Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc.
The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.
Bioclipse will provide functionality for chemo- and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin.
The major features are:
- Import and export in various file formats
- Visual editing of molecular 2D-structures
- 3D-visualization of molecules and proteins
- Editing and visualization of sequences and features (DNA, RNA, proteins etc)
- Graphing and editing of various types of spectra, e. g. NMR, MS
- Retrieval of resources (sequences, proteins, etc) from public data repositories
- Scripting of 3D-visualizations with syntax highlighting and content assistance
- PDB-editor with syntax highlighting for working with PDB files
- CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds
- Chemtree for displaying a hierarchical view of molecular and macromolecular substructures
- Visualization of syandard chemical properties
- Powerful scripting language based on Mozilla Rhino for automating tasks
Integrated, searchable help-system - Connection with external programs, e. g. PyMol
Bioclipse is a rich client, which means it is run on your local computer but also gives the possibility to communicate with servers for data retrieval and computational services. The powerful plugin architecture is based on Eclipse[2], and results in a responsive, integrated user interface designed for simple and intuitive operations that at the same time is easy to extend with custom functionality.
OS: Linux, Unix and Windows
Licence: Open Source (EPL)
