Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as software updates, preferences, help system, 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.
NOTE: Bioclipse is licensed and distributed under the terms of the Eclipse Public License.
Here are some key features of "Bioclipse":
· 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
What's New in This Release: [ read full changelog ]
· The release contains new Decision Support models (such as for ChEMBL and Chemspider), the latest CDK with e.g. improved aromaticity detection, and Bioclipse-R (including R-models for DS), improved core stability based on Eclipse 3.8 and support for Java 1.7, new installation processes for Windows and Mac OS X, and numerous bug fixes.