Bioclipse: an open source workbench for chemo- and bioinformatics

BackgroundThere 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 sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework.ResultsBioclipse 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.ConclusionBioclipse 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.

[1]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[2]  C. Steinbeck,et al.  Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. , 2006, Current pharmaceutical design.

[3]  Egon L. Willighagen,et al.  Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators , 2004, J. Chem. Inf. Model..

[4]  W. Delano.  The PyMOL Molecular Graphics System (2002) , 2002 .

[5]  Morton E. Munk.  Computer-Based Structure Determination: Then and Now , 1998, J. Chem. Inf. Comput. Sci..

[6]  Peter N. Robinson,et al.  HotSwap for bioinformatics: A STRAP tutorial , 2006, BMC Bioinformatics.

[7]  Elarbi Badidi,et al.  AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis , 2003, BMC Bioinformatics.

[8]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the World Wide Web. 4. CML Schema , 2003, J. Chem. Inf. Comput. Sci..

[9]  Pedro Mendes,et al.  ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources , 2001, Bioinform..

[10]  Egon L. Willighagen,et al.  The Blue Obelisk—Interoperability in Chemical Informatics , 2006, J. Chem. Inf. Model..

[11]  Jack A. M. Leunissen,et al.  Evolution of web services in bioinformatics , 2005, Briefings Bioinform..

[12]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[13]  Tim J. Carver,et al.  The design of Jemboss: a graphical user interface to EMBOSS , 2003, Bioinform..

[14]  Christoph Steinbeck,et al.  JChemPaint - Using the collaborative forces of the Internet to develop a free editor for 2D chemical structures , 2000 .

[15]  Egon Willighagen.  Processing CML conventions in Java , 1999 .

[16]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , 1999, J. Chem. Inf. Comput. Sci..

[17]  David J. Reiss,et al.  The Gaggle: An open-source software system for integrating bioinformatics software and data sources , 2006, BMC Bioinformatics.

[18]  Egon L. Willighagen,et al.  The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics , 2003, J. Chem. Inf. Comput. Sci..

[19]  Bart De Moor,et al.  TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis , 2005, Nucleic Acids Res..

[20]  Ed Zintel,et al.  Resources , 1998, IT Prof..

[21]  M. Ghanem,et al.  Web services in the life sciences , 2005, Drug Discovery Today.

[22]  Sameer Velankar,et al.  SOAP-based services provided by the European Bioinformatics Institute , 2005, Nucleic Acids Res..

[23]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[24]  Christoph Gille,et al.  STRAP: editor for STRuctural Alignments of Proteins , 2001, Bioinform..