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Bioclipse: an open source workbench for chemo- and bioinformatics.

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE - BMC Bioinformatics (2007)

Bottom Line: Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality.Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden. ola.spjuth@farmbio.uu.se.

ABSTRACT

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.

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Plugin dependencies. Overview of the plugin dependencies for Bioclipse.
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Related In: Results  -  Collection

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Figure 1: Plugin dependencies. Overview of the plugin dependencies for Bioclipse.

Mentions: Bioclipse is an RCP application extending the Eclipse framework with plugins for chemo- and bioinformatics, and provides a domain-specific platform where the plugins can be integrated (Figure 1). End-users can select desired features from all the Bioclipse plugins, and use them integrated from an intuitive, responsive graphical workbench. For the developer, this is an ideal platform to integrate new components and take advantage of already existing building blocks. Plugins from other Eclipse-based applications could effectively be installed and run within the Bioclipse workbench without modifications, but in order to interact with other components they would require a wrapper for the object model. Bioclipse is developed in Java, a platform-independent programming language which runs on a virtual machine that is freely available for most operating systems (e.g. Windows, Linux, and Mac OS). Several existing application frameworks in bioinformatics have the possibility to add functionality using plugins. However, no previous architecture has the power and flexibility provided by Bioclipse, making it the most advanced integration framework for biosciences available today.


Bioclipse: an open source workbench for chemo- and bioinformatics.

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE - BMC Bioinformatics (2007)

Plugin dependencies. Overview of the plugin dependencies for Bioclipse.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1808478&req=5

Figure 1: Plugin dependencies. Overview of the plugin dependencies for Bioclipse.
Mentions: Bioclipse is an RCP application extending the Eclipse framework with plugins for chemo- and bioinformatics, and provides a domain-specific platform where the plugins can be integrated (Figure 1). End-users can select desired features from all the Bioclipse plugins, and use them integrated from an intuitive, responsive graphical workbench. For the developer, this is an ideal platform to integrate new components and take advantage of already existing building blocks. Plugins from other Eclipse-based applications could effectively be installed and run within the Bioclipse workbench without modifications, but in order to interact with other components they would require a wrapper for the object model. Bioclipse is developed in Java, a platform-independent programming language which runs on a virtual machine that is freely available for most operating systems (e.g. Windows, Linux, and Mac OS). Several existing application frameworks in bioinformatics have the possibility to add functionality using plugins. However, no previous architecture has the power and flexibility provided by Bioclipse, making it the most advanced integration framework for biosciences available today.

Bottom Line: Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality.Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden. ola.spjuth@farmbio.uu.se.

ABSTRACT

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.

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