uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität, Munich, Germany.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.ORCID iD: 0000-0002-8083-2864
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
2009 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 10, 279- p.Article in journal (Refereed) Published
Abstract [en]

BACKGROUND:Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use.

RESULTS:We present a novel approach based on the open standard Extensible Messaging and Presence Protocol (XMPP), consisting of an extension (IO Data) to comprise discovery, asynchronous invocation, and definition of data types in the service. That XMPP cloud services are capable of asynchronous communication implies that clients do not have to poll repetitively for status, but the service sends the results back to the client upon completion. Implementations for Bioclipse and Taverna are presented, as are various XMPP cloud services in bio- and cheminformatics.

CONCLUSION:XMPP with its extensions is a powerful protocol for cloud services that demonstrate several advantages over traditional HTTP-based Web services: 1) services are discoverable without the need of an external registry, 2) asynchronous invocation eliminates the need for ad-hoc solutions like polling, and 3) input and output types defined in the service allows for generation of clients on the fly without the need of an external semantics description. The many advantages over existing technologies make XMPP a highly interesting candidate for next generation online services in bioinformatics.

Place, publisher, year, edition, pages
2009. Vol. 10, 279- p.
Keyword [en]
xmpp, bioclipse, cloud, service, protocol, bioinformatics, cheminformatics, life sciences
National Category
Industrial Biotechnology
Research subject
Pharmaceutical Pharmacology
URN: urn:nbn:se:uu:diva-109290DOI: doi:10.1186/1471-2105-10-279ISI: 000271117300001OAI: oai:DiVA.org:uu-109290DiVA: diva2:271845
Available from: 2009-10-13 Created: 2009-10-13 Last updated: 2015-05-04Bibliographically approved
In thesis
1. Bioclipse: Integration of Data and Software in the Life Sciences
Open this publication in new window or tab >>Bioclipse: Integration of Data and Software in the Life Sciences
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

New high throughput experimental techniques have turned the life sciences into a data-intensive field. Scientists are faced with new types of problems, such as managing voluminous sources of information, integrating heterogeneous data, and applying the proper analysis algorithms; all to end up with reliable conclusions. These challenges call for an infrastructure of algorithms and technologies to supply researchers with the tools and methods necessary to maximize the usefulness of the data. eScience has emerged as a promising technology to take on these challenges, and denotes integrated science carried out in highly distributed network environments, or science that makes use of large data sets and requires high performance computing resources.

In this thesis I present standards, exchange formats, algorithms, and software implementations for empowering researchers in the life sciences with the tools of eScience. The work is centered around Bioclipse - an extensible workbench developed in the frame of this thesis - which provides users with instruments for carrying out integrated research and where technical details are hidden under simple graphical interfaces. Bioclipse is a Rich Client that takes full advantage of the many offerings of eScience, such as networked databases and online services. The benefits of mixing local and remote software in a unifying platform are demonstrated with an integrated approach for predicting metabolic sites in chemical structures. To overcome the limitations of the commonly used technologies for interacting with networked services, I also present a new technology using the XMPP protocol. This enables service discovery and asynchronous communication between the client and server, which is ideal for long-running analyses.

To maximize the usefulness of the available data there is a need for standards, ontologies, and exchange formats, in order to define what information should be captured and how it should be structured and exchanged. A novel format for exchanging QSAR data sets in a fully interoperable and reproducible form is presented, together with an implementation in Bioclipse that takes advantage of eScience components during the setup process.

Bioclipse has been well received by the scientific community, attracted a large group of international users and developers, and has been awarded three international prizes for its innovative character. With continued development, the project has a good chance of becoming an important component in a sustainable infrastructure for the life sciences.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. 53 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, ISSN 1651-6192 ; 111
Bioclipse, integration, life sciences, bioinformatics, cheminformatics, chemoinformatics, eclipse, rich client, xmpp, qsar-ml, web service, standard, ontology
National Category
Bioinformatics and Systems Biology
urn:nbn:se:uu:diva-109305 (URN)978-91-554-7633-5 (ISBN)
Public defence
2009-11-27, B42, Uppsala Biomedical Center (BMC), Husargatan 3, Uppsala, 13:15 (English)
Available from: 2009-11-06 Created: 2009-10-13 Last updated: 2015-05-04Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full texthttp://www.biomedcentral.com/1471-2105/10/279

Search in DiVA

By author/editor
Spjuth, Ola
By organisation
Department of Pharmaceutical Biosciences
In the same journal
BMC Bioinformatics
Industrial Biotechnology

Search outside of DiVA

GoogleGoogle Scholar

Altmetric score

Total: 265 hits
ReferencesLink to record
Permanent link

Direct link