plugin
\ No newline at end of file