The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
Bioclipse uses a plugin architecture that inherits a state-of-the-art plugin architecture, functionality, and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment, and more.
Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality.
Features include:
- Bioinformatics:
- Manage and analyse biological sequences (DNA, RNA, and protein).
- Relies on BioJava to provide core bioinformatics functionality and a graphical editor for sequence alignments.
- Clients for web services.
- Plugin architecture based on Eclipse.
- Cheminformatics in Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. It supports:
- Process large collections of molecules in tables.
- Calculation of various types of property.
- Editing in 2D.
- Pharmacology and drug discovery.
- Advanced tools for interacting with semantic web resources.
- Facilitates working with decision support systems.
- Rich client and takes full advantage of networked resources, such as databases and interoperable Web services, XMPP services.
- Site-of-metabolism prediction.
- Semantic web functionality.
- Browsing of large compound collections.
- Editing of chemical structures.
- Scripting language (Bioclipse Scripting Language, or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others.
- Platform independent.
Website: sourceforge.net/projects/bioclipse
Support: Blog
Developer: The Bioclipse Project
License: Eclipse Public License
Bioclipse is written in Java. Learn Java with our recommended free books and free tutorials.
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