content/introduction/works-with.md

Title:     Works with…
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Taverna directly interfaces with a range of software tools and systems. 
Currently Taverna works with the following:

 - <a href="http://www.biomart.org/" target="_blank">
      <img src="/img/biomart.gif" alt="BioMart" width="61" height="19" /></a>   
   [Biomart][1]
 - <a href="http://sourceforge.net/p/soaplab/wiki/Home/" target="_blank">
      <img src="/img/Soaplab.png" alt="SoapLab" width="33" height="25" /></a>   
   [SoapLab][2]</a>
 - <a href="/documentation/plugins#sadi_plugin">
      <img src="/pages/wp-content/uploads/2011/03/sadi-header-small.png" alt="SADI" /></a>   
   [SADI][3]</a>
 - <a href="http://www.r-project.org/" target="_blank">
      <img src="/img/Rshell.png" alt="RShell" width="29" height="21" /></a>   
   [R][4]</a>   
 - <a href="http://www.bioconductor.org/" target="_blank">
      <img src="/img/logo_bioconductor.gif" alt="Bioconductor" width="130" height="39" /></a>   
   [Bioconductor][5]</a>
 - A number of [third party plugins][6]

<a name="biomart"></a>
##Biomart##
 - <a href="http://www.biomart.org/" target="_blank">
      <img src="/img/biomart.gif" alt="BioMart" width="61" height="19" ></a>   

The [Biomart system][7] is a flexible data warehouse aimed at complex interlinked biological data sets. 
It enables the retrieval of large amounts of genomic data e.g. from Ensembl and Sanger, as well as Uniprot, 
   MSD datasets and many more. 
The [Biomart service][8] is one of the default Taverna services.

<a name="soaplab"></a>
##SoapLab##

 - <a href="http://sourceforge.net/p/soaplab/wiki/Home/" target="_blank">
      <img src="/img/Soaplab.png" alt="SoapLab" width="33" height="25" ></a>   

[SoapLab][9] services are command line applications, wrapped as SOAP services, and served from a Soaplab server.
Soaplab is especially well suited for applications with well described input and output parameters
(such as EMBOSS sequence analysis)

<a name="sadi"></a>
##SADI##

 - <a href="/documentation/plugins/#sadi_plugin">
      <img src="/img/sadi-header-small.png" alt="SADI" ></a>   
Semantic Web services described using the SADI framework

<a name="r"></a>
##R##
 - <a href="http://www.r-project.org/" target="_blank">
      <img src="/img/Rshell.png" alt="RShell" width="29" height="21" ></a>

[R][10] is a popular scripting language oriented towards statistical computing. 
The [Rshell][11] service in Taverna allows your workflow to include services that run R scripts on an 
   R installation.

<a name="bioconductor"></a>
##Bioconductor##

 - <a href="http://www.bioconductor.org/" target="_blank">
      <img src="/img/logo_bioconductor.gif" alt="Bioconductor" width="130" height="39" ></a><br />

[Bioconductor][12] provides tools for the analysis and comprehension of high-throughput genomic data. 
Bioconductor uses the R statistical programming language, and is open source and open development
 
  [1]: #biomart
  [2]: #soaplab
  [3]: #sadi
  [4]: #r
  [5]: #bioconductor
  [6]: /documentation/plugins
  [7]: http://www.biomart.org/
  [8]: http://dev.mygrid.org.uk/wiki/display/taverna/Biomart
  [9]: http://sourceforge.net/p/soaplab/wiki/Home/
  [10]: http://www.r-project.org/
  [11]: http://dev.mygrid.org.uk/wiki/display/taverna23/Rshell
  [12]: http://www.bioconductor.org/