A Workflow Enactment Portal for Bioinformatics Paolo Romano - - PowerPoint PPT Presentation

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a workflow enactment portal for bioinformatics
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A Workflow Enactment Portal for Bioinformatics Paolo Romano - - PowerPoint PPT Presentation

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A Workflow Enactment Portal for Bioinformatics Paolo Romano Bioinformatics and Structural Proteomics National Cancer Research Institute of Genoa, Italy paolo.romano@istge.it Rationale and goals Moving from an interactive to an automated

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A Workflow Enactment Portal for Bioinformatics

Paolo Romano Bioinformatics and Structural Proteomics National Cancer Research Institute of Genoa, Italy paolo.romano@istge.it

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  • P. Romano, DILS '06, 20/7/2006

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Rationale and goals

Moving from an interactive to an automated approach for data integration requires new technologies and tools. Some starting assumptions

XML schemas for the creation of the models of the information, XML based languages for data representation and exchange, Web Services for the interoperability of software Computerised workflows for the definition and execution of

analysis processes

Many workflow management software for bioinformatics applications are being proposed, but they all require knowledge of the systems and skills and time for development

  • f the workflows.
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SLIDE 3
  • P. Romano, DILS '06, 20/7/2006

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Features (i)

We designed biowep, a worlflow enactment portal that:

allows for the carrying out of predefined workflows supports workflows annotation by using a simple

  • ntology for bioinformatics processors (domain,

task, i/o)

implements search and selection of workflows on

the basis of their annotation

supports retrieval of workflows on the basis of

users’ profiling

allows storing and retrieval of workflows’

executions and related results

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SLIDE 4
  • P. Romano, DILS '06, 20/7/2006

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Features (ii)

The system:

is partially based on open source (Taverna WB,

FreeFluo e mySQL)

makes access to data and analysis that are made

available through Web Services

archives workflow either in XScufl o XPDL formats is available under LGPL license requirements: Java SDK + Tomcat + mySQL

Available on-line:

http://bioinformatics.istge.it/biowep/ (reference site) http://bioinformatics.istge.it:8080/biowep/ (portal)

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  • P. Romano, DILS '06, 20/7/2006

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Overall architecture

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  • P. Romano, DILS '06, 20/7/2006

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Workflows

Workflows are:

created by the admin by using Taverna or

BioWMS

archived in the related format in the

repository

updated, when needed (workflow vs version) can be submitted by users or service

providers through the reference site

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  • P. Romano, DILS '06, 20/7/2006

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Workflows’ annotation

Workflows and their main steps are both annotated by using a simple

  • ntology of bioinformatics data and

tasks including

application domains main task input and output data

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SLIDE 8
  • P. Romano, DILS '06, 20/7/2006

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Users’ profiling

Users are classified on the basis of:

their role in the organization

computer scientist / physician /

researcher / patient / officer / …

domains of interest

Workflows are listed according to user profiling and previous executions

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  • P. Romano, DILS '06, 20/7/2006

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Planned activities

End users support (two implementations)

manuals, support through biowep@istge.it

Bug fixing (curation of children diseases) Revision of applications:

administration (end of summer / begin of autumn) visualization of results (end of 2006 / begin of

2007)

Inclusion of further WMS

analysis and selection undergoing