BiBiServ: Practices and Problems WebServices and Workflows on the - - PowerPoint PPT Presentation

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BiBiServ: Practices and Problems WebServices and Workflows on the - - PowerPoint PPT Presentation

May 04, 2023 282 likes •527 views

BiBiServ: Practices and Problems WebServices and Workflows on the Bielefeld University Bioinformatics Server Sven Hartmeier NETTAB 2007 - 13.6.2007 - Pisa, Italy Faculty of Technology - Bielefeld University BiBiServ-Basics... Bi elefeld

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BiBiServ: Practices and Problems

WebServices and Workflows on the Bielefeld University Bioinformatics Server

Sven Hartmeier

Faculty of Technology - Bielefeld University

NETTAB 2007 - 13.6.2007 - Pisa, Italy

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BiBiServ-Basics...

  • Bielefeld University Bioinformatics Server
  • founded in 1996
  • hosts various BioInformatics Tools

developed within several research groups at Bielefeld University

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BiBiServ-Tools

  • currently around 30 tools in the areas of:
  • RNA Structure Research
  • Alignment Computation
  • Genome Comparison
  • Primer Design
  • Evolutionary Relationships
  • Miscellaneous Other Applications
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Used Technologies

  • 1996: HTML/CGI
  • 2003: WebServices using XML-RPC
  • 2004: WebServices using SOAP / WSDL

HTML Interface transformed to „just another WebService Client“

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Architecture

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

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Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

Request

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SLIDE 7

Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

request

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Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

response: Job-ID

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Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

polling

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Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

polling

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Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

Result

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Usage (HTML Interface)

WebServer „BiBiServ“ WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

Result

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WebService Server „BiBiWSServ“ SGE Computation Grid Database Server

Usage: other clients

Perl Client ??? Client C# Client Java Client

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HTML Interface Usage

5.000 16.250 27.500 38.750 50.000 04 05 06 07 08 09 10 11 12 01 02 03 04 05 06 07 08 09 10 11 12 01 02 03 04

2005 2006 2007

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WebService Interface Usage

1.125 2.250 3.375 4.500 04 05 06 07 08 09 10 11 12 01 02 03 04 05 06 07 08 09 10 11 12 01 02 03 04

2005 2006 2007

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HOBIT

  • Helmholtz Open BioInformatics Technology
  • cooperation of 11 german universities and Helmholtz

Institutes as core of a network linking bioinformatics centres together

  • Goal: „To connect bioinformatics applications and

resources in a uniform way to provide an efficient communication tier for resource access.“

  • http://hobit.sourceforge.net/
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Interoperation Obstacles

  • necessary prerequisite:

common communication protocols & common data formats

  • most common bioinformatics data formats:
  • tool specific ASCII or binary files

(but often used for other purposes)

  • no explicit structure
  • no or only implicit semantics

(e.g. lower vs. upper case letters)

  • not easily extendable
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Hobit Schemas

  • extendable XML Schema definitions for

bioinformatics data

  • Basic building blocks for bioinformatical data

types

  • Several higher-level types:
  • SequenceML
  • AlignmentML
  • RNAStructML
  • http://bioschemas.sourceforge.net/
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BioDOM

  • Java Library for creation of data in HOBIT

XML formats + conversion of existing legacy data types

  • easy adaptation of existing tools via:
  • BioDOM Library calls
  • usage of BioDOM WebService
  • http://biodom.sourceforge.net/
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Workflow / Formats Example

BioDOM

EMBLxml TinySeq FASTA

>id agtc uact

SequenceML

mfold

BioDOM BioDOM

RNA- Shapes RNA- Fold

RNAStructML

RNA- Forester

RNAStructAlignmentML RNAMovies

4SALE

PNG/JPG/SVG

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BiBiServices as components

  • hand-coded workflows
  • WSDL-Description -> Taverna, Wildfire
  • jABC / Bio-jETI
  • Virtual BiBiServ
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The (near) Future

  • Better description of services

(WSDL is mostly OK, but not enough)

  • Semantics Layer
  • Integration with other Frameworks

(e.g. BioMoby-S)

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Why we are here...

We are currently looking for generally accepted best practices and open standards

for:

  • adding a semantic layer
  • better service descriptions
  • automated tool discovery methods
  • component interface requirements for

different workflow design tools

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Sven Hartmeier

Faculty of Technology - Bielefeld University shartmei@techfak.uni-bielefeld.de

http://bibiserv.techfak.uni-bielefeld.de/

Thanks for your attention :-)!