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Bioclipse: an open source workbench for chemo- and bioinformatics
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, Pharmaceutical Pharmacology. (Proteochemometric group)ORCID iD: 0000-0002-8083-2864
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, Pharmaceutical Pharmacology. (Proteochemometric group)
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2007 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 8, 59- p.Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

Place, publisher, year, edition, pages
2007. Vol. 8, 59- p.
National Category
Pharmaceutical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-104257DOI: 10.1186/1471-2105-8-59ISI: 000244600100001PubMedID: 17316423OAI: oai:DiVA.org:uu-104257DiVA: diva2:219577
Available from: 2009-05-28 Created: 2009-05-28 Last updated: 2015-09-11Bibliographically approved
In thesis
1. eScience Approaches to Model Selection and Assessment: Applications in Bioinformatics
Open this publication in new window or tab >>eScience Approaches to Model Selection and Assessment: Applications in Bioinformatics
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

High-throughput experimental methods, such as DNA and protein microarrays, have become ubiquitous and indispensable tools in biology and biomedicine, and the number of high-throughput technologies is constantly increasing. They provide the power to measure thousands of properties of a biological system in a single experiment and have the potential to revolutionize our understanding of biology and medicine. However, the high expectations on high-throughput methods are challenged by the problem to statistically model the wealth of data in order to translate it into concrete biological knowledge, new drugs, and clinical practices. In particular, the huge number of properties measured in high-throughput experiments makes statistical model selection and assessment exigent. To use high-throughput data in critical applications, it must be warranted that the models we construct reflect the underlying biology and are not just hypotheses suggested by the data. We must furthermore have a clear picture of the risk of making incorrect decisions based on the models.

The rapid improvements of computers and information technology have opened up new ways of how the problem of model selection and assessment can be approached. Specifically, eScience, i.e. computationally intensive science that is carried out in distributed network envi- ronments, provides computational power and means to efficiently access previously acquired scientific knowledge. This thesis investigates how we can use eScience to improve our chances of constructing biologically relevant models from high-throughput data. Novel methods for model selection and assessment that leverage on computational power and on prior scientific information to "guide" the model selection to models that a priori are likely to be relevant are proposed. In addition, a software system for deploying new methods and make them easily accessible to end users is presented.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. 51 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, ISSN 1651-6192 ; 112
Keyword
bioinformatics, high-throughout biology, eScience, model selection, model assessment
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:uu:diva-109437 (URN)978-91-554-7634-2 (ISBN)
Public defence
2009-11-28, B42, BMC, Husargatan 3, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2009-11-06 Created: 2009-10-15 Last updated: 2011-05-11Bibliographically approved
2. 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.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, ISSN 1651-6192 ; 111
Keyword
Bioclipse, integration, life sciences, bioinformatics, cheminformatics, chemoinformatics, eclipse, rich client, xmpp, qsar-ml, web service, standard, ontology
National Category
Bioinformatics and Systems Biology
Identifiers
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)
Opponent
Supervisors
Available from: 2009-11-06 Created: 2009-10-13 Last updated: 2015-05-04Bibliographically approved

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