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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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Screenshot of the Chemoinformatics Perspective. The Chemoinformatics Perspective showing the BioResource Navigator (on the left), JChemPaint editor with a 2D diagram of ATP (middle), Console echoing messages to the user (bottom), ChemTree view with the atoms and bonds (top right), and the Properties view displaying properties for the selected molecule (bottom right).
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Figure 3: Screenshot of the Chemoinformatics Perspective. The Chemoinformatics Perspective showing the BioResource Navigator (on the left), JChemPaint editor with a 2D diagram of ATP (middle), Console echoing messages to the user (bottom), ChemTree view with the atoms and bonds (top right), and the Properties view displaying properties for the selected molecule (bottom right).

Mentions: The BioResource Navigator is the central component in Bioclipse that allows for navigating BioResources in a hierarchical, tree-like View, similar to browsing local folders and files (Figure 3). It contains basic features such as cut and paste, drag and drop, and wizards for new resources, and provides an extension point where plugins can register actions for appearing in the context menu upon right-click. A basic text-editor and an XML-editor with global actions such as undo, redo, cut, and paste are also provided. Bioclipse further contains a Properties View for visualization of properties of the currently selected objects in the workbench, a console that echoes messages back to the user, and a job scheduler that allows time-consuming tasks to be run in the background and displayed upon completion (Figure 3). Bioclipse also contains various wizards for the creation of new BioResources, global preferences for customizing the workbench, and a searchable, XML-based help-system that ensures the user manual is readily available – all with extension points so that external plugins can make additions to every part.


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)

Screenshot of the Chemoinformatics Perspective. The Chemoinformatics Perspective showing the BioResource Navigator (on the left), JChemPaint editor with a 2D diagram of ATP (middle), Console echoing messages to the user (bottom), ChemTree view with the atoms and bonds (top right), and the Properties view displaying properties for the selected molecule (bottom right).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Screenshot of the Chemoinformatics Perspective. The Chemoinformatics Perspective showing the BioResource Navigator (on the left), JChemPaint editor with a 2D diagram of ATP (middle), Console echoing messages to the user (bottom), ChemTree view with the atoms and bonds (top right), and the Properties view displaying properties for the selected molecule (bottom right).
Mentions: The BioResource Navigator is the central component in Bioclipse that allows for navigating BioResources in a hierarchical, tree-like View, similar to browsing local folders and files (Figure 3). It contains basic features such as cut and paste, drag and drop, and wizards for new resources, and provides an extension point where plugins can register actions for appearing in the context menu upon right-click. A basic text-editor and an XML-editor with global actions such as undo, redo, cut, and paste are also provided. Bioclipse further contains a Properties View for visualization of properties of the currently selected objects in the workbench, a console that echoes messages back to the user, and a job scheduler that allows time-consuming tasks to be run in the background and displayed upon completion (Figure 3). Bioclipse also contains various wizards for the creation of new BioResources, global preferences for customizing the workbench, and a searchable, XML-based help-system that ensures the user manual is readily available – all with extension points so that external plugins can make additions to every part.

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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