Bioclipse 2.4.0 RC2 / 2.2.0

Bioclipse 2.4.0 RC2 / 2.2.0 is known as a convenient and helpful free open source workbench for the life sciences which offers advanced functionality in fields such as cheminformatics, bioinformatics, semantic web, spectrum analysis, drug discovery, safety assessment, and general chemistry education.  

Bioclipse is based on the Eclipse Rich Client Platform (RCP) which means that Bioclipse inherits a state-of-the-art plugin architecture, functionality, and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

Major Features:

1. Cheminformatics
   • Cheminformatics in Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. Bioclipse supports editing in 2D, processing large collections of molecules in tables, calculation of various types of properties, and much more cheminformatics functionality. The Jmol application is integrated in Bioclipse as an editor, and provides advanced interactive 3D visualizations.
2. Bioinformatics
   • Bioinformatics in Bioclipse concerns primarily the management and analysis of biological sequences (DNA, RNA, and protein). Bioinformatics in Bioclipse relies heavily on BioJava, which provides core bioinformatics functionality, and a graphical editor for sequence alignments. Various clients for Web services are also available to facilitate downloading of e.g. biological sequences and annotations, as well as for bioinformatcs analysis.
3. Pharmacology and Drug Discovery
   • ioclipse is equipped with many features that simplify pharmacological research and drug discovery. Quantitative Structure-Activity Relationships (QSAR) is a methodology to relates the responses between several chemical structures and a target, for example to measure the toxicity of drugs in the human body, described by mathematical descriptors and modelled using statistical methods.
4. Semantic Web for the Life Sciences
   • Bioclipse has advanced tools for interacting with semantic web resources. It allows for data integration and retrieval in RDF, OWL, and similar formats, with graphical visualizations.
5. Decision support
   • Bioclipse facilitates working with decision support systems, for example when predicting the susceptibility of a drug for certain patients. By sequencing the DNA of the patient (or e.g. a virus in the patient), it is possible to predict what drugs that would best attack the disease. An example of this is HIVPred, which is implemented as an XMPP cloud service and a plugin in Bioclipse to facilitate invocation.
   • Bioclipse also has a feature for decision support in safety assessment with graphical views and editors for executing and integrating various computational models to predict the safety of chemical compounds.
6. eScience
   • Bioclipse is a rich client and takes full advantage of networked resources, such as databases and interoperable Web services, XMPP services. There is ongoing work to integrate Workflow engines, such as Taverna.
7. Databases in the life sciences
   • Bioclipse has projects aimed at delivering chemical and biological databases to end users. One example is StructureDB.
8. Scripting
   • Bioclispe is equipped with a scripting language (Bioclipse Scripting Language, or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others. BSL is based on JavaScript, and is very powerful in chemical and biological analyses. Bioclipse makes use of Gist and MyExperiment for sharing of scripts.