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Bioclipse 2: A scriptable integration platform for the life sciences
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.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
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2009 (English)In: BMC Bioinformatics, ISSN 1471-2105, Vol. 10, 397- p.Article in journal (Refereed) Published
Abstract [en]

Background: Contemporary biological research integrates neighboring scientific domains to answer complex ques- tions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks.

Results: Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments.

Conclusions: Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today’s powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations or retrieval of data. That Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, and new algorithms, visualizations as well as scripting commands can easily be added. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research. Bioclipse 2 is released under the Eclipse Public License (EPL), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.

Place, publisher, year, edition, pages
2009. Vol. 10, 397- p.
Keyword [en]
Bioclipse, bioinformatics, cheminformatics, scriptable, script, workbench, life science, platform
National Category
Bioinformatics and Systems Biology Pharmaceutical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-109304DOI: 10.1186/1471-2105-10-397ISI: 000273329400001OAI: oai:DiVA.org:uu-109304DiVA: diva2:271875
Available from: 2009-12-16 Created: 2009-10-13 Last updated: 2015-05-12Bibliographically 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.
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
2. Ligand-based Methods for Data Management and Modelling
Open this publication in new window or tab >>Ligand-based Methods for Data Management and Modelling
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Drug discovery is a complicated and expensive process in the billion dollar range. One way of making the drug development process more efficient is better information handling, modelling and visualisation. The majority of todays drugs are small molecules, which interact with drug targets to cause an effect. Since the 1980s large amounts of compounds have been systematically tested by robots in so called high-throughput screening. Ligand-based drug discovery is based on modelling drug molecules. In the field known as Quantitative Structure–Activity Relationship (QSAR) molecules are described by molecular descriptors which are used for building mathematical models. Based on these models molecular properties can be predicted and using the molecular descriptors molecules can be compared for, e.g., similarity. Bioclipse is a workbench for the life sciences which provides ligand-based tools through a point and click interface. 

The aims of this thesis were to research, and develop new or improved ligand-based methods and open source software, and to work towards making these tools available for users through the Bioclipse workbench. To this end, a series of molecular signature studies was done and various Bioclipse plugins were developed.

An introduction to the field is provided in the thesis summary which is followed by five research papers. Paper I describes the Bioclipse 2 software and the Bioclipse scripting language. In Paper II the laboratory information system Brunn for supporting work with dose-response studies on microtiter plates is described. In Paper III the creation of a molecular fingerprint based on the molecular signature descriptor is presented and the new fingerprints are evaluated for target prediction and found to perform on par with industrial standard commercial molecular fingerprints. In Paper IV the effect of different parameter choices when using the signature fingerprint together with support vector machines (SVM) using the radial basis function (RBF) kernel is explored and reasonable default values are found. In Paper V the performance of SVM based QSAR using large datasets with the molecular signature descriptor is studied, and a QSAR model based on 1.2 million substances is created and made available from the Bioclipse workbench.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2015. 73 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy, ISSN 1651-6192 ; 200
Keyword
QSAR, ligand-based drug discovery, bioclipse, information system, cheminformatics, bioinformatics
National Category
Pharmaceutical Sciences Bioinformatics and Systems Biology
Research subject
Pharmaceutical Pharmacology; Bioinformatics
Identifiers
urn:nbn:se:uu:diva-248964 (URN)978-91-554-9237-3 (ISBN)
Public defence
2015-06-05, B22 BMC, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2015-05-12 Created: 2015-04-09 Last updated: 2015-07-07

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