Changes between Version 6 and Version 7 of eGalaxy

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17-02-11 17:33:28 (3 years ago)
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kostas.karasavvas@…
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  • eGalaxy

    v6 v7  
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    66== Introduction == 
    7 The diversity and availability of bioinformatics tools have been increased in the recent years. Some tools deal with the same problem using a different approach, others provide different access mechanisms to the same resources while others provide aggregation mechanisms to make use of a number of tools in a uniform way. For the latter, software pipelining systems, are becoming the norm in bioinformatics. Widely used examples of such systems are Galaxy^1^, a web-portal and framework, and Taverna^2^, a workflow management system. The goal of both of these systems is to provide a platform that bioinformaticians and biologists can use to describe their experiments in a number of well described processing steps, i.e. workflows. 
     7The diversity and availability of bioinformatics tools have increased in recent years. Some tools deal with the same problem using a different approach, others provide different access mechanisms to the same resources while others provide aggregation mechanisms to make use of a number of tools in a uniform way. For the latter, software pipelining systems, are becoming the norm in bioinformatics. Widely used examples of such systems are Galaxy, a web-portal and framework, and Taverna, a workflow management system. The goal of both of these systems is to provide a platform that bioinformaticians and biologists can use to describe their experiments in a number of well described processing steps, i.e. workflows. 
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    9 However, the approach used is different. In Galaxy the focus is on an intuitive and easy to use user interface, a web-based portal, to aggregate several bioinformatics tools and expose them in a uniform way. Taverna is a workflow management system that allows for the orchestration of (primarily) Web Services. It provides good extensibility points to add new functionality (called shims and plugins). It offers a powerful and flexible workflow language that allows for the description of complex workflows that include repetitions, conditionals and other well understood programming language constructs. 
     9However, the approach used is different. In Galaxy the focus is on an intuitive and easy to use user interface, a web-based portal, to aggregate several bioinformatics tools and expose them in a uniform way. Taverna is a workflow management system that allows for the orchestration of a wide range of services. It provides good extensibility points to add new functionality using a plug-in framework. It offers a powerful and flexible workflow language that allows for the description of complex workflows that include repetitions, conditionals and other well understood programming language constructs. 
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    11 Both of the above mentioned systems provide a wide range of functionality out of the box. There is some overlap but the real added value would be if we could combine that functionality and try to get the best of both systems. This work aims to bridge the two by allowing the more expressive but complex Taverna workflows to execute via the simple and intuitive interface that Galaxy offers. To this end we built a Galaxy tool generator that given a Taverna workflow description and a Taverna server^3^ it constructs a Galaxy tool to enable the enactment of that workflow via Galaxy. 
     11Both of the above mentioned systems provide a wide range of functionality out of the box. There is some overlap but the real added value would be if we could combine that functionality and try to get the best of both systems. This work aims to bridge the two by allowing the more expressive but complex Taverna workflows to execute via the simple and intuitive interface that Galaxy offers. To this end we built a Galaxy tool generator that given a Taverna workflow description and a Taverna Server it constructs a Galaxy tool to enable the enactment of that workflow via Galaxy. 
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    13 This generator is available in a workflow repository, myExperiment^4,5^, and it will generate the Galaxy tool behind the scenes. The bioinformatician will just browse the myExperiment repository to identify Taverna workflows that are of interest to him/her and he will be able to download them as Galaxy tools which can then be installed into Galaxy server the usual way.  
     13This generator is available in a workflow repository, myExperiment (www.myexperiment.org), and it will generate the Galaxy tool behind the scenes. The bioinformatician will just browse the myExperiment repository to identify Taverna workflows that are of interest to him/her and he will be able to download them as Galaxy tools which can then be installed into a Galaxy server in the usual way.  
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    15 There are plans to further automate this procedure by accessing the myExperiment site as Galaxy external interface, which will dynamically add the workflows as new tools in Galaxy. 
     15There are plans to further automate this procedure by accessing the myExperiment site as a Galaxy external interface, which will dynamically add the workflows as new tools in Galaxy. 
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     26== Dissemination == 
     27* Presentation at International Symposium on Integrative Bioinformatics 2011, March 21-23 
     28* Submitted at NBIC Conference 2011, April 19-20 
     29* To be submitted at Galaxy Community Conference 2011, May 25-26 
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    2632== Contact == 
    2733Kostas Karasavvas -- kostas (dot) karasavvas (at) nbic (dot) nl