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Exploring Web Services in Life Sciences: A Comprehensive Course

Learn about web services in life sciences, types, models, paradigms, building workflows, and exploring resources. Gain insight into SOAP and REST models, silo-based vs. SOA approaches, and key tools like Taverna and Triana.

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Exploring Web Services in Life Sciences: A Comprehensive Course

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  1. Web Services Programmatic access to Life Sciences resources. Rodrigo Lopez

  2. Outline • What are Web Services. • Types of Web Services. • Lists of Web Services. • Building workflows. Web Services Course CBS, DK.

  3. What are Web Services • Network based tools that permit access to methods… • In a programmatic fashion. • Without using traditional browsers. • Exposing more granularity and thus giving the user more control. • Web Services models… • SOAP/REST models • SOAP is great for embedding methods into complex programs – PERL, Python, Ruby, Java, C/C++, etc. • REST is simpler, easier and provides basic end-points. • http://www.site.dom/param1/param2/data1/... Web Services Course CBS, DK.

  4. Web Services Paradigms • Silo based approach • Services (Tools such as blast, EB-eye, etc.) present methods for their use. • Ideal for running from the command line using simple clients. • Relieve the user from the tool maintenance overhead. The service provider is responsible for this. • SOA – Service Oriented Architecture • Combines SILO-based methods to generate a ‘workflow’. • User decides which tool method to use thus establishing a business relationship with one or several service providers. Web Services Course CBS, DK.

  5. Web Services • We have travelled in WS space since 2004. • Tried, tested and put into production SOAP and REST services for more than 150 discrete applications. • All using the SILO based approach to Web Services. • Intend to migrate into a SOA based architecture during 2007-2008. 5 Web Services Course CBS, DK.

  6. Web Services – our focus • There has been far too much ‘hype’ about WS during the last years. • WS are a just a packaging/messaging technology. • WS are just that: services – and are not meant to be the centre of attention. • Our definition: Bioinformatic WS are just transparent means of running bioinformatic tools that help integrate expensive computation and maintenance into remote analytical pipe-lines and workflows. Web Services Course CBS, DK.

  7. Web Services (1) • Sequence Analysis • Similarity searching. • DNA & Protein sequence analysis. • Genomes – Inquisitor (integr8). • Protein Function prediction • InterProScan • Protein secondary and tertiary structure • PDBSum, MSD-lite, MSD-pro, MSD-motif,… • Proteomics • IntAct • PRIDE • Literature & Ontology services • CiteXplore • Whatizit • ChEBI, SBO,… • Biological models and simulation • BioModels • Future services: • Biological images • EB-eye WS Web Services Course CBS, DK.

  8. Web Services (2) • But there are Web Services from others to exploit, mix and match, complement… • NCBI:http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html • BioMoby: http://biomoby.org/ • KEGG: http://www.genome.jp/kegg/soap/ • DDBJ: http://xml.nig.ac.jp/wsdl/?lang=en • EBI: http://www.ebi.ac.uk/Tools/webservices/ Web Services Course CBS, DK.

  9. Building workflows • Running ‘business transactions’ with Taverna and Triana Web Services Course CBS, DK.

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